https://github.com/histocartography/histocartography
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<h1>Welcome to histocartography’s documentation!<a class="headerlink" href="#welcome-to-histocartography-s-documentation" title="Permalink to this headline">¶</a></h1>
<p><cite>histocartography</cite> is a python-based library designed to facilitate the development of graph-based computational pathology pipelines. The library includes plug-and-play modules to perform:</p>
<ul class="simple">
<li><p>standard histology image pre-processing (e.g., <em>stain normalization</em>, <em>nuclei detection</em>, <em>tissue detection</em>)</p></li>
<li><p>entity-graph representation building (e.g. <em>cell graph</em>, <em>tissue graph</em>, <em>hierarchical graph</em>)</p></li>
<li><p>modeling Graph Neural Networks (e.g. <em>GIN</em>, <em>PNA</em>)</p></li>
<li><p>feature attribution based graph interpretability techniques (e.g. <em>GraphGradCAM</em>, <em>GraphGradCAM++</em>, <em>GNNExplainer</em>)</p></li>
<li><p>visualization tools</p></li>
</ul>
<p>All the functionalities are grouped under a user-friendly API.</p>
<div class="toctree-wrapper compound">
<p class="caption"><span class="caption-text">Contents:</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="api/histocartography.html">histocartography package</a><ul>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.pipeline.html">histocartography.pipeline module</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.pipeline.html#summary">Summary</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.pipeline.html#reference">Reference</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.interpretability.html">histocartography.interpretability package</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.interpretability.base_explainer.html">histocartography.interpretability.base_explainer module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.interpretability.grad_cam.html">histocartography.interpretability.grad_cam module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.interpretability.graph_pruning_explainer.html">histocartography.interpretability.graph_pruning_explainer module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.interpretability.lrp_gnn_explainer.html">histocartography.interpretability.lrp_gnn_explainer module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.interpretability.html#summary">Summary</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.interpretability.html#reference">Reference</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.metrics.html">histocartography.metrics package</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.metrics.metrics.html">histocartography.metrics.metrics module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.metrics.html#summary">Summary</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.metrics.html#reference">Reference</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.ml.html">histocartography.ml package</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.ml.layers.html">histocartography.ml.layers package</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.ml.models.html">histocartography.ml.models package</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.ml.html#summary">Summary</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.ml.html#reference">Reference</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.preprocessing.html">histocartography.preprocessing package</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.assignment_matrix.html">histocartography.preprocessing.assignment_matrix module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.feature_extraction.html">histocartography.preprocessing.feature_extraction module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.graph_builders.html">histocartography.preprocessing.graph_builders module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.io.html">histocartography.preprocessing.io module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.nuclei_concept_extraction.html">histocartography.preprocessing.nuclei_concept_extraction module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.nuclei_extraction.html">histocartography.preprocessing.nuclei_extraction module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.stain_normalizers.html">histocartography.preprocessing.stain_normalizers module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.stats.html">histocartography.preprocessing.stats module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.superpixel.html">histocartography.preprocessing.superpixel module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.tissue_mask.html">histocartography.preprocessing.tissue_mask module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.utils.html">histocartography.preprocessing.utils module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.html#summary">Summary</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.preprocessing.html#reference">Reference</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.utils.html">histocartography.utils package</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.utils.draw_utils.html">histocartography.utils.draw_utils module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.utils.graph.html">histocartography.utils.graph module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.utils.image.html">histocartography.utils.image module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.utils.io.html">histocartography.utils.io module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.utils.torch.html">histocartography.utils.torch module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.utils.html#summary">Summary</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.utils.html#reference">Reference</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.visualization.html">histocartography.visualization package</a><ul>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.visualization.visualization.html">histocartography.visualization.visualization module</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.visualization.html#summary">Summary</a></li>
<li class="toctree-l3"><a class="reference internal" href="api/histocartography.visualization.html#reference">Reference</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.html#summary">Summary</a></li>
<li class="toctree-l2"><a class="reference internal" href="api/histocartography.html#reference">Reference</a></li>
</ul>
</li>
</ul>
</div>
<section id="indices-and-tables">
<h2>Indices and tables<a class="headerlink" href="#indices-and-tables" title="Permalink to this headline">¶</a></h2>
<ul class="simple">
<li><p><a class="reference internal" href="genindex.html"><span class="std std-ref">Index</span></a></p></li>
<li><p><a class="reference internal" href="py-modindex.html"><span class="std std-ref">Module Index</span></a></p></li>
</ul>
</section>
<section id="reference">
<h2>Reference<a class="headerlink" href="#reference" title="Permalink to this headline">¶</a></h2>
<p>If you use <cite>histocartography</cite> in your projects, please cite the following:</p>
<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="nd">@inproceedings</span><span class="p">{</span><span class="n">pati2021</span><span class="p">,</span>
<span class="n">title</span> <span class="o">=</span> <span class="p">{</span><span class="n">Hierarchical</span> <span class="n">Graph</span> <span class="n">Representations</span> <span class="k">for</span> <span class="n">Digital</span> <span class="n">Pathology</span><span class="p">},</span>
<span class="n">author</span> <span class="o">=</span> <span class="p">{</span><span class="n">Pushpak</span> <span class="n">Pati</span><span class="p">,</span> <span class="n">Guillaume</span> <span class="n">Jaume</span><span class="p">,</span> <span class="n">Antonio</span> <span class="n">Foncubierta</span><span class="p">,</span> <span class="n">Florinda</span> <span class="n">Feroce</span><span class="p">,</span> <span class="n">Anna</span> <span class="n">Maria</span> <span class="n">Anniciello</span><span class="p">,</span> <span class="n">Giosuè</span> <span class="n">Scognamiglio</span><span class="p">,</span> <span class="n">Nadia</span> <span class="n">Brancati</span><span class="p">,</span> <span class="n">Maryse</span> <span class="n">Fiche</span><span class="p">,</span> <span class="n">Estelle</span> <span class="n">Dubruc</span><span class="p">,</span> <span class="n">Daniel</span> <span class="n">Riccio</span><span class="p">,</span> <span class="n">Maurizio</span> <span class="n">Di</span> <span class="n">Bonito</span><span class="p">,</span> <span class="n">Giuseppe</span> <span class="n">De</span> <span class="n">Pietro</span><span class="p">,</span> <span class="n">Gerardo</span> <span class="n">Botti</span><span class="p">,</span> <span class="n">Jean</span><span class="o">-</span><span class="n">Philippe</span> <span class="n">Thiran</span><span class="p">,</span> <span class="n">Maria</span> <span class="n">Frucci</span><span class="p">,</span> <span class="n">Orcun</span> <span class="n">Goksel</span><span class="p">,</span> <span class="n">Maria</span> <span class="n">Gabrani</span><span class="p">},</span>
<span class="n">booktitle</span> <span class="o">=</span> <span class="p">{</span><span class="n">https</span><span class="p">:</span><span class="o">//</span><span class="n">arxiv</span><span class="o">.</span><span class="n">org</span><span class="o">/</span><span class="n">pdf</span><span class="o">/</span><span class="mf">2102.11057</span><span class="p">},</span>
<span class="n">year</span> <span class="o">=</span> <span class="p">{</span><span class="mi">2021</span><span class="p">}</span>
<span class="p">}</span>
</pre></div>
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