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---
layout: page
title: Description
permalink: /description/
---
<!-- Slider Start -->
<section id="global-header">
<div class="container">
<div class="row">
<div class="col-md-12">
<div class="block">
<h1>Dataset Description</h1>
</div>
</div>
</div>
</div>
</section>
<section id="description">
<div class="container">
<div class="row">
<div class="col-md-12">
<h1> Dataset format </h1>
<div class="block">
<p>
For every sample, we provide:
</p>
<ul>
<li>The aligned Spatial Transcriptomics data in a standard ScanPy .h5ad file</li>
<li>An H&E WSI in pyramidal generic TIFF</li>
<li>CellViT nuclei segmentation</li>
<li>WSI patches</li>
<li>A JSON file containing metadata for that sample</li>
</ul>
<p>
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.
</p>
<img src="../img/format.png" alt="Img" class="centered-image">
</div>
<body>
<pre>
{
"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
}
</pre>
</body>
</div>
</div>
</div>
</section>