Draft dataset loader Xenium cervical cancer with pathology-based ground truth cell type annotation#41
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Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com>
koenvandenberge
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Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com>
Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com>
Signed-off-by: Robrecht Cannoodt <rcannood@gmail.com>
rcannood
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May 19, 2026
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| param_list: | ||
| - id: ... | ||
| input: s3://hca-op-spatial/datasets/gt_annotated_data/Xenium_Prime_Cervical_Cancer_FFPE_Aligned.zarr | ||
| dataset_name: ... | ||
| dataset_url: ... | ||
| dataset_summary: ... | ||
| dataset_description: ... | ||
| dataset_organism: ... |
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@koenvandenberge Could you fill in this info?
Example from a different task:
- id: tenx_visium/visium/human_colorectal_cancer
input_expression: "https://cf.10xgenomics.com/samples/spatial-exp/2.0.1/CytAssist_11mm_FFPE_Human_Colorectal_Cancer/CytAssist_11mm_FFPE_Human_Colorectal_Cancer_filtered_feature_bc_matrix.h5"
input_spatial: "https://cf.10xgenomics.com/samples/spatial-exp/2.0.1/CytAssist_11mm_FFPE_Human_Colorectal_Cancer/CytAssist_11mm_FFPE_Human_Colorectal_Cancer_spatial.tar.gz"
dataset_name: 10X Visium - Human Colorectal Cancer
dataset_summary: Gene expression library of Human Colorectal Cancer (CytAssist FFPE) using the Human Whole Transcriptome Probe Set
dataset_description: "The tissue was sectioned as described in the Visium CytAssist Spatial Gene Expression for FFPE Tissue Preparation Guide (CG000518). Tissue section of 5 µm was placed on a standard glass slide, then stained following the Deparaffinization, H&E Staining, Imaging & Decrosslinking Demonstrated Protocol (CG000520). The glass slide with tissue section was processed via Visium CytAssist instrument to transfer analytes to a Visium CytAssist Spatial Gene Expression Slide v2, with 11 mm capture areas following the Visium CytAssist Spatial Gene Expression Reagent Kits User Guide (CG000495)."
dataset_url: # url to dataset, if available
dataset_reference_doi: # doi for dataset, if available
dataset_organism: homo_sapiens
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Done, thanks for the pointers.
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Describe your changes
Initial edits to add a dataset loader for the public Xenium cervical cancer dataset.
Checklist before requesting a review
[x ] I have performed a self-review of my code
Check the correct box. Does this PR contain:
Proposed changes are described in the CHANGELOG.md
CI Tests succeed and look good!