Dataset format

For every sample, we provide:

• The aligned Spatial Transcriptomics data in a standard ScanPy .h5ad file
• An H&E WSI in pyramidal generic TIFF
• CellViT nuclei segmentation
• WSI patches
• A JSON file containing metadata for that sample

An example showing the metadata for a HEST sample is given below. A more detailed description of each sample is provided in the original paper.

        {
            "dataset_title": "FFPE Human Ovarian Cancer Data with Human Immuno-Oncology Profiling Panel and Custom Add-on",
            "id": "TENX142",
            "image_filename": "TENX142.tif",
            "organ": "Ovary",
            "disease_state": "Cancer",
            "oncotree_code": "HGSOC",
            "species": "Homo sapiens",
            "patient": "",
            "st_technology": "Xenium",
            "data_publication_data": "2024-05-15",
            "license": "Creative Commons Attribution",
            "study_link": "null,
            "download_page_link1": "https://www.10xgenomics.com/datasets/ffpe-human-ovarian-cancer-data-with-human-immuno-oncology-profiling-panel-and-custom-add-on-1-standard",
            "inter_spot_dist": "100",
            "spot_diameter": "55",
            "spots_under_tissue": "3743",
            "nb_genes": "541",
            "treatment_comment": null,
            "pixel_size_um_embedded": 0.273769293411857,
            "pixel_size_um_estimated": 0.273706493143168,
            "fullres_height": 17064,
            "fullres_width": 16800,
            "spots_under_tissue": 2524,
            "spot_estimate_dist": 6,
            "spot_diameter": 55.0,
            "inter_spot_dist": 100.0,
            "adata_nb_col": 541,
            "fullres_px_width": 21806,
            "fullres_px_height": 37330
        }