hubmapconsortium · BirdMachine · Apr 6, 2026 · Apr 6, 2026 · Apr 6, 2026 · Apr 6, 2026
diff --git a/.gitignore b/.gitignore
@@ -6,3 +6,5 @@ node_modules
 scripts/metaBuilder/metaJSON/old
 scripts/metaBuilder/toMD/old/
 scripts/metaBuilder/__pycache__/
+docs/assays/metadata/.directory
+docs/.directory
diff --git a/docs/_includes/page.html b/docs/_includes/page.html
@@ -30,7 +30,10 @@
     <link rel="stylesheet" href="/css/bootstrap.min.css"/>
     <script src="/js/popper.min.js" crossorigin="anonymous"></script>
     <script src="/js/bootstrap.min.js" crossorigin="anonymous"></script>
-
+      {% if page.url contains "assays/metadata" %}
+        <script src="/js/new-releases.js"></script>
+        <link rel="stylesheet" href="/css/releaseHighlight.css" />
+      {% endif %}
     {% seo %}
   </head>
   <body data-js-gtm>

diff --git a/docs/_includes/pageAlt.html b/docs/_includes/pageAlt.html
@@ -0,0 +1,62 @@
+
+<!-- This template page was auto generated, do not edit directly--><!DOCTYPE html>
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+    <!-- Google Tag Manager-->
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+    {% include {{ include.page_header }} %}
+    {% include {{ include.page_sidebar }} %}
+        <div class="c-container" role="main">{% if include.page_breadcrumbs %}
+          <div class="c-breadcrumbs js-app--breadcrumbs" role="navigation" aria-label="Breadcrumbs">
+            <div class="c-breadcrumbs__main js-breadcrumbs__main"></div>
+          </div>{% endif %}
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diff --git a/docs/_layouts/page-triary-newreleases.html b/docs/_layouts/page-triary-newreleases.html
@@ -0,0 +1 @@
+{% include pageAlt.html page_header="headers/standard.html" page_sidebar="empty.html" page_extra_js="/js/new-releases.js"  %}
diff --git a/docs/_layouts/page-triary.html b/docs/_layouts/page-triary.html
@@ -0,0 +1 @@
+{% include pageAlt.html page_header="headers/standard.html" page_sidebar="empty.html"  %}
diff --git a/docs/assays/metadata/10XMultiome.md b/docs/assays/metadata/10XMultiome.md
diff --git a/docs/assays/metadata/ATACseq.md b/docs/assays/metadata/ATACseq.md
diff --git a/docs/assays/metadata/AutoFluorescence.md b/docs/assays/metadata/AutoFluorescence.md
diff --git a/docs/assays/metadata/CODEX.md b/docs/assays/metadata/CODEX.md
diff --git a/docs/assays/metadata/Cell-DIVE.md b/docs/assays/metadata/Cell-DIVE.md
@@ -0,0 +1,62 @@
+---
+layout: page-triary
+---
+
+# Cell DIVE Metadata Attributes
+
+Fields that are collected for Cell DIVE data, available at ```Dataset.metadata.<attribute>```
+&nbsp;
+
+<span style="color:red" title="Required">*</span><span class="requiredNote"> indicates a required field</span>
+
+| Attribute | Type | Description | Allowable Values |
+|------|------|-------------|-------------------|
+| parent_sample_id | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | Unique HuBMAP or SenNet identifier of the sample (i.e., block, section or suspension) used to perform this assay. For example, for a RNAseq assay, the parent would be the suspension, whereas, for one of the imaging assays, the parent would be the tissue section. If an assay comes from multiple parent samples then this should be a comma separated list. Example: HBM386.ZGKG.235, HBM672.MKPK.442 or SNT232.UBHJ.322, SNT329.ALSK.102 |  |
+| lab_id | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | A locally assigned identifier provided by the data provider for the dataset. It is used to reference an external metadata record that may be maintained independently, enabling traceability and supporting provenance tracking. Example: Visium_9OLC_A4_S1 |  |
+| preparation_protocol_doi <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | DOI for the protocols.io page that describes the assay or sample procurment and preparation. For example for an imaging assay, the protocol might include staining of a section through the creation of an OME-TIFF file. In this case the protocol would include any image processing steps required to create the OME-TIFF file. Example: https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1 | ```https://dx.doi.org/10.17504/protocols.io.eq2lyno9qvx9/v1``` |
+| dataset_type <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | The specific type of dataset being produced. | ```10X Multiome``` ```2D Imaging Mass Cytometry``` ```ATACseq``` ```Auto-fluorescence``` ```Cell DIVE``` ```CODEX``` ```Confocal``` ```CosMx``` ```CyCIF``` ```DBiT``` ```DESI``` ```Enhanced Stimulated Raman Spectroscopy (SRS)``` ```GeoMx (nCounter)``` ```GeoMx (NGS)``` ```HiFi-Slide``` ```Histology``` ```LC-MS``` ```Light Sheet``` ```MALDI``` ```MERFISH``` ```MIBI``` ```Molecular Cartography``` ```MUSIC``` ```nanoSPLITS``` ```PhenoCycler``` ```Resolve``` ```RNAseq``` ```RNAseq (with probes)``` ```Second Harmonic Generation (SHG)``` ```SIMS``` ```SNARE-seq2``` ```Stereo-seq``` ```Thick section Multiphoton MxIF``` ```Visium (no probes)``` ```Visium (with probes)``` ```Xenium``` |
+| analyte_class <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | Analytes are the target molecules being measured with the assay. | ```Chromatin``` ```DNA``` ```DNA + RNA``` ```Endogenous fluorophores``` ```Fluorochrome``` ```Lipid``` ```Metabolite``` ```Nucleic acid and protein``` ```Peptide``` ```Polysaccharide``` ```Protein``` ```RNA``` |
+| is_targeted <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-dot" title="Radio" aria-label="Radio"></i> | Specifies whether or not a specific molecule(s) is/are targeted for detection/measurement by the assay ("Yes" or "No"). The CODEX analyte is protein. | ```Yes``` ```No``` |
+| acquisition_instrument_vendor <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | An acquisition instrument is the device that contains the signal detection hardware and signal processing software. Assays generate signals such as light of various intensities or color or signals representing the molecular mass. | ```Akoya Biosciences``` ```Andor``` ```BGI Genomics``` ```Bruker``` ```Cytiva``` ```Evident Scientific (Olympus)``` ```GE Healthcare``` ```Hamamatsu``` ```Huron Digital Pathology``` ```Illumina``` ```In-House``` ```Ionpath``` ```Keyence``` ```Leica Biosystems``` ```Leica Microsystems``` ```Motic``` ```NanoString``` ```Resolve Biosciences``` ```Sciex``` ```Standard BioTools (Fluidigm)``` ```Thermo Fisher Scientific``` ```Zeiss Microscopy``` |
+| acquisition_instrument_model <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | Manufacturers of an acquisition instrument may offer various versions (models) of that instrument with different features or sensitivities. Differences in features or sensitivities may be relevant to processing or interpretation of the data. | ```Aperio AT2``` ```Aperio CS2``` ```Axio Observer 3``` ```Axio Observer 5``` ```Axio Observer 7``` ```Axio Scan.Z1``` ```BZ-X710``` ```BZ-X800``` ```BZ-X810``` ```CosMx Spatial Molecular Imager``` ```Custom: Multiphoton``` ```Digital Spatial Profiler``` ```DM6 B``` ```DNBSEQ-T7``` ```EVOS M7000``` ```HiSeq 2500``` ```HiSeq 4000``` ```Hyperion Imaging System``` ```IN Cell Analyzer 2200``` ```Lightsheet 7``` ```MALDI timsTOF Flex Prototype``` ```MIBIscope``` ```MoticEasyScan One``` ```NanoZoomer 2.0-HT``` ```NanoZoomer S210``` ```NanoZoomer S360``` ```NanoZoomer S60``` ```NanoZoomer-SQ``` ```NextSeq 2000``` ```NextSeq 500``` ```NextSeq 550``` ```NovaSeq 6000``` ```NovaSeq X``` ```NovaSeq X Plus``` ```Orbitrap Eclipse Tribrid``` ```Orbitrap Fusion Lumos Tribrid``` ```Phenocycler-Fusion 1.0``` ```Phenocycler-Fusion 2.0``` ```PhenoImager Fusion``` ```Q Exactive``` ```Q Exactive HF``` ```Q Exactive UHMR``` ```QTRAP 5500``` ```Resolve Biosciences Molecular Cartography``` ```SCN400``` ```STELLARIS 5``` ```TissueScope LE Slide Scanner``` ```Unknown``` ```VS200 Slide Scanner``` ```Xenium Analyzer``` ```Zyla 4.2 sCMOS``` |
+| source_storage_duration_value | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | How long was the source material stored, prior to this sample being processed? For assays applied to tissue sections, this would be how long the tissue section (e.g., slide) was stored, prior to the assay beginning (e.g., imaging). For assays applied to suspensions such as sequencing, this would be how long the suspension was stored before library construction began. |  |
+| source_storage_duration_unit <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | The time duration unit of measurement | ```hour``` ```month``` ```day``` ```minute``` ```year``` |
+| time_since_acquisition_instrument_calibration_value | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | The amount of time since the acqusition instrument was last serviced by the vendor. This provides a metric for assessing drift in data capture. |  |
+| time_since_acquisition_instrument_calibration_unit | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | The time unit of measurement | ```Column-by-column``` ```Not applicable``` ```Row-by-row``` ```Snake-by-columns``` ```Snake-by-rows``` |
+| contributors_path | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | The path to the file with the ORCID IDs for all contributors of this dataset (e.g., "./extras/contributors.tsv" or "./contributors.tsv"). This is an internal metadata field that is just used for ingest. |  |
+| data_path | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | The top level directory containing the raw and/or processed data. For a single dataset upload this might be "." where as for a data upload containing multiple datasets, this would be the directory name for the respective dataset. For instance, if the data is within a directory called "TEST001-RK" use syntax "./TEST001-RK" for this field. If there are multiple directory levels, use the format "./TEST001-RK/Run1/Pass2" in which "Pass2" is the subdirectory where the single dataset's data is stored. This is an internal metadata field that is just used for ingest. |  |
+| antibodies_path | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | This is the location of the antibodies.tsv file relative to the root of the top level of the upload directory structure. This path should begin with "." and would likely be something like "./extras/antibodies.tsv". |  |
+| number_of_antibodies | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | Number of antibodies |  |
+| number_of_channels | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | Number of fluorescent channels imaged during each cycle. |  |
+| number_of_biomarker_imaging_rounds | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | Number of imaging rounds to capture the tagged biomarkers. For CODEX a biomarker imaging round consists of 1. oligo application, 2. fluor application, 3. washes. For Cell DIVE a biomarker imaging round consists of 1. staining of a biomarker via secondary detection or direct conjugate and 2. dye inactivation. |  |
+| number_of_total_imaging_rounds | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | The total number of acquisitions performed on microscope to collect autofluorescence/background or stained signal (e.g., histology). |  |
+| slide_id | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | A unique ID denoting the slide used. This allows users the ability to determine which tissue sections were processed together on the same slide. It is recommended that data providers prefix the ID with the center name, to prevent values overlapping across centers. |  |
+| cell_boundary_marker_or_stain <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | If a marker or stain was used to identify all cell boundaries in the tissue, then the name of the marker or stain should be included here. The name of the antibody-targeted molecule marker or non-antibody targeted molecule stain included here must be identical to what is found in the imaging data. For example, with the PhenoCycler, this name must match the value found in the XPD output file. If multiple marker or stains are used to identify all cell boundaries, then a comma separated list should be used here. | ```NAKATPASE``` ```CD298``` ```Not applicable``` |
+| nuclear_marker_or_stain <span style="color:red" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | For markers, an antibody-targetted molecule present in or around the cell nucleus, the protein or gene symbol that identifies the antibody target that is used as the nuclear marker. This symbol must match the antibody target that is either generated from the panel used or entered with custom panels. Preferably, if using a custom antibody marker, this symbol should be the HGNC symbol (https://www.genenames.org/).   For non-protein targets this is the stain name (e.g., DAPI) and, when appropriate, associated staining kit and vendor. For the PhenoCycler, this symbol must match the value found in the XPD output file. | ```DAPI``` ```Not applicable``` |
+| metadata_schema_id | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | The string that serves as the definitive identifier for the metadata schema version and is readily interpretable by computers for data validation and processing. Example: 22bc762a-5020-419d-b170-24253ed9e8d9 |  |
+
+
+&nbsp;
+
+## Deprecated Attributes
+&nbsp;
+
+<span style="color:#00000061" title="Required"></span><span class="requiredNote"> indicates a field that was previously required</span>
+
+| Attribute | Type | Description | Allowable Values |
+|------|------|-------------|-------------------|
+| assay_category <span style="color:#00000061" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | Each assay is placed into one of the following 4 general categories: generation of images of microscopic entities, identification & quantitation of molecules by mass spectrometry, imaging mass spectrometry, and determination of nucleotide sequence. | ```sequence``` |
+| description | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | Free-text description of this assay. |  |
+| donor_id | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | HuBMAP Display ID of the donor of the assayed tissue. |  |
+| execution_datetime | <i class="fa-solid fa-calendar" title="Datetime" aria-label="Datetime"></i> | Start date and time of assay, typically a date-time stamped folder generated by the acquisition instrument. YYYY-MM-DD hh:mm, where YYYY is the year, MM is the month with leading 0s, and DD is the day with leading 0s, hh is the hour with leading zeros, mm are the minutes with leading zeros. |  |
+| operator | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | Name of the person responsible for executing the assay. |  |
+| operator_email | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | Email address for the operator. |  |
+| overall_protocols_io_doi | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | DOI for protocols.io referring to the overall protocol for the assay. |  |
+| pi | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | Name of the principal investigator responsible for the data. |  |
+| pi_email | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | Email address for the principal investigator. |  |
+| processing_protocols_io_doi | <i class="fa-solid fa-font" title="Textfield" aria-label="Textfield"></i> | DOI for analysis protocols.io for this assay. |  |
+| resolution_x_unit | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | The unit of measurement of width of a pixel.(nm) | ```mm``` ```um``` ```nm``` |
+| resolution_x_value | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | The width of a pixel. (Akoya pixel is 377nm square) |  |
+| resolution_y_unit | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | The unit of measurement of height of a pixel. (nm) | ```mm``` ```um``` ```nm``` |
+| resolution_y_value | <i class="fa-solid fa-hashtag" title="Numeric" aria-label="Numeric"></i> | The height of a pixel. (Akoya pixel is 377nm square) |  |
+| version <span style="color:#00000061" title="Required" aria-label="Required">*</span> | <i class="fa-solid fa-circle-nodes" title="Allowable Value" aria-label="Allowable Value"></i> | Version of the schema to use when validating this metadata. | ```1``` |
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		{% include pageAlt.html page_header="headers/standard.html" page_sidebar="empty.html" page_extra_js="/js/new-releases.js" %}