From 39ceca945f9a81963ca88a25c8403f5d50eab006 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 14:02:33 -0300 Subject: [PATCH 01/62] docs: add qupath to viewers closes #526 --- resources/tools/index.md | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 1c24977e..4b854a46 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -4,14 +4,16 @@ A list of tools and libraries with OME-Zarr support. These are developed by vari ## Contents -- [Tools with a graphical interface (ex. a website)](#tools-with-a-graphical-interface) +- [Tools](#tools) + - [Contents](#contents) + - [Tools with a graphical interface](#tools-with-a-graphical-interface) - [Zarr viewers](#zarr-viewers) - - [Zarr converters](#zarr-converters-with-a-ui) -- [Tools for the programmatically inclined](#tools-for-the-programmatically-inclined) + - [Zarr converters (with a UI)](#zarr-converters-with-a-ui) + - [Tools for the programmatically inclined](#tools-for-the-programmatically-inclined) - [Zarr converters](#zarr-converters) - - [Zarr readers and writers](#zarr-readers--writers) - - [Validating Zarr](#zarr-validation) -- [Other zarr tools and libraries](#other-tools-and-libraries) + - [Zarr readers \& writers](#zarr-readers--writers) + - [Zarr validation](#zarr-validation) + - [Other tools and libraries](#other-tools-and-libraries) ## Tools with a graphical interface @@ -32,6 +34,7 @@ Want to view a Zarr? Use one of these. | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | | Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | | Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | | Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | From 798267f93c658f5ed3903fc98508d579baf18267 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 14:05:01 -0300 Subject: [PATCH 02/62] docs: add odon to viewers closes #527 --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 4b854a46..65f31f14 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -33,7 +33,8 @@ Want to view a Zarr? Use one of these. | Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer |\ +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | | Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | From bdf03aaccad6cd1a09799b00b9867366fdc3e491 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 14:08:01 -0300 Subject: [PATCH 03/62] docs: add biomero to tools closes #504 --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index 65f31f14..f8ad1d53 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -114,6 +114,7 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | | mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | | Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | +| NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | From 1cddc5907fba062e0586078c0a1e4c819785f804 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 15:33:29 -0300 Subject: [PATCH 04/62] docs: reorganize the data resources - removed the statistics for number of files and size (often not verifiable, incorrect and hard to keep updated) - split the resources into categories, somewhat similar to the tools section --- resources/data/index.md | 81 +++++++++++++++++++++++++++-------------- 1 file changed, 54 insertions(+), 27 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index 72b3286e..b8c741e8 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -1,27 +1,54 @@ -Data Resources -============== - -| Catalog | Hosting | Zarr Files | Size | -| ------------------------------------------------------------------------ | -----------------------------------------------------| ------------ | -------- | -| [BIA Samples](https://bit.ly/bia-ome-ngff-samples) | EBI | 90 | 200 GB | -| [BioFile Finder](https://bff.allencell.org/datasets) | AWS Open Data Program & others | 78091 | ? TB | -| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | AWS Open Data Program | 37585 | 70 TB | -| [Cell Painting Gallery](https://github.com/broadinstitute/cellpainting-gallery) | AWS Open Data Program | 136 | 20 TB | -| [CZB-Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | czbiohub | 5 | 1.2 TB | -| [DANDI](https://dandiarchive.org/dandiset/000108) ([identifiers.org][dandi2],[github][dandi3]) | AWS Open Data Program | 3914 | 355 TB | -| [JAX](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory | 17000 | 192 TB | -| [Glencoe](https://glencoesoftware.com/ngff) | Glencoe Software, Inc. | 8 | 165 GB | -| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | EBI | 88 | 3 TB | -| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | EBI | 1644 | 47 TB | -| [MoBIE](https://mobie.github.io/specs/ngff.html) | EMBL-HD | 21 | 2 TB | -| [Neural Dynamics](https://registry.opendata.aws/allen-nd-open-data/) | AWS Open Data Program | 90 | 200 TB | -| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) | AWS Open Data Program | 624 | 372 GB | -| [Sanger](https://www.sanger.ac.uk/project/ome-zarr/) | Sanger, UK | 10 | 1 TB | -| [SpatialData](https://github.com/scverse/spatialdata-notebooks/tree/main/datasets) | EMBL-HD | 10 | 25 GB | -| [SSBD](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | SSBD | 5000 | 20 TB | -| [webKnossos](https://zarr.webknossos.org) | scalable minds | 69 | 70 TB | - -OME-Zarr 0.5 data has been collected during [the OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/). - -[dandi2]: https://identifiers.org/DANDI:000108 -[dandi3]: https://github.com/dandisets/000108 +# Data Resources + +Looking for test data? [IDR Samples](https://idr.github.io/ome-ngff-samples/) aims at covering the different corners of the specification. + +After this quick reference, you can find a diverse set of data resources in OME-Zarr format, illustrating the range of scientific stories enabled by the format. + +Do you have a data resource in OME-Zarr format that you would like to share? Is there something missing? Please submit an [issue](https://github.com/ome/ngff/issues) or [pull request](https://github.com/ome/ngff/pulls) to update this list. + +## Sample data + +Resources curating OME-Zarr sample data, for demonstration and testing purposes. + +| Resource | Description +| ------------------------------------------------------------------------ | ---------------------------------------------------| +| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | +| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html)| Sample OME-Zarr datasets from the BioImage Archive for testing | +| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | +| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes. | + | [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format. | + +## Data portals + +Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available. + +| Resource | Description +| ------------------------------------------------------------------------ | ---------------------------------------------------| +| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | +| [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support.| +| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | +| [webknossos Zarr Gallery](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis.| +| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data. | + +## Datasets + +These are datasets available in OME-Zarr format, hosted in various locations. They are representative of different types of scientific stories enabled by OME-Zarr. +|Resource | Description +| ------------------------------------------------------------------------ | ---------------------------------------------------| +| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | + +## Atlases + +These are "atlas"-like datasets, which provide a comprehensive view of a particular biological system. + +| Resource | Description| +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | + +# Other resources +These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. + +| Resource | Description +| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data +| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes.| +| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | +|[SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | From be22872f6a5625397670e910743fab44d63090bd Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 15:39:19 -0300 Subject: [PATCH 05/62] Add pointer to the Zarr documentation motivated by the mention of zarrs in #525 --- resources/tools/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index f8ad1d53..a3837160 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -2,6 +2,8 @@ A list of tools and libraries with OME-Zarr support. These are developed by various members of the NGFF community. If you think your tool/library should be listed here, please [open a pull request](https://github.com/ome/ngff). +For tools supporting the core Zarr specification, agnostic to NGFF, see the [Zarr documentation](https://zarr.dev/implementations/). + ## Contents - [Tools](#tools) From 3e63cb49ff186e0aeb9d2ebcbb5b401e4fcb7ca2 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 16:27:58 -0300 Subject: [PATCH 06/62] docs: add atlas/stories content --- resources/data/index.md | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index b8c741e8..bef1bb4d 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -39,10 +39,23 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th ## Atlases -These are "atlas"-like datasets, which provide a comprehensive view of a particular biological system. +These are "atlas"-like datasets, which provide a comprehensive view of a particular biological system. The metadata-rich, streaming-friendly nature of OME-Zarr makes it ideal for sharing and visualizing large, complex datasets that are often associated with atlases. -| Resource | Description| -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | +The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https://www.nature.com/articles/s41592-024-02371-x)) demonstrates how OME-Zarr can be used in the context of deploying such atlases in the context of spatial transcriptomics. The examples, however, cover also other types of data, including volumetric electron microscopy, expansion microscopy and light sheet imaging. + + +## + + +| Resource | Description| Publication| Sample | +| ------------------------------------------------------------------------ | ---------------------------------------------------| ---------------------------------------------------| ---------------------------------------------------| +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging |-|-| +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). ||[vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/)|-|-|-| +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) |-|[Ben-Simon et al., 2025](https://www.cell.com/cell/fulltext/S0092-8674(25)00513-6)|-| +| [Platynereis cell atlas](https://platynereis.com/resources/image/)|-|[Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017)| [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D)| +| [OpenOrganelle](https://openorganelle.janelia.org/)|An open-access volume electron microscopy atlas of whole cells and tissues|[Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4)| [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D)| +**** # Other resources These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. From b9c513c3c867a8e01ab74eb18d14a72fdeffdbf8 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 16:32:21 -0300 Subject: [PATCH 07/62] docs: fix formatting of tables --- resources/data/index.md | 68 +++++++++++++++++++++-------------------- 1 file changed, 35 insertions(+), 33 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index bef1bb4d..06904f10 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -10,32 +10,33 @@ Do you have a data resource in OME-Zarr format that you would like to share? Is Resources curating OME-Zarr sample data, for demonstration and testing purposes. -| Resource | Description -| ------------------------------------------------------------------------ | ---------------------------------------------------| -| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | -| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html)| Sample OME-Zarr datasets from the BioImage Archive for testing | -| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | -| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes. | - | [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format. | +| Resource | Description | +| ------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------- | +| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | +| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | +| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | +| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes | +| [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format | ## Data portals Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available. -| Resource | Description -| ------------------------------------------------------------------------ | ---------------------------------------------------| -| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | -| [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support.| -| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | -| [webknossos Zarr Gallery](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis.| -| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data. | +| Resource | Description | +| -------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | +| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | +| [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support | +| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | +| [webknossos Zarr Gallery](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis. | +| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data | ## Datasets -These are datasets available in OME-Zarr format, hosted in various locations. They are representative of different types of scientific stories enabled by OME-Zarr. -|Resource | Description -| ------------------------------------------------------------------------ | ---------------------------------------------------| -| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | +These are datasets available in OME-Zarr format, hosted in various locations. They represent some of the different scientific stories enabled by OME-Zarr. + +| Resource | Description | +| --------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- | +| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | ## Atlases @@ -43,25 +44,26 @@ These are "atlas"-like datasets, which provide a comprehensive view of a particu The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https://www.nature.com/articles/s41592-024-02371-x)) demonstrates how OME-Zarr can be used in the context of deploying such atlases in the context of spatial transcriptomics. The examples, however, cover also other types of data, including volumetric electron microscopy, expansion microscopy and light sheet imaging. - ## +| Resource | Description | Publication | Sample | +| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) | +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - | +| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D) | +| [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D) | -| Resource | Description| Publication| Sample | -| ------------------------------------------------------------------------ | ---------------------------------------------------| ---------------------------------------------------| ---------------------------------------------------| -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging |-|-| -| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). ||[vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) -| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/)|-|-|-| -| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) |-|[Ben-Simon et al., 2025](https://www.cell.com/cell/fulltext/S0092-8674(25)00513-6)|-| -| [Platynereis cell atlas](https://platynereis.com/resources/image/)|-|[Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017)| [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D)| -| [OpenOrganelle](https://openorganelle.janelia.org/)|An open-access volume electron microscopy atlas of whole cells and tissues|[Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4)| [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D)| -**** +--- # Other resources + These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. -| Resource | Description -| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data -| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes.| -| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | -|[SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | +| Resource | Description | +| ----------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | +| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data | +| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes. | +| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | +| [SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | From 793fdc4e24ea3782d1b266321c4090b3696fbbe4 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 5 Jun 2026 08:47:31 -0300 Subject: [PATCH 08/62] fix: change neuroglancer links to proxy see github.com/German-BioImaging/ome-zarr-ideas/issues/115 --- resources/data/index.md | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index 06904f10..55b847c3 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -10,8 +10,8 @@ Do you have a data resource in OME-Zarr format that you would like to share? Is Resources curating OME-Zarr sample data, for demonstration and testing purposes. -| Resource | Description | -| ------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | | [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | | [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | @@ -22,8 +22,8 @@ Resources curating OME-Zarr sample data, for demonstration and testing purposes. Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available. -| Resource | Description | -| -------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | | [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support | | [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | @@ -34,8 +34,8 @@ Imaging data portals with curated OME-Zarr data, including public repositories. These are datasets available in OME-Zarr format, hosted in various locations. They represent some of the different scientific stories enabled by OME-Zarr. -| Resource | Description | -| --------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | ## Atlases @@ -46,14 +46,16 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ ## -| Resource | Description | Publication | Sample | -| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | -| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) | -| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | -| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - | -| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D) | -| [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D) | +| Resource | Description | Publication | Sample | +| ----------- | ----------------- | -------------------- | ----------- | +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) +| +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - +| +| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | +| [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://tiago.bio.br/links?go=open-organelle) | --- @@ -61,8 +63,8 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. -| Resource | Description | -| ----------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data | | [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes. | | [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | From ed05e910e7e82fc95410ae517b5e8cd9a17f213d Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Tue, 2 Jun 2026 11:54:31 +0100 Subject: [PATCH 09/62] Add kfb2zarr to Zarr converters --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index a3837160..487ff851 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -67,6 +67,7 @@ Check out the [readers and writers below](#zarr-readers--writers) to interact wi | BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | | EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | | ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | +| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | | multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | | nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | | Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | From 23cee0288a9207130f6a8085bbb6e8054c87580f Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 10:07:57 -0300 Subject: [PATCH 10/62] docs: fix odon logo --- resources/tools/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 487ff851..ee9bb00a 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -36,7 +36,7 @@ Want to view a Zarr? Use one of these. | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | | Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer |\ -| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | | Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | From b3a64f4fa7cd195d0213ee577b0f66c7ffee1a76 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 10:57:26 -0300 Subject: [PATCH 11/62] docs: Add Zallery closes #531 --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index ee9bb00a..b38978ad 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -121,4 +121,5 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Create searchable web-based OME-Zarr image galleries. | +| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Create searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | From 7732df8ea8f712992720b9331961fe84cf10d8c2 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 10:58:01 -0300 Subject: [PATCH 12/62] docs: update ngff-zarr link ping @thewtex --- resources/tools/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index b38978ad..23c46a0f 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -88,7 +88,7 @@ Want to read or write a Zarr? Use one of these tools. | Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | | BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | | iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | -| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/thewtex/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | +| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | | ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | | omero-zarr-pixel-buffer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/omero-zarr-pixel-buffer) | An OMERO server extension for reading OME-Zarr data from local or S3 storage. | | ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | From da8e8bde8e863423d0d2ffeec91ec5a83fded17e Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 11:07:46 -0300 Subject: [PATCH 13/62] docs: Add zowser --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 23c46a0f..f51c738b 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -121,5 +121,6 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Create searchable web-based OME-Zarr image galleries developed by Janelia. | | Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | +| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | From 000ff50d154003c6b0b7af27502f17f8f831eef5 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 11:34:33 -0300 Subject: [PATCH 14/62] Add Squid to tools Closes #530 --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index f51c738b..9378f682 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -121,6 +121,7 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | +| Squid | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Cephla-Lab/Squid)| An open-source confocal microscope with software to acquire and write OME-Zarr data. | | Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | | Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | | Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | From b75fccb7b0c6fabc0ca490b1f12be1d0a57febff Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 09:36:05 -0300 Subject: [PATCH 15/62] docs: add multiview stitcher Co-authored-by: m-albert --- resources/tools/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 9378f682..92e4419c 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -111,11 +111,11 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | Name | Link | Description | | -------- | ------- | ------- | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | -| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | +| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. || Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | | Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | | mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | +| multiview-stitcher | [multiview-stitcher logo]((https://github.com/multiview-stitcher/multiview-stitcher)) | Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. | | Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | | NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | From 6d2eb4c94d81bfcc7d0575db514e3cb3c3c305e8 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 10:38:06 -0300 Subject: [PATCH 16/62] fix: re-add fractal --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 92e4419c..e2674c18 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -111,7 +111,8 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | Name | Link | Description | | -------- | ------- | ------- | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. || Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | +| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | +| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | | Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | | mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | From 81a7b09fe9f8bd347662e496b27cd935c67990bf Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 15:25:16 -0300 Subject: [PATCH 17/62] docs: refactor the "other" category into /ecosystem Also adds mentions of BIDS (#514), Zowser, HuggingFace Hub, the thumbnails convention, RO-Crate and BioCroissant. --- resources/data/index.md | 2 +- resources/ecosystem/index.md | 75 ++++++++++++++++++++++++++++++++++++ resources/index.md | 5 +-- resources/tools/index.md | 25 ++++-------- 4 files changed, 85 insertions(+), 22 deletions(-) create mode 100644 resources/ecosystem/index.md diff --git a/resources/data/index.md b/resources/data/index.md index 55b847c3..aeef7a0b 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -16,7 +16,7 @@ Resources curating OME-Zarr sample data, for demonstration and testing purposes. | [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | | [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | | [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes | -| [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format | +| [OME 2024 NGFF challenge](https://ome.github.io/) | Close to 500 TB of data in the OME-Zarr 0.5 format | ## Data portals diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md new file mode 100644 index 00000000..6899a9fb --- /dev/null +++ b/resources/ecosystem/index.md @@ -0,0 +1,75 @@ +# Ecosystem + +Workflows and data formats that adopt OME-Zarr and build upon it for extended capabilities and interoperabilitieswith additional systems. + +It extends the [tools](../tools/index.md) section by including projects that are not necessarily tools for viewing, writing, reading, converting, validating or processing OME-Zarr data, but that are still part of a ecosystem of projects with first-class, dedicated support for OME-Zarr. + +It fits microscope acquisition software, analysis pipelines, standards and extensions, gallery-like displays, integrative workflows, and the like. + +## Standards and extensions + +| Name | Link | Description | Status | +| -------- | ------- | ------- | ------ | +| SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | [published](https://www.nature.com/articles/s41592-024-02212-x) | +| BIDS | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) | A community-developed standard for organizing and describing neuroscientific data, currently adding support for OME-Zarr. | [work in progress](https://github.com/bids-standard/bids-specification/pull/2392) | + + +## Gallery-like displays + +Tooling for sharing collections of OME-Zarr datasets in different ways. + +| Name | Link | Description | +| -------- | ------- | ------- | +| BioFileFinder | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/AllenInstitute/biofile-finder) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support. | +| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | +| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | +| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | + + +## Microscope acquisition software + +| Name | Link | Description | +| -------- | ------- | ------- | +| mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | +| Squid | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Cephla-Lab/Squid)| An open-source confocal microscope with software to acquire and write OME-Zarr data. | + +## Integrative workflows + +Tools that integrate OME-Zarr into workflows that support OME-Zarr as either as an input, output or intermediate format for processing/management pipelines. + +| Name | Link | Description | +| -------- | ------- | ------- | +| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | +| Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | +| Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | +| Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | +| multiview-stitcher | [multiview-stitcher logo]((https://github.com/multiview-stitcher/multiview-stitcher)) | Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. | +| NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| +| omero-zarr-pixel-buffer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/omero-zarr-pixel-buffer) | An OMERO server extension for reading OME-Zarr data from local or S3 storage. | + +## Data sharing + +Platforms with dedicated support for sharing OME-Zarr datasets, open to public data submission. + +| Name | Link | Description | +| -------- | ------- | ------- | +| BioImage Archive | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://www.ebi.ac.uk/bioimage-archive/) | A public repository for bioimaging data, with support for submissions of OME-Zarr datasets. | +| HuggingFace Hub | [![image](https://www.google.com/s2/favicons?sz=256&domain_url=huggingface.co)](https://huggingface.co/datasets) | A platform for sharing machine-learning datasets, with [ongoing updates](https://github.com/huggingface/datasets/pull/8135) for first-class support for OME-Zarr datasets. | + +Of course, many other platforms support sharing OME-Zarr datasets, but don't necessarily parse the OME metadata or provide any kind of custom support.One may share OME-Zarr datasets and get a DOI (but no S3-like access) in platforms like [Zenodo](https://zenodo.org), [Figshare](https://figshare.com), [Dryad](https://datadryad.org), etc. + +Conversely, one may not get a DOI, but may be able to share datasets with S3-like access for streaming/testing in platforms like [HuggingFace Buckets](https://huggingface.co/buckets), [Cloudflare R2](https://www.cloudflare.com/developer-platform/r2/), [AWS S3](https://aws.amazon.com/s3/), [Google Cloud Storage](https://cloud.google.com/storage), [Microsoft Azure Blob Storage](https://azure.microsoft.com/en-us/products/storage/blobs/), etc. Some of them offer free tiers for small and medium public datasets, as well as programs for supporting open science data sharing (like [AWS Open Data](https://aws.amazon.com/opendata/), [Google Cloud Public Datasets](https://cloud.google.com/datasets), [Microsoft Azure Open Datasets](https://azure.microsoft.com/en-us/services/open-datasets/), etc). + +## Extended metadata frameworks + +While these projects do not *adopt* OME-Zarr, they are resources studied in the context of extending the metadata capabilities of OME-Zarr. + +They are all projects which users of OME-Zarr may find useful to be aware of for workflows that require more complex metadata management, or for integration with other ecosystems. + + +| Name | Link | Description | Status | +| -------- | ------- | ------- | ------ | +| Thumbnails convention | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/clbarnes/zarr-convention-thumbnails) | A convention for storing thumbnail images in PNG or JPEG format alongside OME-Zarr datasets. | [work in progress](https://github.com/clbarnes/zarr-convention-thumbnails)| +| RO-Crate | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://www.researchobject.org/ro-crate/) | An approach to packaging research data with metadata with pilots for OME-Zarr integration. | [work in progress](https://www.researchobject.org/ro-crate/ome) (see also the [ome2024-ngff-challenge](https://github.com/ome/ome2024-ngff-challenge/)) | +| BioCroissant | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mlcommons/BioCroissant) | A community effort to extend the [Croissant](https://github.com/mlcommons/croissant) standard for packaging and sharing machine learning datasets in biology. | [work in progress](https://github.com/mlcommons/BioCroissant/discussions/5)| diff --git a/resources/index.md b/resources/index.md index 53ef8247..5c31cb79 100644 --- a/resources/index.md +++ b/resources/index.md @@ -7,12 +7,11 @@ */index ``` -This section provides resources related to OME-Zarr for users from all experience levels. +This section provides resources related to OME-Zarr for users from all experience levels. * [Data Resources](data/index.md) - A list of publicly available OME-Zarr datasets for testing and exploration. * [Publications](publications/index.md) - Publications and preprints related to OME-Zarr and NGFF. * [Tools](tools/index.md) - A list of tools for viewing, reading, writing, converting, validating and processing OME-Zarr data. * [Learning and Teaching Resources](learning-and-teaching-material/index.md) - A collection of tutorials, guides, slides, notebooks and other materials for OME-Zarr. * [OME-Zarr Ambassador Toolkit](ambassador-toolkit/index.md) - Slides, talking points and FAQs for confidently giving talks about OME-Zarr. - - +* [Ecosystem](ecosystem/index.md) - Workflows and data formats that adopt OME-Zarr and build upon it diff --git a/resources/tools/index.md b/resources/tools/index.md index e2674c18..825d0973 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -4,6 +4,8 @@ A list of tools and libraries with OME-Zarr support. These are developed by vari For tools supporting the core Zarr specification, agnostic to NGFF, see the [Zarr documentation](https://zarr.dev/implementations/). +While some tools would fit multiple categories, we assigned each tool to a single candidate best matching category. + ## Contents - [Tools](#tools) @@ -15,7 +17,7 @@ For tools supporting the core Zarr specification, agnostic to NGFF, see the [Zar - [Zarr converters](#zarr-converters) - [Zarr readers \& writers](#zarr-readers--writers) - [Zarr validation](#zarr-validation) - - [Other tools and libraries](#other-tools-and-libraries) + - [Rendering libraries](#rendering-libraries) ## Tools with a graphical interface @@ -90,7 +92,6 @@ Want to read or write a Zarr? Use one of these tools. | iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | | ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | | ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | -| omero-zarr-pixel-buffer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/omero-zarr-pixel-buffer) | An OMERO server extension for reading OME-Zarr data from local or S3 storage. | | ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | | ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py)| A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | | Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | @@ -105,24 +106,12 @@ Want to validate a Zarr? Use one of these. | ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | | yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | -## Other tools and libraries +## Rendering libraries -Tools that do not explicitly fit into any of the above categories (ex. Zarr computation workflow orchestrators) +Libraries that support the rendering and navigation of OME-Zarr data, but that are not themselves applications with a graphical user interface. | Name | Link | Description | | -------- | ------- | ------- | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | -| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | -| Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | -| Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | -| mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | -| multiview-stitcher | [multiview-stitcher logo]((https://github.com/multiview-stitcher/multiview-stitcher)) | Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. | -| Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | -| NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| + | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | -| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | -| SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | -| Squid | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Cephla-Lab/Squid)| An open-source confocal microscope with software to acquire and write OME-Zarr data. | -| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | -| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | +| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | From 987a072b2e53c2fc45dfc931f7477e3135a130aa Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 15:38:38 -0300 Subject: [PATCH 18/62] chore: use the OME icon as a browser favicon --- conf.py | 2 ++ images/favicon-16x16.png | Bin 0 -> 753 bytes 2 files changed, 2 insertions(+) create mode 100644 images/favicon-16x16.png diff --git a/conf.py b/conf.py index 29fcaf35..a92d3d0e 100644 --- a/conf.py +++ b/conf.py @@ -78,6 +78,8 @@ "use_download_button": True, } +html_favicon = "images/favicon-16x16.png" + html_static_path = ["_static"] html_css_files = [ diff --git a/images/favicon-16x16.png b/images/favicon-16x16.png new file mode 100644 index 0000000000000000000000000000000000000000..d894595a9a13bf5649835ca6ce2a80070e421393 GIT binary patch literal 753 zcmeAS@N?(olHy`uVBq!ia0vp^0wB!63?wyl`GbKJOS+@4BLl<6e(pbstU$g(vPY0F z14ES>14Ba#1H&(%P{RubhEf9thF1v;3|2E37{m+a>32_C|GG6UMZJAQx zjUtu#vR>`?G#u`0*x%Ezm+d_(>(wR`F-^99A5aZM8Biq}Th^^puqz!+9B2X%J1!ru=CT=||85(}dB~vQgjrX4HDAzm+k$nAlZ&j*i!Z+W`6X-YZL>}{hE2Ea8%}&O z|1@!u$?10rt`)55p}P8Ab0)k`?qB}GYNBuR!a1v^I!$qY5<7oM=+tk&x!Ep>T)QT) zX+O}dswJ)wB`Jv|saDBFsX&Us$iT=@*U(7U&^*M@z{=Rr%Gg-jz`)ADK&9X>Fg+k? z$jwj5OsmALAyn7Z0;nOpDkP#LD6w3jpeR2rGbdG{q_QAYA+w+)nSr5V&f`x!9ED*T z8mIhEpYePe#K5e~t(VL#tSsz3S%g_w!KK0Ea0;{X<`9L`H?EvGa^{H45%$v!9t*tm Z7+#4BmV9zDoeH#q!PC{xWt~$(69Djs0g(Uz literal 0 HcmV?d00001 From 15777559e4fc2215f044a46342d617ef45d44b11 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 16:51:33 -0300 Subject: [PATCH 19/62] Add links to fileglancer and biofilefinder docs --- resources/ecosystem/index.md | 16 +++++++--------- resources/tools/index.md | 1 - 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index 6899a9fb..96acc7fe 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -17,15 +17,13 @@ It fits microscope acquisition software, analysis pipelines, standards and exten ## Gallery-like displays Tooling for sharing collections of OME-Zarr datasets in different ways. - | Name | Link | Description | | -------- | ------- | ------- | -| BioFileFinder | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/AllenInstitute/biofile-finder) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support. | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | -| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | -| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | - +| BioFileFinder | website | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support. | +| Fileglancer | website | A webapp for browsing, sharing, and viewing OME-Zarr images. | +| Zallery | GitHub | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | +| Zarrcade | GitHub | Searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zowser | GitHub | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | ## Microscope acquisition software @@ -54,8 +52,8 @@ Platforms with dedicated support for sharing OME-Zarr datasets, open to public d | Name | Link | Description | | -------- | ------- | ------- | -| BioImage Archive | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://www.ebi.ac.uk/bioimage-archive/) | A public repository for bioimaging data, with support for submissions of OME-Zarr datasets. | -| HuggingFace Hub | [![image](https://www.google.com/s2/favicons?sz=256&domain_url=huggingface.co)](https://huggingface.co/datasets) | A platform for sharing machine-learning datasets, with [ongoing updates](https://github.com/huggingface/datasets/pull/8135) for first-class support for OME-Zarr datasets. | +| BioImage Archive | [BioImage Archive logo](https://www.ebi.ac.uk/bioimage-archive/) | A public repository for bioimaging data, with support for submissions of OME-Zarr datasets. | +| HuggingFace Hub | [HuggingFace Hub logo](https://huggingface.co/datasets) | A platform for sharing machine-learning datasets, with [ongoing updates](https://github.com/huggingface/datasets/pull/8135) for first-class support for OME-Zarr datasets. | Of course, many other platforms support sharing OME-Zarr datasets, but don't necessarily parse the OME metadata or provide any kind of custom support.One may share OME-Zarr datasets and get a DOI (but no S3-like access) in platforms like [Zenodo](https://zenodo.org), [Figshare](https://figshare.com), [Dryad](https://datadryad.org), etc. diff --git a/resources/tools/index.md b/resources/tools/index.md index 825d0973..abdc04f4 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -112,6 +112,5 @@ Libraries that support the rendering and navigation of OME-Zarr data, but that a | Name | Link | Description | | -------- | ------- | ------- | - | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | From 1bf4563a171acf197ac86daecd3587e1b1a0b66b Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 17:01:52 -0300 Subject: [PATCH 20/62] Add CT Herculaneum Scrolls (closes #500) --- resources/data/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/resources/data/index.md b/resources/data/index.md index aeef7a0b..7ea214a1 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -37,6 +37,8 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th | Resource | Description | | ---- | ---------------------- | | [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | +| [Herculaneum Scrolls](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) [source](https://github.com/ScrollPrize/open-data)| Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format.| + ## Atlases From a6c084ba5dfc14648371753741c0a43a67342b74 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 17:05:40 -0300 Subject: [PATCH 21/62] Add VoDaSuRe to data (closes #524) --- resources/data/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/data/index.md b/resources/data/index.md index 7ea214a1..5b611df3 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -38,7 +38,7 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th | ---- | ---------------------- | | [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | | [Herculaneum Scrolls](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) [source](https://github.com/ScrollPrize/open-data)| Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format.| - +| [VoDaSuRe](https://augusthoeg.github.io/VoDaSuRe/)| A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe))| ## Atlases From 43e2b55301a94a5a1ef5c0776658f500854e5794 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 17:24:50 -0300 Subject: [PATCH 22/62] Fill the gaps in the Atlases section --- resources/data/index.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index 5b611df3..4c4dc2d0 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -50,13 +50,11 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ | Resource | Description | Publication | Sample | | ----------- | ----------------- | -------------------- | ----------- | -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | -| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) -| -| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | -| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - -| -| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | [Lange et al., 2024](https://doi.org/https://doi.org/10.1016/j.cell.2024.09.047) | [zebrahub](https://zebrahub.sf.czbiohub.org/ngv?name=ZMNS001) | +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ([highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)) | [Mikus et al., 2024](https://doi.org/10.1101/2024.10.18.618984) | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0)| +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | Atlas of organs using Hierarchical Phase-Contrast Tomography (HiP-CT) | [Walsh et al., 2026](https://www.science.org/doi/10.1126/sciadv.adz2240) | [Human Organ Atlas](https://human-organ-atlas.esrf.fr/datasets/2439291070) | +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | A searchable web tool representing information and data on enhancer-adeno-associated viruses (enhancer AAVs) and mouse transgenes | [Ben-Simon et al., 2025]() | [atlas](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens/3PILF5KFKGJILDK30H2) +| [Platynereis cell atlas](https://platynereis.com/resources/image/) | An expression atlas registered to a whole-body electron microscopy volume of the nereid *Platynereis dumerilii* | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | | [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://tiago.bio.br/links?go=open-organelle) | --- From 87741405720495c0bf3deefd1a4bcb6033143683 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 11 Jun 2026 17:11:19 -0300 Subject: [PATCH 23/62] fix: remove wrong W3C branding, re-add OME They were lost in the migration from bs to Markdown. The old bikeshed documents were not rendering correctly --- boilerplate/copyright.include | 4 +++ boilerplate/header.include | 31 +++++++++++++++++ conf.py | 64 +++++++++++++++++++++++------------ 3 files changed, 78 insertions(+), 21 deletions(-) create mode 100644 boilerplate/copyright.include create mode 100644 boilerplate/header.include diff --git a/boilerplate/copyright.include b/boilerplate/copyright.include new file mode 100644 index 00000000..f0def708 --- /dev/null +++ b/boilerplate/copyright.include @@ -0,0 +1,4 @@ +Copyright © 2020-[YEAR] +OME® +(U. Dundee). +OME trademark rules apply. diff --git a/boilerplate/header.include b/boilerplate/header.include new file mode 100644 index 00000000..79b2fd56 --- /dev/null +++ b/boilerplate/header.include @@ -0,0 +1,31 @@ + + + + + + [TITLE] + + + +
+ + OME logo (6 circles in a hexagon) + +

[TITLE]

+

[LONGSTATUS], +

+
+
+

+
+
+ +
+ +

Status of this document

+
+
+ + +
diff --git a/conf.py b/conf.py index 29fcaf35..ede96b62 100644 --- a/conf.py +++ b/conf.py @@ -17,15 +17,12 @@ "myst_parser", "sphinx_reredirects", "sphinx_design", - "sphinxcontrib.bibtex"] + "sphinxcontrib.bibtex", +] bibtex_bibfiles = ["references.bib"] source_suffix = [".rst", ".md"] myst_heading_anchors = 5 -myst_enable_extensions = [ - "deflist", - "strikethrough", - "colon_fence" - ] +myst_enable_extensions = ["deflist", "strikethrough", "colon_fence"] templates_path = ["_templates"] exclude_patterns = [ @@ -57,7 +54,7 @@ "latest/index": "../specifications/0.5/index.html", "latest/": "../specifications/0.5/index.html", "dev/index": "../specifications/dev/index.html", - "dev/": "../specifications/dev/index.html" + "dev/": "../specifications/dev/index.html", } # -- Options for HTML output ------------------------------------------------- @@ -93,6 +90,7 @@ "_html_extra", ] + def build_served_html(): import glob import subprocess @@ -102,34 +100,58 @@ def build_served_html(): from pathlib import Path os.chdir(Path(__file__).parent) - versions = [d for d in os.listdir("specifications") if os.path.isdir(os.path.join("specifications", d))] + versions = [ + d + for d in os.listdir("specifications") + if os.path.isdir(os.path.join("specifications", d)) + ] for version in versions: # copy schemas to _html_extra - os.makedirs(f'_html_extra/{version}/schemas', exist_ok=True) - schemas = glob.glob(f'specifications/{version}/**/*.schema', recursive=True) + os.makedirs(f"_html_extra/{version}/schemas", exist_ok=True) + schemas = glob.glob(f"specifications/{version}/**/*.schema", recursive=True) for schema in schemas: - shutil.copy2(schema, f'_html_extra/{version}/schemas/') - print(f'✅ Copied schemas for version {version}') - + shutil.copy2(schema, f"_html_extra/{version}/schemas/") + print(f"✅ Copied schemas for version {version}") + # find 'pre_build.py' in 'specifications' subdirectories - script = glob.glob(f'specifications/{version}/**/pre_build.py', recursive=True)[0] + script = glob.glob(f"specifications/{version}/**/pre_build.py", recursive=True)[ + 0 + ] + + # Inject shared OME boilerplate next to index.bs so the legacy Bikeshed + # build renders OME branding instead of falling back to the W3C default. + # Kept here in the superproject so we never have to edit, commit, and + # bump every ngff-spec version submodule (the includes were lost exactly + # that way during the ngff -> ngff-spec migration). + spec_dir = os.path.dirname(script) + for inc in ("header.include", "copyright.include"): + src = os.path.join("boilerplate", inc) + if os.path.exists(src): + shutil.copy2(src, os.path.join(spec_dir, inc)) + print(f"✅ Injected {inc} for version {version}") + else: + print( + f"⚠️ Missing boilerplate/{inc}; {version} will use Bikeshed defaults" + ) subprocess.check_call([sys.executable, script]) - print('✅ Built rendered examples/schemas for version', version) + print("✅ Built rendered examples/schemas for version", version) # build jupyter-book docs in specification submodules - myst_file = glob.glob(f'specifications/{version}/**/myst.yml', recursive=True)[0] - bikeshed_output = f'specifications/{version}/index.html' + myst_file = glob.glob(f"specifications/{version}/**/myst.yml", recursive=True)[ + 0 + ] + bikeshed_output = f"specifications/{version}/index.html" # copy built html files to _html_extra try: if os.path.exists(bikeshed_output): - shutil.copy2(bikeshed_output, f'_html_extra/{version}/index.html') - print(f'✅ Found legacy bikeshed, serving as extra html for {version}') + shutil.copy2(bikeshed_output, f"_html_extra/{version}/index.html") + print(f"✅ Found legacy bikeshed, serving as extra html for {version}") except Exception as e: - print(f'⚠️ Could not copy served html for version {version}: {e}') + print(f"⚠️ Could not copy served html for version {version}: {e}") + build_served_html() - \ No newline at end of file From 15ab4dea2ce6395fff7bdf8a10df1881b8f7232e Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 11 Jun 2026 17:24:36 -0300 Subject: [PATCH 24/62] update bikeshed and Python versions --- readthedocs.yml | 4 ++-- requirements.txt | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/readthedocs.yml b/readthedocs.yml index 4f2967e9..f643b380 100644 --- a/readthedocs.yml +++ b/readthedocs.yml @@ -3,7 +3,7 @@ version: 2 build: os: ubuntu-24.04 tools: - python: "3.10" + python: "3.13" nodejs: "22" submodules: @@ -21,4 +21,4 @@ python: install: - requirements: requirements.txt - method: pip - path: specifications/dev \ No newline at end of file + path: specifications/dev diff --git a/requirements.txt b/requirements.txt index 3479fbfd..19336c7f 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,4 +1,4 @@ -bikeshed<4.2 +bikeshed myst-parser pydata-sphinx-theme json-schema-for-humans From 98e98789df650581b61ea7a767ffef21604c592e Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 12 Jun 2026 15:55:34 -0300 Subject: [PATCH 25/62] docs: reorganize FIJI libraries --- resources/tools/index.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index abdc04f4..2fa46d48 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -30,14 +30,16 @@ Want to view a Zarr? Use one of these. | Name | Link | Description | | -------- | ------- | ------- | -| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | -| FIJI (MoBIE / BigDataViewer) | [FIJI logo](https://mobie.github.io/) | [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | -| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | +| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | +| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | +| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data.| | ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | | Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer |\ +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | | Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | From 15fc2f392058c9fb57d71984b26792721a93dc6d Mon Sep 17 00:00:00 2001 From: Kevin Yamauchi Date: Tue, 16 Jun 2026 08:44:53 +0200 Subject: [PATCH 26/62] Add ez-zarr library to reader/writer table --- resources/tools/index.md | 111 +++++++++++++++++++-------------------- 1 file changed, 55 insertions(+), 56 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 2fa46d48..cf2fb6f7 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -19,7 +19,6 @@ While some tools would fit multiple categories, we assigned each tool to a singl - [Zarr validation](#zarr-validation) - [Rendering libraries](#rendering-libraries) - ## Tools with a graphical interface ### Zarr viewers @@ -28,32 +27,31 @@ Want to view a Zarr? Use one of these. [Check this out](https://ome.github.io/ome-ngff-tools/) to see viewer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| -------- | ------- | ------- | -| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | -| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | -| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | -| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | -| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data.| -| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | -| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | -| Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | -| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | -| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| -| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | -| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | -| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | -| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | -| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | - +| Name | Link | Description | +| ------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | +| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | +| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | +| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data. | +| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | +| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | +| Microscopy Nodes | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | +| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust. | +| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | +| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | +| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | +| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | +| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | ### Zarr converters (with a UI) Want to convert your file to Zarr? Use one of these tools that has a user interface. -| Name | Link | Description | -| -------- | ------- | ------- | +| Name | Link | Description | +| -------------- | ------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | | NGFF-Converter | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/NGFF-Converter) | A desktop application for conversion of bioimage formats into OME-Zarr or OME-TIFF. | ## Tools for the programmatically inclined @@ -64,20 +62,20 @@ Want to convert from a different file format to a Zarr? Use one of these tools. Check out the [readers and writers below](#zarr-readers--writers) to interact with Zarrs in others ways as well conversion. -| Name | Link | Description | -| -------- | ------- | ------- | -| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | -| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | -| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | -| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | -| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | -| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | -| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | -| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | -| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | -| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | -| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | -| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | +| Name | Link | Description | +| ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------- | ----------------- | +| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | +| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | +| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | +| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | +| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | +| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | +| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | +| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | +| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | +| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | +| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | +| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | ### Zarr readers & writers @@ -85,34 +83,35 @@ Want to read or write a Zarr? Use one of these tools. [Check this out](https://github.com/jwindhager/ome-ngff-readers-writers/) to see reader/writer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| -------- | ------- | ------- | -| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | -| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | -| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | -| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | -| iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | -| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | -| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | -| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | -| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py)| A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | -| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | +| Name | Link | Description | +| ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | +| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | +| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | +| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | +| iohub | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | +| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | +| ez-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fmicompbio/ez_zarr) | A Python and R package for reading and plotting OME-Zarr images. | +| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | +| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | +| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py) | A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | +| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | ### Zarr validation Want to validate a Zarr? Use one of these. -| Name | Link | Description | -| -------- | ------- | ------- | -| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | -| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | -| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | +| Name | Link | Description | +| ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------- | +| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | +| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | +| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | ## Rendering libraries Libraries that support the rendering and navigation of OME-Zarr data, but that are not themselves applications with a graphical user interface. -| Name | Link | Description | -| -------- | ------- | ------- | +| Name | Link | Description | +| ----------------- | ----------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------- | | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | -| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | +| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | From 55d6464819e9f7bb58afe582b2ea06b8cb62ce72 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 16 Jun 2026 08:59:06 -0300 Subject: [PATCH 27/62] fix: fix alphabetical ordering --- resources/tools/index.md | 112 ++++++++++++++++++++------------------- specifications/dev | 2 +- 2 files changed, 58 insertions(+), 56 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index cf2fb6f7..48949ee2 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -19,6 +19,7 @@ While some tools would fit multiple categories, we assigned each tool to a singl - [Zarr validation](#zarr-validation) - [Rendering libraries](#rendering-libraries) + ## Tools with a graphical interface ### Zarr viewers @@ -27,31 +28,32 @@ Want to view a Zarr? Use one of these. [Check this out](https://ome.github.io/ome-ngff-tools/) to see viewer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| ------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | -| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | -| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | -| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | -| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data. | -| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | -| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | -| Microscopy Nodes | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | -| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | -| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust. | -| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | -| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | -| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | -| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | -| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | +| Name | Link | Description | +| -------- | ------- | ------- | +| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | +| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | +| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | +| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data.| +| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | +| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | +| Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | +| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| +| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | +| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | +| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | +| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | +| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | + ### Zarr converters (with a UI) Want to convert your file to Zarr? Use one of these tools that has a user interface. -| Name | Link | Description | -| -------------- | ------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | +| Name | Link | Description | +| -------- | ------- | ------- | | NGFF-Converter | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/NGFF-Converter) | A desktop application for conversion of bioimage formats into OME-Zarr or OME-TIFF. | ## Tools for the programmatically inclined @@ -62,20 +64,20 @@ Want to convert from a different file format to a Zarr? Use one of these tools. Check out the [readers and writers below](#zarr-readers--writers) to interact with Zarrs in others ways as well conversion. -| Name | Link | Description | -| ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------- | ----------------- | -| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | -| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | -| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | -| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | -| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | -| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | -| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | -| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | -| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | -| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | -| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | -| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | +| Name | Link | Description | +| -------- | ------- | ------- | +| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | +| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | +| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | +| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | +| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | +| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | +| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | +| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | +| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | +| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | +| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | +| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | ### Zarr readers & writers @@ -83,35 +85,35 @@ Want to read or write a Zarr? Use one of these tools. [Check this out](https://github.com/jwindhager/ome-ngff-readers-writers/) to see reader/writer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | -| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | -| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | -| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | -| iohub | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | -| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | -| ez-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fmicompbio/ez_zarr) | A Python and R package for reading and plotting OME-Zarr images. | -| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | -| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | -| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py) | A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | -| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | +| Name | Link | Description | +| -------- | ------- | ------- | +| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | +| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | +| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | +| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | +| ez-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fmicompbio/ez_zarr) | A Python and R package for reading and plotting OME-Zarr images. | +| iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | +| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | +| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | +| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | +| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py)| A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | +| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | ### Zarr validation Want to validate a Zarr? Use one of these. -| Name | Link | Description | -| ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------- | -| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | -| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | -| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | +| Name | Link | Description | +| -------- | ------- | ------- | +| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | +| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | +| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | ## Rendering libraries Libraries that support the rendering and navigation of OME-Zarr data, but that are not themselves applications with a graphical user interface. -| Name | Link | Description | -| ----------------- | ----------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------- | +| Name | Link | Description | +| -------- | ------- | ------- | | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | -| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | +| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | diff --git a/specifications/dev b/specifications/dev index 44ffdf77..2f8be18e 160000 --- a/specifications/dev +++ b/specifications/dev @@ -1 +1 @@ -Subproject commit 44ffdf7742bcef5147fb320175e9432dccc9dabf +Subproject commit 2f8be18ead24401ed346954a603acdbdf8d68b89 From 2450406f198edf098c23188d184ba1ec8a4e2ec1 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 16 Jun 2026 09:12:39 -0300 Subject: [PATCH 28/62] set specifications/dev to 44ffdf7 --- specifications/dev | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/specifications/dev b/specifications/dev index 2f8be18e..44ffdf77 160000 --- a/specifications/dev +++ b/specifications/dev @@ -1 +1 @@ -Subproject commit 2f8be18ead24401ed346954a603acdbdf8d68b89 +Subproject commit 44ffdf7742bcef5147fb320175e9432dccc9dabf From 546018c791e751bdbff179eb752e0a1006b50012 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 16 Jun 2026 09:19:18 -0300 Subject: [PATCH 29/62] docs: add idetik Closes #539 --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index 48949ee2..0b6cef25 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -117,3 +117,4 @@ Libraries that support the rendering and navigation of OME-Zarr data, but that a | -------- | ------- | ------- | | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | +| idetik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/chanzuckerberg/idetik) | A library for building web-based image viewers. | From ca5c79f8e575ef1f985e688311a67afc60fb9cec Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 14:02:33 -0300 Subject: [PATCH 30/62] docs: add qupath to viewers closes #526 --- resources/tools/index.md | 15 +++++++++------ 1 file changed, 9 insertions(+), 6 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 1c24977e..4b854a46 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -4,14 +4,16 @@ A list of tools and libraries with OME-Zarr support. These are developed by vari ## Contents -- [Tools with a graphical interface (ex. a website)](#tools-with-a-graphical-interface) +- [Tools](#tools) + - [Contents](#contents) + - [Tools with a graphical interface](#tools-with-a-graphical-interface) - [Zarr viewers](#zarr-viewers) - - [Zarr converters](#zarr-converters-with-a-ui) -- [Tools for the programmatically inclined](#tools-for-the-programmatically-inclined) + - [Zarr converters (with a UI)](#zarr-converters-with-a-ui) + - [Tools for the programmatically inclined](#tools-for-the-programmatically-inclined) - [Zarr converters](#zarr-converters) - - [Zarr readers and writers](#zarr-readers--writers) - - [Validating Zarr](#zarr-validation) -- [Other zarr tools and libraries](#other-tools-and-libraries) + - [Zarr readers \& writers](#zarr-readers--writers) + - [Zarr validation](#zarr-validation) + - [Other tools and libraries](#other-tools-and-libraries) ## Tools with a graphical interface @@ -32,6 +34,7 @@ Want to view a Zarr? Use one of these. | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | | Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | | Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | | Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | From 948b571ac2d0f27b18ee49d371d2d4abc55b6473 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 14:05:01 -0300 Subject: [PATCH 31/62] docs: add odon to viewers closes #527 --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 4b854a46..65f31f14 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -33,7 +33,8 @@ Want to view a Zarr? Use one of these. | Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer |\ +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | | Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | From aa2e431f5b19b222f4b6099529ea61037b01cd43 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 14:08:01 -0300 Subject: [PATCH 32/62] docs: add biomero to tools closes #504 --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index 65f31f14..f8ad1d53 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -114,6 +114,7 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | | mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | | Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | +| NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | From c037c6b556dc78de5b5cc4051519c8a824839bf9 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 15:33:29 -0300 Subject: [PATCH 33/62] docs: reorganize the data resources - removed the statistics for number of files and size (often not verifiable, incorrect and hard to keep updated) - split the resources into categories, somewhat similar to the tools section --- resources/data/index.md | 81 +++++++++++++++++++++++++++-------------- 1 file changed, 54 insertions(+), 27 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index 72b3286e..b8c741e8 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -1,27 +1,54 @@ -Data Resources -============== - -| Catalog | Hosting | Zarr Files | Size | -| ------------------------------------------------------------------------ | -----------------------------------------------------| ------------ | -------- | -| [BIA Samples](https://bit.ly/bia-ome-ngff-samples) | EBI | 90 | 200 GB | -| [BioFile Finder](https://bff.allencell.org/datasets) | AWS Open Data Program & others | 78091 | ? TB | -| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | AWS Open Data Program | 37585 | 70 TB | -| [Cell Painting Gallery](https://github.com/broadinstitute/cellpainting-gallery) | AWS Open Data Program | 136 | 20 TB | -| [CZB-Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | czbiohub | 5 | 1.2 TB | -| [DANDI](https://dandiarchive.org/dandiset/000108) ([identifiers.org][dandi2],[github][dandi3]) | AWS Open Data Program | 3914 | 355 TB | -| [JAX](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory | 17000 | 192 TB | -| [Glencoe](https://glencoesoftware.com/ngff) | Glencoe Software, Inc. | 8 | 165 GB | -| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | EBI | 88 | 3 TB | -| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | EBI | 1644 | 47 TB | -| [MoBIE](https://mobie.github.io/specs/ngff.html) | EMBL-HD | 21 | 2 TB | -| [Neural Dynamics](https://registry.opendata.aws/allen-nd-open-data/) | AWS Open Data Program | 90 | 200 TB | -| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) | AWS Open Data Program | 624 | 372 GB | -| [Sanger](https://www.sanger.ac.uk/project/ome-zarr/) | Sanger, UK | 10 | 1 TB | -| [SpatialData](https://github.com/scverse/spatialdata-notebooks/tree/main/datasets) | EMBL-HD | 10 | 25 GB | -| [SSBD](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | SSBD | 5000 | 20 TB | -| [webKnossos](https://zarr.webknossos.org) | scalable minds | 69 | 70 TB | - -OME-Zarr 0.5 data has been collected during [the OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/). - -[dandi2]: https://identifiers.org/DANDI:000108 -[dandi3]: https://github.com/dandisets/000108 +# Data Resources + +Looking for test data? [IDR Samples](https://idr.github.io/ome-ngff-samples/) aims at covering the different corners of the specification. + +After this quick reference, you can find a diverse set of data resources in OME-Zarr format, illustrating the range of scientific stories enabled by the format. + +Do you have a data resource in OME-Zarr format that you would like to share? Is there something missing? Please submit an [issue](https://github.com/ome/ngff/issues) or [pull request](https://github.com/ome/ngff/pulls) to update this list. + +## Sample data + +Resources curating OME-Zarr sample data, for demonstration and testing purposes. + +| Resource | Description +| ------------------------------------------------------------------------ | ---------------------------------------------------| +| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | +| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html)| Sample OME-Zarr datasets from the BioImage Archive for testing | +| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | +| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes. | + | [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format. | + +## Data portals + +Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available. + +| Resource | Description +| ------------------------------------------------------------------------ | ---------------------------------------------------| +| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | +| [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support.| +| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | +| [webknossos Zarr Gallery](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis.| +| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data. | + +## Datasets + +These are datasets available in OME-Zarr format, hosted in various locations. They are representative of different types of scientific stories enabled by OME-Zarr. +|Resource | Description +| ------------------------------------------------------------------------ | ---------------------------------------------------| +| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | + +## Atlases + +These are "atlas"-like datasets, which provide a comprehensive view of a particular biological system. + +| Resource | Description| +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | + +# Other resources +These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. + +| Resource | Description +| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data +| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes.| +| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | +|[SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | From f865a1e9ad88e7b04250661592dc83fe5deebbd2 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 15:39:19 -0300 Subject: [PATCH 34/62] Add pointer to the Zarr documentation motivated by the mention of zarrs in #525 --- resources/tools/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index f8ad1d53..a3837160 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -2,6 +2,8 @@ A list of tools and libraries with OME-Zarr support. These are developed by various members of the NGFF community. If you think your tool/library should be listed here, please [open a pull request](https://github.com/ome/ngff). +For tools supporting the core Zarr specification, agnostic to NGFF, see the [Zarr documentation](https://zarr.dev/implementations/). + ## Contents - [Tools](#tools) From 991dd0bd5d1b8d99ae170e6e5d0b477543a93bff Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 16:27:58 -0300 Subject: [PATCH 35/62] docs: add atlas/stories content --- resources/data/index.md | 19 ++++++++++++++++--- 1 file changed, 16 insertions(+), 3 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index b8c741e8..bef1bb4d 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -39,10 +39,23 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th ## Atlases -These are "atlas"-like datasets, which provide a comprehensive view of a particular biological system. +These are "atlas"-like datasets, which provide a comprehensive view of a particular biological system. The metadata-rich, streaming-friendly nature of OME-Zarr makes it ideal for sharing and visualizing large, complex datasets that are often associated with atlases. -| Resource | Description| -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | +The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https://www.nature.com/articles/s41592-024-02371-x)) demonstrates how OME-Zarr can be used in the context of deploying such atlases in the context of spatial transcriptomics. The examples, however, cover also other types of data, including volumetric electron microscopy, expansion microscopy and light sheet imaging. + + +## + + +| Resource | Description| Publication| Sample | +| ------------------------------------------------------------------------ | ---------------------------------------------------| ---------------------------------------------------| ---------------------------------------------------| +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging |-|-| +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). ||[vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/)|-|-|-| +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) |-|[Ben-Simon et al., 2025](https://www.cell.com/cell/fulltext/S0092-8674(25)00513-6)|-| +| [Platynereis cell atlas](https://platynereis.com/resources/image/)|-|[Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017)| [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D)| +| [OpenOrganelle](https://openorganelle.janelia.org/)|An open-access volume electron microscopy atlas of whole cells and tissues|[Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4)| [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D)| +**** # Other resources These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. From 439f00d3b93e57a6d7e3580d4a667b3a01b0a526 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Thu, 4 Jun 2026 16:32:21 -0300 Subject: [PATCH 36/62] docs: fix formatting of tables --- resources/data/index.md | 68 +++++++++++++++++++++-------------------- 1 file changed, 35 insertions(+), 33 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index bef1bb4d..06904f10 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -10,32 +10,33 @@ Do you have a data resource in OME-Zarr format that you would like to share? Is Resources curating OME-Zarr sample data, for demonstration and testing purposes. -| Resource | Description -| ------------------------------------------------------------------------ | ---------------------------------------------------| -| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | -| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html)| Sample OME-Zarr datasets from the BioImage Archive for testing | -| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | -| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes. | - | [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format. | +| Resource | Description | +| ------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------- | +| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | +| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | +| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | +| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes | +| [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format | ## Data portals Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available. -| Resource | Description -| ------------------------------------------------------------------------ | ---------------------------------------------------| -| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | -| [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support.| -| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | -| [webknossos Zarr Gallery](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis.| -| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data. | +| Resource | Description | +| -------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | +| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | +| [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support | +| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | +| [webknossos Zarr Gallery](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis. | +| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data | ## Datasets -These are datasets available in OME-Zarr format, hosted in various locations. They are representative of different types of scientific stories enabled by OME-Zarr. -|Resource | Description -| ------------------------------------------------------------------------ | ---------------------------------------------------| -| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | +These are datasets available in OME-Zarr format, hosted in various locations. They represent some of the different scientific stories enabled by OME-Zarr. + +| Resource | Description | +| --------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- | +| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | ## Atlases @@ -43,25 +44,26 @@ These are "atlas"-like datasets, which provide a comprehensive view of a particu The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https://www.nature.com/articles/s41592-024-02371-x)) demonstrates how OME-Zarr can be used in the context of deploying such atlases in the context of spatial transcriptomics. The examples, however, cover also other types of data, including volumetric electron microscopy, expansion microscopy and light sheet imaging. - ## +| Resource | Description | Publication | Sample | +| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) | +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - | +| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D) | +| [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D) | -| Resource | Description| Publication| Sample | -| ------------------------------------------------------------------------ | ---------------------------------------------------| ---------------------------------------------------| ---------------------------------------------------| -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging |-|-| -| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). ||[vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) -| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/)|-|-|-| -| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) |-|[Ben-Simon et al., 2025](https://www.cell.com/cell/fulltext/S0092-8674(25)00513-6)|-| -| [Platynereis cell atlas](https://platynereis.com/resources/image/)|-|[Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017)| [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D)| -| [OpenOrganelle](https://openorganelle.janelia.org/)|An open-access volume electron microscopy atlas of whole cells and tissues|[Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4)| [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D)| -**** +--- # Other resources + These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. -| Resource | Description -| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data -| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes.| -| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | -|[SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | +| Resource | Description | +| ----------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | +| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data | +| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes. | +| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | +| [SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | From a8e2dd3f36b42e6f9699d0812df180c18a82f100 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 5 Jun 2026 08:47:31 -0300 Subject: [PATCH 37/62] fix: change neuroglancer links to proxy see github.com/German-BioImaging/ome-zarr-ideas/issues/115 --- resources/data/index.md | 34 ++++++++++++++++++---------------- 1 file changed, 18 insertions(+), 16 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index 06904f10..55b847c3 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -10,8 +10,8 @@ Do you have a data resource in OME-Zarr format that you would like to share? Is Resources curating OME-Zarr sample data, for demonstration and testing purposes. -| Resource | Description | -| ------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | | [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | | [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | @@ -22,8 +22,8 @@ Resources curating OME-Zarr sample data, for demonstration and testing purposes. Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available. -| Resource | Description | -| -------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | | [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support | | [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | @@ -34,8 +34,8 @@ Imaging data portals with curated OME-Zarr data, including public repositories. These are datasets available in OME-Zarr format, hosted in various locations. They represent some of the different scientific stories enabled by OME-Zarr. -| Resource | Description | -| --------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | ## Atlases @@ -46,14 +46,16 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ ## -| Resource | Description | Publication | Sample | -| --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | -| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) | -| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | -| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - | -| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https%3A%2F%2Fneuroglancer-demo.appspot.com%2F%23%21%7B%22dimensions%22%3A%7B%22x%22%3A%5B1e-8%252C%22m%22%5D%252C%22y%22%3A%5B1e-8%252C%22m%22%5D%252C%22z%22%3A%5B2.5e-8%252C%22m%22%5D%7D%252C%22position%22%3A%5B19076.947265625%252C14208%252C4272%5D%252C%22crossSectionScale%22%3A36.598234443678%252C%22projectionScale%22%3A32768%252C%22layers%22%3A%5B%7B%22type%22%3A%22image%22%252C%22source%22%3A%22https%3A%2F%2Fs3.embl.de%2Fi2k-2020%2Fplaty-raw.ome.zarr%22%252C%22tab%22%3A%22source%22%252C%22opacity%22%3A1%252C%22blend%22%3A%22additive%22%252C%22shader%22%3A%22%23uicontrol%20invlerp%20contrast%5Cn%23uicontrol%20vec3%20color%20color%5Cnvoid%20main%28%29%20%7B%5Cn%2520%20float%20contrast_value%20%3D%20contrast%28%29%253B%5Cn%2520%20if%20%28VOLUME_RENDERING%29%20%7B%5Cn%2520%2520%2520%20emitRGBA%28vec4%28color%20%2A%20contrast_value%252C%20contrast_value%29%29%253B%5Cn%2520%20%7D%5Cn%2520%20else%20%7B%5Cn%2520%2520%2520%20emitRGB%28color%20%2A%20contrast_value%29%253B%5Cn%2520%20%7D%5Cn%7D%5Cn%22%252C%22shaderControls%22%3A%7B%22contrast%22%3A%7B%22range%22%3A%5B135%252C184%5D%252C%22window%22%3A%5B123%252C196%5D%7D%7D%252C%22volumeRenderingDepthSamples%22%3A256%252C%22name%22%3A%22OME-NGFF%22%7D%5D%252C%22layout%22%3A%224panel%22%252C%22helpPanel%22%3A%7B%22row%22%3A2%7D%252C%22settingsPanel%22%3A%7B%22row%22%3A3%7D%252C%22toolPalettes%22%3A%7B%22Shader%20controls%22%3A%7B%22side%22%3A%22left%22%252C%22row%22%3A1%252C%22query%22%3A%22type%3AshaderControl%22%7D%7D%7D) | -| [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://neuroglancer-demo.appspot.com/#!%7B%22dimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22position%22:%5B19998.5%2C3998.5%2C18624.5%5D%2C%22crossSectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22crossSectionScale%22:50%2C%22projectionOrientation%22:%5B1%2C0%2C0%2C0%5D%2C%22projectionScale%22:65536%2C%22layers%22:%5B%7B%22type%22:%22image%22%2C%22source%22:%22zarr://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.zarr/recon-1/em/fibsem-uint8/%22%2C%22tab%22:%22rendering%22%2C%22opacity%22:0.75%2C%22blend%22:%22additive%22%2C%22shader%22:%22#uicontrol%20invlerp%20normalized%28range=%5B203%2C%20238%5D%2C%20window=%5B0%2C%20255%5D%29%5Cn#uicontrol%20vec3%20color%20color%28default=%5C%22white%5C%22%29%5Cnvoid%20main%28%29%7BemitRGB%28color%20%2A%20normalized%28%29%29%3B%7D%22%2C%22name%22:%22fibsem-uint16%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/vesicle_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/vesicle_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22vesicle_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/pm_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/pm_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ffa500%22%2C%22name%22:%22pm_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%7B%22url%22:%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/nucleus_seg%22%2C%22transform%22:%7B%22outputDimensions%22:%7B%22x%22:%5B1e-9%2C%22m%22%5D%2C%22y%22:%5B1e-9%2C%22m%22%5D%2C%22z%22:%5B1e-9%2C%22m%22%5D%7D%2C%22inputDimensions%22:%7B%22x%22:%5B4e-9%2C%22m%22%5D%2C%22y%22:%5B4e-9%2C%22m%22%5D%2C%22z%22:%5B3.36e-9%2C%22m%22%5D%7D%7D%7D%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/nucleus_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff0000%22%2C%22name%22:%22nucleus_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/mito_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/mito_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#008000%22%2C%22name%22:%22mito_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/golgi_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/golgi_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#00ffff%22%2C%22name%22:%22golgi_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/er_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/er_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#0000ff%22%2C%22name%22:%22er_seg%22%7D%2C%7B%22type%22:%22segmentation%22%2C%22source%22:%5B%22n5://s3://janelia-cosem-datasets/jrc_macrophage-2/jrc_macrophage-2.n5/labels/endo_seg%22%2C%22precomputed://s3://janelia-cosem-datasets/jrc_macrophage-2/neuroglancer/mesh/endo_seg%22%5D%2C%22tab%22:%22source%22%2C%22segments%22:%5B%5D%2C%22segmentDefaultColor%22:%22#ff00ff%22%2C%22name%22:%22endo_seg%22%7D%5D%2C%22selectedLayer%22:%7B%22visible%22:true%2C%22layer%22:%22fibsem-uint16%22%7D%2C%22crossSectionBackgroundColor%22:%22#000000%22%2C%22layout%22:%224panel%22%7D) | +| Resource | Description | Publication | Sample | +| ----------- | ----------------- | -------------------- | ----------- | +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) +| +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - +| +| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | +| [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://tiago.bio.br/links?go=open-organelle) | --- @@ -61,8 +63,8 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. -| Resource | Description | -| ----------------------------------------------------------------------------------------------------------------------------------------------------- | -------------------------------------------------------------------------------------------------------------------------- | +| Resource | Description | +| ---- | ---------------------- | | [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data | | [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes. | | [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | From ec46634910d790863c5e2580b8fca39c3880b49c Mon Sep 17 00:00:00 2001 From: Cameron Lloyd Date: Tue, 2 Jun 2026 11:54:31 +0100 Subject: [PATCH 38/62] Add kfb2zarr to Zarr converters --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index a3837160..487ff851 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -67,6 +67,7 @@ Check out the [readers and writers below](#zarr-readers--writers) to interact wi | BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | | EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | | ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | +| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | | multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | | nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | | Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | From 0366258bd3c87cea9626d9c6748b731327de3904 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 10:07:57 -0300 Subject: [PATCH 39/62] docs: fix odon logo --- resources/tools/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 487ff851..ee9bb00a 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -36,7 +36,7 @@ Want to view a Zarr? Use one of these. | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | | Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer |\ -| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | | Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | From 282b302a43f3c3745a32c18bbfdcb7320a3ed268 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 10:57:26 -0300 Subject: [PATCH 40/62] docs: Add Zallery closes #531 --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index ee9bb00a..b38978ad 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -121,4 +121,5 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Create searchable web-based OME-Zarr image galleries. | +| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Create searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | From c7b9399b62379af7337a8e9ae0a2ebca1fe6b594 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 10:58:01 -0300 Subject: [PATCH 41/62] docs: update ngff-zarr link ping @thewtex --- resources/tools/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index b38978ad..23c46a0f 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -88,7 +88,7 @@ Want to read or write a Zarr? Use one of these tools. | Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | | BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | | iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | -| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/thewtex/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | +| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | | ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | | omero-zarr-pixel-buffer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/omero-zarr-pixel-buffer) | An OMERO server extension for reading OME-Zarr data from local or S3 storage. | | ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | From 7e35c44276b7a40de7a442febf32db1a24e839e9 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 11:07:46 -0300 Subject: [PATCH 42/62] docs: Add zowser --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 23c46a0f..f51c738b 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -121,5 +121,6 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Create searchable web-based OME-Zarr image galleries developed by Janelia. | | Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | +| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | From 472240bf69d25c27e50e8aefdc24c024b669680a Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Mon, 8 Jun 2026 11:34:33 -0300 Subject: [PATCH 43/62] Add Squid to tools Closes #530 --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index f51c738b..9378f682 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -121,6 +121,7 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | | SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | +| Squid | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Cephla-Lab/Squid)| An open-source confocal microscope with software to acquire and write OME-Zarr data. | | Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | | Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | | Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | From 74579452f74486e06730c3e9efaad90685dda2c4 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 09:36:05 -0300 Subject: [PATCH 44/62] docs: add multiview stitcher Co-authored-by: m-albert --- resources/tools/index.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 9378f682..92e4419c 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -111,11 +111,11 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | Name | Link | Description | | -------- | ------- | ------- | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | -| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | +| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. || Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | | Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | | mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | +| multiview-stitcher | [multiview-stitcher logo]((https://github.com/multiview-stitcher/multiview-stitcher)) | Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. | | Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | | NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | From 541ed45eb2ff655f827b5136c0909343b39d5694 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 10:38:06 -0300 Subject: [PATCH 45/62] fix: re-add fractal --- resources/tools/index.md | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 92e4419c..e2674c18 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -111,7 +111,8 @@ Tools that do not explicitly fit into any of the above categories (ex. Zarr comp | Name | Link | Description | | -------- | ------- | ------- | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. || Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | +| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | +| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | | Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | | mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | From ee6b1db9e212712bf360bde78e04065306def324 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 15:25:16 -0300 Subject: [PATCH 46/62] docs: refactor the "other" category into /ecosystem Also adds mentions of BIDS (#514), Zowser, HuggingFace Hub, the thumbnails convention, RO-Crate and BioCroissant. --- resources/data/index.md | 2 +- resources/ecosystem/index.md | 75 ++++++++++++++++++++++++++++++++++++ resources/index.md | 5 +-- resources/tools/index.md | 25 ++++-------- 4 files changed, 85 insertions(+), 22 deletions(-) create mode 100644 resources/ecosystem/index.md diff --git a/resources/data/index.md b/resources/data/index.md index 55b847c3..aeef7a0b 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -16,7 +16,7 @@ Resources curating OME-Zarr sample data, for demonstration and testing purposes. | [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | | [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | | [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes | -| [OME 2024 NGFF challenge](https://ome.github.io/ome2024-ngff-challenge/) | Close to 500 TB of data in the OME-Zarr 0.5 format | +| [OME 2024 NGFF challenge](https://ome.github.io/) | Close to 500 TB of data in the OME-Zarr 0.5 format | ## Data portals diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md new file mode 100644 index 00000000..6899a9fb --- /dev/null +++ b/resources/ecosystem/index.md @@ -0,0 +1,75 @@ +# Ecosystem + +Workflows and data formats that adopt OME-Zarr and build upon it for extended capabilities and interoperabilitieswith additional systems. + +It extends the [tools](../tools/index.md) section by including projects that are not necessarily tools for viewing, writing, reading, converting, validating or processing OME-Zarr data, but that are still part of a ecosystem of projects with first-class, dedicated support for OME-Zarr. + +It fits microscope acquisition software, analysis pipelines, standards and extensions, gallery-like displays, integrative workflows, and the like. + +## Standards and extensions + +| Name | Link | Description | Status | +| -------- | ------- | ------- | ------ | +| SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | [published](https://www.nature.com/articles/s41592-024-02212-x) | +| BIDS | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://bids-specification.readthedocs.io/en/stable/common-principles.html#imaging-files) | A community-developed standard for organizing and describing neuroscientific data, currently adding support for OME-Zarr. | [work in progress](https://github.com/bids-standard/bids-specification/pull/2392) | + + +## Gallery-like displays + +Tooling for sharing collections of OME-Zarr datasets in different ways. + +| Name | Link | Description | +| -------- | ------- | ------- | +| BioFileFinder | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/AllenInstitute/biofile-finder) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support. | +| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | +| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | +| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | + + +## Microscope acquisition software + +| Name | Link | Description | +| -------- | ------- | ------- | +| mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | +| Squid | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Cephla-Lab/Squid)| An open-source confocal microscope with software to acquire and write OME-Zarr data. | + +## Integrative workflows + +Tools that integrate OME-Zarr into workflows that support OME-Zarr as either as an input, output or intermediate format for processing/management pipelines. + +| Name | Link | Description | +| -------- | ------- | ------- | +| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | +| Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | +| Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | +| Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | +| multiview-stitcher | [multiview-stitcher logo]((https://github.com/multiview-stitcher/multiview-stitcher)) | Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. | +| NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| +| omero-zarr-pixel-buffer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/omero-zarr-pixel-buffer) | An OMERO server extension for reading OME-Zarr data from local or S3 storage. | + +## Data sharing + +Platforms with dedicated support for sharing OME-Zarr datasets, open to public data submission. + +| Name | Link | Description | +| -------- | ------- | ------- | +| BioImage Archive | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://www.ebi.ac.uk/bioimage-archive/) | A public repository for bioimaging data, with support for submissions of OME-Zarr datasets. | +| HuggingFace Hub | [![image](https://www.google.com/s2/favicons?sz=256&domain_url=huggingface.co)](https://huggingface.co/datasets) | A platform for sharing machine-learning datasets, with [ongoing updates](https://github.com/huggingface/datasets/pull/8135) for first-class support for OME-Zarr datasets. | + +Of course, many other platforms support sharing OME-Zarr datasets, but don't necessarily parse the OME metadata or provide any kind of custom support.One may share OME-Zarr datasets and get a DOI (but no S3-like access) in platforms like [Zenodo](https://zenodo.org), [Figshare](https://figshare.com), [Dryad](https://datadryad.org), etc. + +Conversely, one may not get a DOI, but may be able to share datasets with S3-like access for streaming/testing in platforms like [HuggingFace Buckets](https://huggingface.co/buckets), [Cloudflare R2](https://www.cloudflare.com/developer-platform/r2/), [AWS S3](https://aws.amazon.com/s3/), [Google Cloud Storage](https://cloud.google.com/storage), [Microsoft Azure Blob Storage](https://azure.microsoft.com/en-us/products/storage/blobs/), etc. Some of them offer free tiers for small and medium public datasets, as well as programs for supporting open science data sharing (like [AWS Open Data](https://aws.amazon.com/opendata/), [Google Cloud Public Datasets](https://cloud.google.com/datasets), [Microsoft Azure Open Datasets](https://azure.microsoft.com/en-us/services/open-datasets/), etc). + +## Extended metadata frameworks + +While these projects do not *adopt* OME-Zarr, they are resources studied in the context of extending the metadata capabilities of OME-Zarr. + +They are all projects which users of OME-Zarr may find useful to be aware of for workflows that require more complex metadata management, or for integration with other ecosystems. + + +| Name | Link | Description | Status | +| -------- | ------- | ------- | ------ | +| Thumbnails convention | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/clbarnes/zarr-convention-thumbnails) | A convention for storing thumbnail images in PNG or JPEG format alongside OME-Zarr datasets. | [work in progress](https://github.com/clbarnes/zarr-convention-thumbnails)| +| RO-Crate | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://www.researchobject.org/ro-crate/) | An approach to packaging research data with metadata with pilots for OME-Zarr integration. | [work in progress](https://www.researchobject.org/ro-crate/ome) (see also the [ome2024-ngff-challenge](https://github.com/ome/ome2024-ngff-challenge/)) | +| BioCroissant | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mlcommons/BioCroissant) | A community effort to extend the [Croissant](https://github.com/mlcommons/croissant) standard for packaging and sharing machine learning datasets in biology. | [work in progress](https://github.com/mlcommons/BioCroissant/discussions/5)| diff --git a/resources/index.md b/resources/index.md index 53ef8247..5c31cb79 100644 --- a/resources/index.md +++ b/resources/index.md @@ -7,12 +7,11 @@ */index ``` -This section provides resources related to OME-Zarr for users from all experience levels. +This section provides resources related to OME-Zarr for users from all experience levels. * [Data Resources](data/index.md) - A list of publicly available OME-Zarr datasets for testing and exploration. * [Publications](publications/index.md) - Publications and preprints related to OME-Zarr and NGFF. * [Tools](tools/index.md) - A list of tools for viewing, reading, writing, converting, validating and processing OME-Zarr data. * [Learning and Teaching Resources](learning-and-teaching-material/index.md) - A collection of tutorials, guides, slides, notebooks and other materials for OME-Zarr. * [OME-Zarr Ambassador Toolkit](ambassador-toolkit/index.md) - Slides, talking points and FAQs for confidently giving talks about OME-Zarr. - - +* [Ecosystem](ecosystem/index.md) - Workflows and data formats that adopt OME-Zarr and build upon it diff --git a/resources/tools/index.md b/resources/tools/index.md index e2674c18..825d0973 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -4,6 +4,8 @@ A list of tools and libraries with OME-Zarr support. These are developed by vari For tools supporting the core Zarr specification, agnostic to NGFF, see the [Zarr documentation](https://zarr.dev/implementations/). +While some tools would fit multiple categories, we assigned each tool to a single candidate best matching category. + ## Contents - [Tools](#tools) @@ -15,7 +17,7 @@ For tools supporting the core Zarr specification, agnostic to NGFF, see the [Zar - [Zarr converters](#zarr-converters) - [Zarr readers \& writers](#zarr-readers--writers) - [Zarr validation](#zarr-validation) - - [Other tools and libraries](#other-tools-and-libraries) + - [Rendering libraries](#rendering-libraries) ## Tools with a graphical interface @@ -90,7 +92,6 @@ Want to read or write a Zarr? Use one of these tools. | iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | | ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | | ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | -| omero-zarr-pixel-buffer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/omero-zarr-pixel-buffer) | An OMERO server extension for reading OME-Zarr data from local or S3 storage. | | ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | | ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py)| A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | | Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | @@ -105,24 +106,12 @@ Want to validate a Zarr? Use one of these. | ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | | yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | -## Other tools and libraries +## Rendering libraries -Tools that do not explicitly fit into any of the above categories (ex. Zarr computation workflow orchestrators) +Libraries that support the rendering and navigation of OME-Zarr data, but that are not themselves applications with a graphical user interface. | Name | Link | Description | | -------- | ------- | ------- | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | -| Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | -| Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | -| Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | -| mesoSPIM-control | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/mesoSPIM/mesoSPIM-control) | Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. | -| multiview-stitcher | [multiview-stitcher logo]((https://github.com/multiview-stitcher/multiview-stitcher)) | Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. | -| Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | -| NL-BIOMERO| [NL-BIOMERO logo](https://github.com/NL-BioImaging/NL-BIOMERO) | An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web.| + | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | -| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnnails and images. | -| SpatialData | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/scverse/spatialdata) | An open and universal framework for processing spatial omics data. | -| Squid | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Cephla-Lab/Squid)| An open-source confocal microscope with software to acquire and write OME-Zarr data. | -| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | -| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | +| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | From be54c8fd4f4965d22491103df0bbcf904d0c48be Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 9 Jun 2026 15:38:38 -0300 Subject: [PATCH 47/62] chore: use the OME icon as a browser favicon --- conf.py | 2 ++ images/favicon-16x16.png | Bin 0 -> 753 bytes 2 files changed, 2 insertions(+) create mode 100644 images/favicon-16x16.png diff --git a/conf.py b/conf.py index ede96b62..55152f5e 100644 --- a/conf.py +++ b/conf.py @@ -75,6 +75,8 @@ "use_download_button": True, } +html_favicon = "images/favicon-16x16.png" + html_static_path = ["_static"] html_css_files = [ diff --git a/images/favicon-16x16.png b/images/favicon-16x16.png new file mode 100644 index 0000000000000000000000000000000000000000..d894595a9a13bf5649835ca6ce2a80070e421393 GIT binary patch literal 753 zcmeAS@N?(olHy`uVBq!ia0vp^0wB!63?wyl`GbKJOS+@4BLl<6e(pbstU$g(vPY0F z14ES>14Ba#1H&(%P{RubhEf9thF1v;3|2E37{m+a>32_C|GG6UMZJAQx zjUtu#vR>`?G#u`0*x%Ezm+d_(>(wR`F-^99A5aZM8Biq}Th^^puqz!+9B2X%J1!ru=CT=||85(}dB~vQgjrX4HDAzm+k$nAlZ&j*i!Z+W`6X-YZL>}{hE2Ea8%}&O z|1@!u$?10rt`)55p}P8Ab0)k`?qB}GYNBuR!a1v^I!$qY5<7oM=+tk&x!Ep>T)QT) zX+O}dswJ)wB`Jv|saDBFsX&Us$iT=@*U(7U&^*M@z{=Rr%Gg-jz`)ADK&9X>Fg+k? z$jwj5OsmALAyn7Z0;nOpDkP#LD6w3jpeR2rGbdG{q_QAYA+w+)nSr5V&f`x!9ED*T z8mIhEpYePe#K5e~t(VL#tSsz3S%g_w!KK0Ea0;{X<`9L`H?EvGa^{H45%$v!9t*tm Z7+#4BmV9zDoeH#q!PC{xWt~$(69Djs0g(Uz literal 0 HcmV?d00001 From b6962c405eb0166ccc7f02bad010523856369f5e Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 16:51:33 -0300 Subject: [PATCH 48/62] Add links to fileglancer and biofilefinder docs --- resources/ecosystem/index.md | 16 +++++++--------- resources/tools/index.md | 1 - 2 files changed, 7 insertions(+), 10 deletions(-) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index 6899a9fb..96acc7fe 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -17,15 +17,13 @@ It fits microscope acquisition software, analysis pipelines, standards and exten ## Gallery-like displays Tooling for sharing collections of OME-Zarr datasets in different ways. - | Name | Link | Description | | -------- | ------- | ------- | -| BioFileFinder | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/AllenInstitute/biofile-finder) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support. | -| Fileglancer | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/fileglancer) | A webapp for browsing, sharing, and viewing OME-Zarr images. | -| Zallery | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://openssbd.github.io/zallery/) | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | -| Zarrcade | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/JaneliaSciComp/zarrcade) | Searchable web-based OME-Zarr image galleries developed by Janelia. | -| Zowser | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/lubianat/zowser) | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | - +| BioFileFinder | website | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support. | +| Fileglancer | website | A webapp for browsing, sharing, and viewing OME-Zarr images. | +| Zallery | GitHub | A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). | +| Zarrcade | GitHub | Searchable web-based OME-Zarr image galleries developed by Janelia. | +| Zowser | GitHub | A gallery template for sharing sets of images built upon the [ome2024-ngff-challenge](https://ome.github.io/ome2024-ngff-challenge/). | ## Microscope acquisition software @@ -54,8 +52,8 @@ Platforms with dedicated support for sharing OME-Zarr datasets, open to public d | Name | Link | Description | | -------- | ------- | ------- | -| BioImage Archive | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://www.ebi.ac.uk/bioimage-archive/) | A public repository for bioimaging data, with support for submissions of OME-Zarr datasets. | -| HuggingFace Hub | [![image](https://www.google.com/s2/favicons?sz=256&domain_url=huggingface.co)](https://huggingface.co/datasets) | A platform for sharing machine-learning datasets, with [ongoing updates](https://github.com/huggingface/datasets/pull/8135) for first-class support for OME-Zarr datasets. | +| BioImage Archive | [BioImage Archive logo](https://www.ebi.ac.uk/bioimage-archive/) | A public repository for bioimaging data, with support for submissions of OME-Zarr datasets. | +| HuggingFace Hub | [HuggingFace Hub logo](https://huggingface.co/datasets) | A platform for sharing machine-learning datasets, with [ongoing updates](https://github.com/huggingface/datasets/pull/8135) for first-class support for OME-Zarr datasets. | Of course, many other platforms support sharing OME-Zarr datasets, but don't necessarily parse the OME metadata or provide any kind of custom support.One may share OME-Zarr datasets and get a DOI (but no S3-like access) in platforms like [Zenodo](https://zenodo.org), [Figshare](https://figshare.com), [Dryad](https://datadryad.org), etc. diff --git a/resources/tools/index.md b/resources/tools/index.md index 825d0973..abdc04f4 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -112,6 +112,5 @@ Libraries that support the rendering and navigation of OME-Zarr data, but that a | Name | Link | Description | | -------- | ------- | ------- | - | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | From 79bf3f0b39a030b1916af78f1e6f62f2109a807f Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 17:01:52 -0300 Subject: [PATCH 49/62] Add CT Herculaneum Scrolls (closes #500) --- resources/data/index.md | 2 ++ 1 file changed, 2 insertions(+) diff --git a/resources/data/index.md b/resources/data/index.md index aeef7a0b..7ea214a1 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -37,6 +37,8 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th | Resource | Description | | ---- | ---------------------- | | [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | +| [Herculaneum Scrolls](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) [source](https://github.com/ScrollPrize/open-data)| Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format.| + ## Atlases From a7aebe462fc80daa706fea9d7145cd07f3ba77fb Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 17:05:40 -0300 Subject: [PATCH 50/62] Add VoDaSuRe to data (closes #524) --- resources/data/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/data/index.md b/resources/data/index.md index 7ea214a1..5b611df3 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -38,7 +38,7 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th | ---- | ---------------------- | | [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | | [Herculaneum Scrolls](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) [source](https://github.com/ScrollPrize/open-data)| Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format.| - +| [VoDaSuRe](https://augusthoeg.github.io/VoDaSuRe/)| A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe))| ## Atlases From 2b853b2c39d48d550890f0911ae31c55728572d4 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Wed, 10 Jun 2026 17:24:50 -0300 Subject: [PATCH 51/62] Fill the gaps in the Atlases section --- resources/data/index.md | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index 5b611df3..4c4dc2d0 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -50,13 +50,11 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ | Resource | Description | Publication | Sample | | ----------- | ----------------- | -------------------- | ----------- | -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | - | - | -| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ( [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)). | - | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) -| -| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | - | - | - | -| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | - | [Ben-Simon et al., 2025]() | - -| -| [Platynereis cell atlas](https://platynereis.com/resources/image/) | - | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | +| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | [Lange et al., 2024](https://doi.org/https://doi.org/10.1016/j.cell.2024.09.047) | [zebrahub](https://zebrahub.sf.czbiohub.org/ngv?name=ZMNS001) | +| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ([highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)) | [Mikus et al., 2024](https://doi.org/10.1101/2024.10.18.618984) | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0)| +| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | Atlas of organs using Hierarchical Phase-Contrast Tomography (HiP-CT) | [Walsh et al., 2026](https://www.science.org/doi/10.1126/sciadv.adz2240) | [Human Organ Atlas](https://human-organ-atlas.esrf.fr/datasets/2439291070) | +| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | A searchable web tool representing information and data on enhancer-adeno-associated viruses (enhancer AAVs) and mouse transgenes | [Ben-Simon et al., 2025]() | [atlas](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens/3PILF5KFKGJILDK30H2) +| [Platynereis cell atlas](https://platynereis.com/resources/image/) | An expression atlas registered to a whole-body electron microscopy volume of the nereid *Platynereis dumerilii* | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | | [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://tiago.bio.br/links?go=open-organelle) | --- From 8aee78bed3de1d8a1c3429760535c79432475213 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 12 Jun 2026 15:55:34 -0300 Subject: [PATCH 52/62] docs: reorganize FIJI libraries --- resources/tools/index.md | 10 ++++++---- 1 file changed, 6 insertions(+), 4 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index abdc04f4..2fa46d48 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -30,14 +30,16 @@ Want to view a Zarr? Use one of these. | Name | Link | Description | | -------- | ------- | ------- | -| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | -| FIJI (MoBIE / BigDataViewer) | [FIJI logo](https://mobie.github.io/) | [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | -| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | +| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | +| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | +| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data.| | ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | | Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | | napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer |\ +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | | Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| | QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | | syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | From 3ad30ec7f09e86645ddee2f17372e8914ab80396 Mon Sep 17 00:00:00 2001 From: Kevin Yamauchi Date: Tue, 16 Jun 2026 08:44:53 +0200 Subject: [PATCH 53/62] Add ez-zarr library to reader/writer table --- resources/tools/index.md | 111 +++++++++++++++++++-------------------- 1 file changed, 55 insertions(+), 56 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 2fa46d48..cf2fb6f7 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -19,7 +19,6 @@ While some tools would fit multiple categories, we assigned each tool to a singl - [Zarr validation](#zarr-validation) - [Rendering libraries](#rendering-libraries) - ## Tools with a graphical interface ### Zarr viewers @@ -28,32 +27,31 @@ Want to view a Zarr? Use one of these. [Check this out](https://ome.github.io/ome-ngff-tools/) to see viewer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| -------- | ------- | ------- | -| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | -| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | -| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | -| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | -| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data.| -| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | -| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | -| Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | -| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | -| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| -| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | -| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | -| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | -| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | -| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | - +| Name | Link | Description | +| ------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | +| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | +| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | +| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data. | +| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | +| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | +| Microscopy Nodes | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | +| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust. | +| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | +| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | +| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | +| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | +| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | ### Zarr converters (with a UI) Want to convert your file to Zarr? Use one of these tools that has a user interface. -| Name | Link | Description | -| -------- | ------- | ------- | +| Name | Link | Description | +| -------------- | ------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | | NGFF-Converter | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/NGFF-Converter) | A desktop application for conversion of bioimage formats into OME-Zarr or OME-TIFF. | ## Tools for the programmatically inclined @@ -64,20 +62,20 @@ Want to convert from a different file format to a Zarr? Use one of these tools. Check out the [readers and writers below](#zarr-readers--writers) to interact with Zarrs in others ways as well conversion. -| Name | Link | Description | -| -------- | ------- | ------- | -| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | -| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | -| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | -| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | -| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | -| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | -| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | -| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | -| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | -| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | -| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | -| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | +| Name | Link | Description | +| ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------- | ----------------- | +| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | +| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | +| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | +| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | +| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | +| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | +| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | +| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | +| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | +| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | +| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | +| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | ### Zarr readers & writers @@ -85,34 +83,35 @@ Want to read or write a Zarr? Use one of these tools. [Check this out](https://github.com/jwindhager/ome-ngff-readers-writers/) to see reader/writer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| -------- | ------- | ------- | -| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | -| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | -| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | -| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | -| iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | -| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | -| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | -| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | -| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py)| A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | -| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | +| Name | Link | Description | +| ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | +| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | +| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | +| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | +| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | +| iohub | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | +| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | +| ez-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fmicompbio/ez_zarr) | A Python and R package for reading and plotting OME-Zarr images. | +| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | +| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | +| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py) | A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | +| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | ### Zarr validation Want to validate a Zarr? Use one of these. -| Name | Link | Description | -| -------- | ------- | ------- | -| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | -| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | -| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | +| Name | Link | Description | +| ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------- | +| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | +| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | +| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | ## Rendering libraries Libraries that support the rendering and navigation of OME-Zarr data, but that are not themselves applications with a graphical user interface. -| Name | Link | Description | -| -------- | ------- | ------- | +| Name | Link | Description | +| ----------------- | ----------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------- | | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | -| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | +| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | From 3aa9b1fe4ad2d043e3b2b47b5dca89d57a97943d Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 16 Jun 2026 08:59:06 -0300 Subject: [PATCH 54/62] fix: fix alphabetical ordering --- resources/tools/index.md | 112 ++++++++++++++++++++------------------- specifications/dev | 2 +- 2 files changed, 58 insertions(+), 56 deletions(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index cf2fb6f7..48949ee2 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -19,6 +19,7 @@ While some tools would fit multiple categories, we assigned each tool to a singl - [Zarr validation](#zarr-validation) - [Rendering libraries](#rendering-libraries) + ## Tools with a graphical interface ### Zarr viewers @@ -27,31 +28,32 @@ Want to view a Zarr? Use one of these. [Check this out](https://ome.github.io/ome-ngff-tools/) to see viewer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| ------------------------------------- | -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | -| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | -| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | -| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | -| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data. | -| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | -| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | -| Microscopy Nodes | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | -| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | -| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | -| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust. | -| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | -| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | -| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | -| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | -| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | +| Name | Link | Description | +| -------- | ------- | ------- | +| AGAVE | [AGAVE logo](https://www.allencell.org/pathtrace-rendering.html) | Desktop application for viewing multichannel volume data powered by your GPU | +| FIJI (MoBIE) | [MoBIE logo](https://mobie.github.io/) | MoBIE is a [FIJI](https://fiji.sc/) plug-in for exploring and sharing big multi-modal image and associated tabular data | +| FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | +| FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | +| FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data.| +| ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | +| Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | +| Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | +| napari | [napari logo](https://github.com/ome/napari-ome-zarr) | [napari](https://napari.org/) plug-in for viewing Zarr | +| Neuroglancer | [Neuroglancer logo](https://github.com/google/neuroglancer) | A browser-based volume viewer | +| Odon | [Odon logo](https://github.com/alexcoulton/odon) | A spatial proteomics OME-Zarr viewer built in Rust.| +| QuPath | [QuPath logo](https://github.com/qupath/qupath) | Open source software for digital pathology image analysis | +| syGlass | [syGlass logo](https://www.syglass.io/) | A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support. | +| Viv (Avivator, Vizarr, Vitessce, ...) | [Viv logo](https://github.com/hms-dbmi/viv) | A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the [Avivator](https://avivator.gehlenborglab.org), [Vizarr](https://github.com/hms-dbmi/vizarr) and [Vitessce](http://vitessce.io) image viewers, among others | +| Vol-E | [Vol-E logo](https://vole.allencell.org/) | A browser-based volume viewer | +| WEBKNOSSOS | [WEBKNOSSOS logo](https://home.webknossos.org/) | An open-source tool for annotating and exploring large 3D image datasets | + ### Zarr converters (with a UI) Want to convert your file to Zarr? Use one of these tools that has a user interface. -| Name | Link | Description | -| -------------- | ------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------- | +| Name | Link | Description | +| -------- | ------- | ------- | | NGFF-Converter | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/NGFF-Converter) | A desktop application for conversion of bioimage formats into OME-Zarr or OME-TIFF. | ## Tools for the programmatically inclined @@ -62,20 +64,20 @@ Want to convert from a different file format to a Zarr? Use one of these tools. Check out the [readers and writers below](#zarr-readers--writers) to interact with Zarrs in others ways as well conversion. -| Name | Link | Description | -| ------------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | ---------------------------------------------------------------------------------------------------------------------------------------------- | ----------------- | -| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | -| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | -| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | -| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | -| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | -| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | -| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | -| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | -| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | -| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | -| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | -| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | +| Name | Link | Description | +| -------- | ------- | ------- | +| BatchConvert | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/BatchConvert) | A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr. | +| bioformats2raw | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/glencoesoftware/bioformats2raw) | Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification. | +| BioIO Conversion | [BioIO logo](https://github.com/bioio-devs/bioio-conversion) | CLI & scripting tool for easily converting images to OME-Zarr. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) | +| EuBI-Bridge | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/Euro-BioImaging/EuBI-Bridge) | A tool for distributed conversion of microscopic image collections into the OME-Zarr format. | +| ITKIOOMEZarrNGFF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/InsightSoftwareConsortium/ITKIOOMEZarrNGFF) | An ITK external module for IO of images stored in OME-Zarr file format. | Reading & Writing | +| kfb2zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/camlloyd/kfb2zarr) | Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr. | +| multiscale-spatial-image | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/spatial-image/multiscale-spatial-image) | Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. | Reading & Writing | +| nd2 | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/tlambert03/nd2) | A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation. | +| Nextflow (nf-omezarr) | [Nextflow logo](https://github.com/JaneliaSciComp/nf-omezarr) | A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw | +| PyMIF | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/grinic/pymif) | A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr. | +| stack-to-chunk | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://stack-to-chunk.readthedocs.io) | A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency. | +| stack_to_multiscale_ngff | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/CBI-PITT/stack_to_multiscale_ngff) | A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr. | ### Zarr readers & writers @@ -83,35 +85,35 @@ Want to read or write a Zarr? Use one of these tools. [Check this out](https://github.com/jwindhager/ome-ngff-readers-writers/) to see reader/writer compatibility with various OME-Zarr features & versions. -| Name | Link | Description | -| ----------- | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- | -| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | -| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | -| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | -| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | -| iohub | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | -| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | -| ez-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fmicompbio/ez_zarr) | A Python and R package for reading and plotting OME-Zarr images. | -| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | -| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | -| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py) | A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | -| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | +| Name | Link | Description | +| -------- | ------- | ------- | +| bfio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/bfio) | A Python interface to Bioformats using jpype for direct access to the library. | +| bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | +| Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | +| BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | +| ez-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fmicompbio/ez_zarr) | A Python and R package for reading and plotting OME-Zarr images. | +| iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | +| ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | +| ngio | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://biovisioncenter.github.io/ngio/stable/) | Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates | +| ome-writers | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/pymmcore-plus/ome-writers) | A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends. | +| ome-zarr-py | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/ome-zarr-py)| A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. | +| Zarr.NET | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BiologyTools/Zarr.NET) | A native .NET library for reading and writing Zarr microscopy data. | ### Zarr validation Want to validate a Zarr? Use one of these. -| Name | Link | Description | -| ------------------ | ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ | -------------------------------------------------------------------------------------------------------------------------------------------------------- | -| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | -| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | -| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | +| Name | Link | Description | +| -------- | ------- | ------- | +| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | +| ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | +| yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | ## Rendering libraries Libraries that support the rendering and navigation of OME-Zarr data, but that are not themselves applications with a graphical user interface. -| Name | Link | Description | -| ----------------- | ----------------------------------------------------------------------------------------------------------------- | ------------------------------------------------------------------- | +| Name | Link | Description | +| -------- | ------- | ------- | | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | -| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | +| ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | diff --git a/specifications/dev b/specifications/dev index 44ffdf77..2f8be18e 160000 --- a/specifications/dev +++ b/specifications/dev @@ -1 +1 @@ -Subproject commit 44ffdf7742bcef5147fb320175e9432dccc9dabf +Subproject commit 2f8be18ead24401ed346954a603acdbdf8d68b89 From 21bd1f39b0fb387092b8fdf5f2ef0e59bf9141e2 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 16 Jun 2026 09:12:39 -0300 Subject: [PATCH 55/62] set specifications/dev to 44ffdf7 --- specifications/dev | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/specifications/dev b/specifications/dev index 2f8be18e..44ffdf77 160000 --- a/specifications/dev +++ b/specifications/dev @@ -1 +1 @@ -Subproject commit 2f8be18ead24401ed346954a603acdbdf8d68b89 +Subproject commit 44ffdf7742bcef5147fb320175e9432dccc9dabf From cc69b0217ecb4aedb43bcde94f1cccf1d90662a5 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 16 Jun 2026 09:19:18 -0300 Subject: [PATCH 56/62] docs: add idetik Closes #539 --- resources/tools/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/tools/index.md b/resources/tools/index.md index 48949ee2..0b6cef25 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -117,3 +117,4 @@ Libraries that support the rendering and navigation of OME-Zarr data, but that a | -------- | ------- | ------- | | OMEZarrTileSource | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/TissUUmaps/OMEZarrTileSource) | An OpenSeadragon tile source for the OME-Zarr bioimage file format. | | ome-zarr.js | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioNGFF/ome-zarr.js) | A JavaScript library for simple rendering of thumbnails and images. | +| idetik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/chanzuckerberg/idetik) | A library for building web-based image viewers. | From 1e5072b91f88f5e6d05ceffdca6a248edbbc0d9d Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Tue, 16 Jun 2026 09:35:32 -0300 Subject: [PATCH 57/62] fix: fix link to the OME logo --- resources/tools/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/tools/index.md b/resources/tools/index.md index 0b6cef25..5ee64dae 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -105,7 +105,7 @@ Want to validate a Zarr? Use one of these. | Name | Link | Description | | -------- | ------- | ------- | -| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | +| ome-ngff-validator | [OME NGFF Validator logo](https://ome.github.io/ome-ngff-validator/) | Web page for validating OME-Zarr files. | | ome-zarr-models | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome-zarr-models/ome-zarr-models-py) | Python package and command line interface that can validate OME-Zarr files | | yaozarrs | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/imaging-formats/yaozarrs) | Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O | From f643b9760544ab79035496af8cd76e597b753527 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 19 Jun 2026 08:53:06 -0300 Subject: [PATCH 58/62] feat: add links to data resources --- resources/data/index.md | 66 ++++++++++++++++++++--------------------- 1 file changed, 33 insertions(+), 33 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index 4c4dc2d0..abb75eaf 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -10,35 +10,35 @@ Do you have a data resource in OME-Zarr format that you would like to share? Is Resources curating OME-Zarr sample data, for demonstration and testing purposes. -| Resource | Description | -| ---- | ---------------------- | -| [IDR Samples](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | -| [BIA Samples](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | -| [Sanger Institute Samples ](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | -| [SSBD samples](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes | -| [OME 2024 NGFF challenge](https://ome.github.io/) | Close to 500 TB of data in the OME-Zarr 0.5 format | +| Name | Link | Description | +| -------- | ------- | ------- | +| IDR Samples | [IDR Samples logo](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | +| BIA Samples | [BIA Samples logo](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | +| Sanger Institute Samples | [Sanger Institute Samples logo](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | +| SSBD samples | [SSBD samples logo](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes | +| OME 2024 NGFF challenge | [OME 2024 NGFF challenge logo](https://ome.github.io/) | Close to 500 TB of data in the OME-Zarr 0.5 format | ## Data portals Imaging data portals with curated OME-Zarr data, including public repositories. The content in the repositories may grow with time as new datasets become available. -| Resource | Description | -| ---- | ---------------------- | -| [CryoET Data Portal](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | -| [BioFile Finder](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support | -| [JAX OMERO](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | -| [webknossos Zarr Gallery](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis. | -| [IDR Studies](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data | +| Name | Link | Description | +| -------- | ------- | ------- | +| CryoET Data Portal | [CryoET Data Portal logo](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | +| BioFile Finder | [BioFile Finder logo](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support | +| JAX OMERO | [JAX OMERO logo](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | +| webknossos Zarr Gallery | [webknossos Zarr Gallery logo](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis. | +| IDR Studies | [IDR Studies logo](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data | ## Datasets These are datasets available in OME-Zarr format, hosted in various locations. They represent some of the different scientific stories enabled by OME-Zarr. -| Resource | Description | -| ---- | ---------------------- | -| [Open SciVis](https://registry.opendata.aws/ome-zarr-open-scivis/) [source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. | -| [Herculaneum Scrolls](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) [source](https://github.com/ScrollPrize/open-data)| Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format.| -| [VoDaSuRe](https://augusthoeg.github.io/VoDaSuRe/)| A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe))| +| Name | Link | Description | +| -------- | ------- | ------- | +| Open SciVis | [Open SciVis logo](https://registry.opendata.aws/ome-zarr-open-scivis/) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. ([source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets)) | +| Herculaneum Scrolls | [Herculaneum Scrolls logo](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) | Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format. ([source](https://github.com/ScrollPrize/open-data)) | +| VoDaSuRe | [VoDaSuRe logo](https://augusthoeg.github.io/VoDaSuRe/) | A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe)) | ## Atlases @@ -48,14 +48,14 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ ## -| Resource | Description | Publication | Sample | -| ----------- | ----------------- | -------------------- | ----------- | -| [Zebrahub](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | [Lange et al., 2024](https://doi.org/https://doi.org/10.1016/j.cell.2024.09.047) | [zebrahub](https://zebrahub.sf.czbiohub.org/ngv?name=ZMNS001) | -| [ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes](https://www.dudinlab.com/exame) (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095)) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets ([highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)) | [Mikus et al., 2024](https://doi.org/10.1101/2024.10.18.618984) | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0)| -| [The Human Organ Atlas](https://human-organ-atlas.esrf.fr/) | Atlas of organs using Hierarchical Phase-Contrast Tomography (HiP-CT) | [Walsh et al., 2026](https://www.science.org/doi/10.1126/sciadv.adz2240) | [Human Organ Atlas](https://human-organ-atlas.esrf.fr/datasets/2439291070) | -| [The Genetic Tools Atlas](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | A searchable web tool representing information and data on enhancer-adeno-associated viruses (enhancer AAVs) and mouse transgenes | [Ben-Simon et al., 2025]() | [atlas](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens/3PILF5KFKGJILDK30H2) -| [Platynereis cell atlas](https://platynereis.com/resources/image/) | An expression atlas registered to a whole-body electron microscopy volume of the nereid *Platynereis dumerilii* | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | -| [OpenOrganelle](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://tiago.bio.br/links?go=open-organelle) | +| Name | Link | Description | Publication | Sample | +| -------- | ------- | ------- | ------- | ------- | +| Zebrahub | [Zebrahub logo](https://zebrahub.ds.czbiohub.org/imaging) | Multimodal atlas of zebrafish development including light-sheet imaging | [Lange et al., 2024](https://doi.org/https://doi.org/10.1016/j.cell.2024.09.047) | [zebrahub](https://zebrahub.sf.czbiohub.org/ngv?name=ZMNS001) | +| ExÂME: Expansion Microscopy Atlas of Microbial Eukayotes | [ExÂME logo](https://www.dudinlab.com/exame) | An atlas of expansion microscopy images of microbial eukaryotes, including OME-Zarr datasets (see also [S-BIAD2095](https://www.ebi.ac.uk/biostudies/bioimages/studies/S-BIAD2095); [highlight](https://www.nature.com/immersive/d41586-026-00901-5/index.html)) | [Mikus et al., 2024](https://doi.org/10.1101/2024.10.18.618984) | [vizarr](https://uk1s3.embassy.ebi.ac.uk/bia-zarr-test/vizarr/index.html?source=https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD2095/d39625f2-590d-4e19-9f61-37489318b1c0/3c55c404-49e4-4e9d-bb76-c028b08835d3.ome.zarr/0) | +| The Human Organ Atlas | [The Human Organ Atlas logo](https://human-organ-atlas.esrf.fr/) | Atlas of organs using Hierarchical Phase-Contrast Tomography (HiP-CT) | [Walsh et al., 2026](https://www.science.org/doi/10.1126/sciadv.adz2240) | [Human Organ Atlas](https://human-organ-atlas.esrf.fr/datasets/2439291070) | +| The Genetic Tools Atlas | [The Genetic Tools Atlas logo](https://brain-map.org/bkp/experiment/genetic-tools/genetic-tools-atlas) | A searchable web tool representing information and data on enhancer-adeno-associated viruses (enhancer AAVs) and mouse transgenes | [Ben-Simon et al., 2025]() | [atlas](https://knowledge.brain-map.org/data/7CVKSF7QGAKIQ8LM5LC/specimens/3PILF5KFKGJILDK30H2) | +| Platynereis cell atlas | [Platynereis cell atlas logo](https://platynereis.com/resources/image/) | An expression atlas registered to a whole-body electron microscopy volume of the nereid *Platynereis dumerilii* | [Vergara et al., 2021](https://doi.org/10.1016/j.cell.2021.07.017) | [neuroglancer](https://tiago.bio.br/links?go=platy-atlas) | +| OpenOrganelle | [OpenOrganelle logo](https://openorganelle.janelia.org/) | An open-access volume electron microscopy atlas of whole cells and tissues | [Xu et al., 2021](https://www.nature.com/articles/s41586-021-03992-4) | [neuroglancer](https://tiago.bio.br/links?go=open-organelle) | --- @@ -63,9 +63,9 @@ The [WebAtlas pipeline](https://cellatlas.io/webatlas) ([Li et al, 2024](https:/ These are resources that may not be exclusively OME-Zarr, but include some OME-Zarr data that may be of interest to the community. -| Resource | Description | -| ---- | ---------------------- | -| [DANDI](https://dandiarchive.org/), e.g. [000108](https://dandiarchive.org/dandiset/000108) | BRAIN Initiative archive for publishing and sharing neurophysiology data | -| [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery), e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes. | -| [AIND - Mouse Neuroanatomy and Physiology Data](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | -| [SpatialData datasets](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | +| Name | Link | Description | +| -------- | ------- | ------- | +| DANDI | [DANDI logo](https://dandiarchive.org/) | BRAIN Initiative archive for publishing and sharing neurophysiology data (e.g. [000108](https://dandiarchive.org/dandiset/000108)) | +| Cell Painting Gallery | [Cell Painting Gallery logo](https://broadinstitute.github.io/cellpainting-gallery) | A collection of datasets from the Cell Painting assay, a high-content image-based assay for profiling cellular phenotypes (e.g. [cpg0004-lincs](https://idr.github.io/idr0125-way-cellpainting/)). | +| AIND - Mouse Neuroanatomy and Physiology Data | [AIND logo](https://registry.opendata.aws/allen-nd-open-data/) | Datasets from the Allen Institute for Neural Dynamics, including OME-Zarr. | +| SpatialData datasets | [SpatialData datasets logo](https://spatialdata.scverse.org/en/latest/tutorials/notebooks/datasets/README.html) | A collection of spatial omics datasets using the SpatialData specification, which includes OME-Zarr. | From eb33d39299c7e611d8b5e85a2b422742ccdad61e Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 19 Jun 2026 08:53:28 -0300 Subject: [PATCH 59/62] feat: add hoct closes #541, ping @JoOkuma --- resources/ecosystem/index.md | 1 + 1 file changed, 1 insertion(+) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index 96acc7fe..c7bc06a6 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -39,6 +39,7 @@ Tools that integrate OME-Zarr into workflows that support OME-Zarr as either as | Name | Link | Description | | -------- | ------- | ------- | | Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | +| hoct | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/royerlab/hoct) | Higher-Order Cell Tracking is a predictive deep learning model for tracking cells from segments and images. | | Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | | Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | From 46c8409cc4e25def75b518c76dd34043b2763193 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 19 Jun 2026 09:08:32 -0300 Subject: [PATCH 60/62] feat: add clearscale and re-position ilastik closes #542 --- resources/ecosystem/index.md | 1 - resources/tools/index.md | 2 ++ 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/resources/ecosystem/index.md b/resources/ecosystem/index.md index c7bc06a6..10f38025 100644 --- a/resources/ecosystem/index.md +++ b/resources/ecosystem/index.md @@ -40,7 +40,6 @@ Tools that integrate OME-Zarr into workflows that support OME-Zarr as either as | -------- | ------- | ------- | | Fractal | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://fractal-analytics-platform.github.io/) | A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. | | hoct | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/royerlab/hoct) | Higher-Order Cell Tracking is a predictive deep learning model for tracking cells from segments and images. | -| Ilastik | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/ilastik) | An interactive learning and segmentation toolkit | | Nyxus | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/PolusAI/nyxus) | A scalable library for calculating features from intensity-label image data. | | Mastodon | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://mastodon.readthedocs.io/) | A large-scale tracking and track-editing framework for large, multi-view images. | | multiview-stitcher | [multiview-stitcher logo]((https://github.com/multiview-stitcher/multiview-stitcher)) | Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. | diff --git a/resources/tools/index.md b/resources/tools/index.md index 5ee64dae..484b95bc 100644 --- a/resources/tools/index.md +++ b/resources/tools/index.md @@ -35,6 +35,7 @@ Want to view a Zarr? Use one of these. | FIJI (BigDataViewer) | [FIJI logo](https://imagej.net/plugins/bdv/) | BigDataViewer ships with [FIJI](https://fiji.sc/) and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels | | FIJI (n5-ij) | [FIJI logo](https://github.com/saalfeldlab/n5-ij) | n5-ij is a [FIJI](https://fiji.sc/) plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API | | FIJI (ome-zarr-fiji) | [FIJI logo](https://github.com/BioImageTools/ome-zarr-fiji-java) | ome-zarr-fiji is a [FIJI](https://fiji.sc/) plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data.| +| Ilastik | [Ilastik logo](https://www.ilastik.org) | An interactive learning and segmentation toolkit | | ITKWidgets | [ITKWidgets logo](https://github.com/InsightSoftwareConsortium/itkwidgets) | Python tool for interactively viewing images (ex. in Jupyter) | | Kiln | [kiln logo](https://github.com/MPanknin/kiln-render) | A WebGPU-native out-of-core rendering system for virtualized volumetric data | | Microscopy Nodes |[![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/aafkegros/MicroscopyNodes) | [Blender](https://www.blender.org/) add-on for visualizing high-dimensional microscopy data | @@ -91,6 +92,7 @@ Want to read or write a Zarr? Use one of these tools. | bia-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/BioImage-Archive/bia-zarr) | A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection. | | Bio-Formats | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ome/bioformats) | A standalone Java library for reading and writing life sciences image file formats. Requires [OMEZarrReader](https://github.com/ome/ZarrReader) | | BioIO | [BioIO logo](https://github.com/bioio-devs/bioio) | Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires [bioio-ome-zarr](https://github.com/bioio-devs/bioio-ome-zarr) (formerly [AICSImageIO](https://github.com/AllenCellModeling/aicsimageio)) | +| clearscale | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/ilastik/clearscale) | Python library for handling OME metadata without learning the spec | | ez-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fmicompbio/ez_zarr) | A Python and R package for reading and plotting OME-Zarr images. | | iohub| [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/czbiohub-sf/iohub) | Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata | | ngff-zarr | [![image](https://github.githubassets.com/favicons/favicon.svg)](https://github.com/fideus-labs/ngff-zarr) | A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. | From 496cfa0403fd3cbac65d5b62e9d4777e417949c4 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 19 Jun 2026 09:17:44 -0300 Subject: [PATCH 61/62] fix: fix broken logos --- resources/data/index.md | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/resources/data/index.md b/resources/data/index.md index abb75eaf..e541d6d6 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -13,10 +13,10 @@ Resources curating OME-Zarr sample data, for demonstration and testing purposes. | Name | Link | Description | | -------- | ------- | ------- | | IDR Samples | [IDR Samples logo](https://idr.github.io/ome-ngff-samples/) | A comprehensive set of OME-Zarr samples from IDR, covering all OME-Zarr versions | -| BIA Samples | [BIA Samples logo](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | +| BIA Samples | [BIA Samples logo](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/omengff.html) | Sample OME-Zarr datasets from the BioImage Archive for testing | | Sanger Institute Samples | [Sanger Institute Samples logo](https://www.sanger.ac.uk/project/ome-zarr/) | Datasets from the Sanger Institute that have been converted to OME-Zarr to test and encourage the file format | | SSBD samples | [SSBD samples logo](https://ssbd.riken.jp/ssbd-ome-ngff-samples) | Sample OME-Zarr datasets from the Systems Science of Biological Dynamics database (SSBD) for testing and demonstration purposes | -| OME 2024 NGFF challenge | [OME 2024 NGFF challenge logo](https://ome.github.io/) | Close to 500 TB of data in the OME-Zarr 0.5 format | +| OME 2024 NGFF challenge | [OME 2024 NGFF challenge logo](https://ome.github.io/) | Close to 500 TB of data in the OME-Zarr 0.5 format | ## Data portals @@ -26,7 +26,7 @@ Imaging data portals with curated OME-Zarr data, including public repositories. | -------- | ------- | ------- | | CryoET Data Portal | [CryoET Data Portal logo](https://cryoetdataportal.czscience.com) | Cryo-electron tomography (cryoET) data repository | | BioFile Finder | [BioFile Finder logo](https://bff.allencell.org/datasets) | A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support | -| JAX OMERO | [JAX OMERO logo](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | +| JAX OMERO | [JAX OMERO logo](https://images.jax.org/webclient/userdata/?experimenter=-1) | The Jackson Laboratory public OMERO instance, links to OME-Zarr files are available in the key-value | | webknossos Zarr Gallery | [webknossos Zarr Gallery logo](https://zarr.webknossos.org) | A collection of mostly Electron Microscopy OME-Zarr datasets from webKnossos, a platform for large-scale 3D image data visualization and analysis. | | IDR Studies | [IDR Studies logo](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/idr_ngff_data.html) | A collection of OME-Zarr datasets from the Image Data Resource (IDR), a public repository for bioimaging data | @@ -38,7 +38,7 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th | -------- | ------- | ------- | | Open SciVis | [Open SciVis logo](https://registry.opendata.aws/ome-zarr-open-scivis/) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. ([source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets)) | | Herculaneum Scrolls | [Herculaneum Scrolls logo](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) | Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format. ([source](https://github.com/ScrollPrize/open-data)) | -| VoDaSuRe | [VoDaSuRe logo](https://augusthoeg.github.io/VoDaSuRe/) | A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe)) | +| VoDaSuRe | ![image](https://github.githubassets.com/favicons/favicon.svg)](https://augusthoeg.github.io/VoDaSuRe/) | A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe)) | ## Atlases From b35310aa3b0ac7f26d97e2290a598100629db387 Mon Sep 17 00:00:00 2001 From: Tiago Lubiana Date: Fri, 19 Jun 2026 09:41:00 -0300 Subject: [PATCH 62/62] fix broken markup in vodasure --- resources/data/index.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/resources/data/index.md b/resources/data/index.md index e541d6d6..98d996d9 100644 --- a/resources/data/index.md +++ b/resources/data/index.md @@ -38,7 +38,7 @@ These are datasets available in OME-Zarr format, hosted in various locations. Th | -------- | ------- | ------- | | Open SciVis | [Open SciVis logo](https://registry.opendata.aws/ome-zarr-open-scivis/) | A collection of of volumetric datasets in OME-Zarr format, including several CT scans. ([source](https://github.com/InsightSoftwareConsortium/OMEZarrOpenSciVisDatasets)) | | Herculaneum Scrolls | [Herculaneum Scrolls logo](https://registry.opendata.aws/vesuvius-challenge-herculaneum-scrolls/) | Scrolls carbonized by Mount Vesuvius eruptions imaged via X-ray micro-CT, made available in OME-Zarr format. ([source](https://github.com/ScrollPrize/open-data)) | -| VoDaSuRe | ![image](https://github.githubassets.com/favicons/favicon.svg)](https://augusthoeg.github.io/VoDaSuRe/) | A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe)) | +| VoDaSuRe | ![image](https://github.githubassets.com/favicons/favicon.svg)(https://augusthoeg.github.io/VoDaSuRe/) | A large-scale dataset covering volumetric super-resolution data with micro-CT ([arXiv](https://arxiv.org/abs/2603.23153); [dataset](https://huggingface.co/datasets/AugustHoeg/VoDaSuRe)) | ## Atlases