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<ul><li class="navigation__item"><a href="/STimage-1K4M/docs/00_about">About</a></li><li class="navigation__item"><a href="/STimage-1K4M/docs/01-make-meta">Document</a></li></ul>
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<article itemscope itemtype="http://schema.org/Article"><div class="article__header"><header><h1>STimage-1K4M Dataset</h1></header></div><meta itemprop="headline" content="STimage-1K4M Dataset"><meta itemprop="author" content="Jiawen CHen"/><div class="js-article-content"><div class="layout--article"><!-- start custom article top snippet -->
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<div class="article__content" itemprop="articleBody"><p>Welcome to the STimage-1K4M Dataset repository. This dataset is designed to foster research in the field of spatial transcriptomics, combining high-resolution histopathology images with detailed gene expression data.</p>
<p><img src="doc_data/f1.png" alt="teaser" title="teaser" /></p>
<h2 id="dataset-description">Dataset Description</h2>
<p>STimage-1K4M consists of 1,149 spatial transcriptomics slides, totaling over 4 million spots with paired gene expression data. This dataset includes:</p>
<ul>
<li>Images.</li>
<li>Gene expression profiles matched with high-resolution histopathology images.</li>
<li>Spatial coordinates for each spot.</li>
</ul>
<p>See example folder for an example slide from Andersson et al. (pmid: 34650042).</p>
<h2 id="getting-started">Getting Started</h2>
<p>To use the STimage-1K4M dataset in your research, please access the dataset via <a href="https://huggingface.co/datasets/jiawennnn/STimage-1K4M">Hugging Face</a>.</p>
<h2 id="data-structure">Data structure</h2>
<p>The data structure is organized as follows:</p>
<div class="language-bash highlighter-rouge"><div class="highlight"><pre class="highlight"><code>├── annotation <span class="c"># Pathologist annotation</span>
├── meta <span class="c"># Test files (alternatively `spec` or `tests`)</span>
│ ├── bib.txt <span class="c"># the bibtex for all studies with pmid included in the dataset</span>
│ ├── meta_all_gene.csv <span class="c"># The meta information</span>
├── ST <span class="c"># Include all data for tech: Spatial Transcriptomics</span>
│ ├── coord <span class="c"># Include the spot coordinates &amp; spot radius of each slide</span>
│ ├── gene_exp <span class="c"># Include the gene expression of each slide</span>
│ └── image <span class="c"># Include the image each slide</span>
├── Visium <span class="c"># Include all data for tech: Visium, same structure as ST</span>
├── VisiumHD <span class="c"># Include all data for tech: VisiumHD, same structure as ST</span>
</code></pre></div></div>
<h2 id="document">Document</h2>
<p>The code for data processing and reproducing evaluation result in the paper are in <a href="01-make-meta">Document</a>.</p>
<h2 id="acknowledgement">Acknowledgement</h2>
<p>The fine-tuning and evaluation codes borrows heavily from <a href="https://github.com/openai/CLIP/issues/83">CLIP</a> and <a href="https://github.com/PathologyFoundation/plip/">PLIP</a>.</p>
<h2 id="citation">Citation</h2>
<div class="language-plaintext highlighter-rouge"><div class="highlight"><pre class="highlight"><code>@misc{chen2024stimage1k4m,
title={STimage-1K4M: A histopathology image-gene expression dataset for spatial transcriptomics},
author={Jiawen Chen and Muqing Zhou and Wenrong Wu and Jinwei Zhang and Yun Li and Didong Li},
year={2024},
eprint={2406.06393},
archivePrefix={arXiv},
primaryClass={cs.CV}
}
</code></pre></div></div>
<h2 id="license">License</h2>
<p>All code is licensed under the MIT License - see the LICENSE.md file for details.</p>
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