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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>
<ul class="current">
<li class="toctree-l1 current"><a class="current reference internal" href="#">Installation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../overview/">Overview</a></li>
<li class="toctree-l1"><a class="reference internal" href="../quickstart/">Quickstart</a></li>
<li class="toctree-l1"><a class="reference internal" href="../project_setup/">Setting up a Project</a></li>
<li class="toctree-l1"><a class="reference internal" href="../datasets_and_val/">Datasets</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slide_processing/">Slide Processing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../training/">Training</a></li>
<li class="toctree-l1"><a class="reference internal" href="../evaluation/">Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../posthoc/">Layer Activations</a></li>
<li class="toctree-l1"><a class="reference internal" href="../uq/">Uncertainty Quantification</a></li>
<li class="toctree-l1"><a class="reference internal" href="../features/">Generating Features</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mil/">Multiple-Instance Learning (MIL)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../ssl/">Self-Supervised Learning (SSL)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../stylegan/">Generative Networks (GANs)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../saliency/">Saliency Maps</a></li>
<li class="toctree-l1"><a class="reference internal" href="../segmentation/">Tissue Segmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../cellseg/">Cell Segmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../custom_loops/">Custom Training Loops</a></li>
<li class="toctree-l1"><a class="reference internal" href="../studio/">Slideflow Studio: Live Visualization</a></li>
<li class="toctree-l1"><a class="reference internal" href="../troubleshooting/">Troubleshooting</a></li>
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<p class="caption" role="heading"><span class="caption-text">Developer Notes</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../tfrecords/">TFRecords: Reading and Writing</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataloaders/">Dataloaders: Sampling and Augmentation</a></li>
<li class="toctree-l1"><a class="reference internal" href="../custom_extractors/">Custom Feature Extractors</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tile_labels/">Strong Supervision with Tile Labels</a></li>
<li class="toctree-l1"><a class="reference internal" href="../plugins/">Creating a Slideflow Plugin</a></li>
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<p class="caption" role="heading"><span class="caption-text">API</span></p>
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<li class="toctree-l1"><a class="reference internal" href="../slideflow/">slideflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="../project/">slideflow.Project</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataset/">slideflow.Dataset</a></li>
<li class="toctree-l1"><a class="reference internal" href="../dataset_features/">slideflow.DatasetFeatures</a></li>
<li class="toctree-l1"><a class="reference internal" href="../heatmap/">slideflow.Heatmap</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model_params/">slideflow.ModelParams</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mosaic/">slideflow.Mosaic</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slidemap/">slideflow.SlideMap</a></li>
<li class="toctree-l1"><a class="reference internal" href="../biscuit/">slideflow.biscuit</a></li>
<li class="toctree-l1"><a class="reference internal" href="../slideflow_cellseg/">slideflow.cellseg</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io/">slideflow.io</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io_tensorflow/">slideflow.io.tensorflow</a></li>
<li class="toctree-l1"><a class="reference internal" href="../io_torch/">slideflow.io.torch</a></li>
<li class="toctree-l1"><a class="reference internal" href="../gan/">slideflow.gan</a></li>
<li class="toctree-l1"><a class="reference internal" href="../grad/">slideflow.grad</a></li>
<li class="toctree-l1"><a class="reference internal" href="../mil_module/">slideflow.mil</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model/">slideflow.model</a></li>
<li class="toctree-l1"><a class="reference internal" href="../model_tensorflow/">slideflow.model.tensorflow</a></li>
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<li class="toctree-l1"><a class="reference internal" href="../studio_module/">slideflow.studio</a></li>
</ul>
<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>
<ul>
<li class="toctree-l1"><a class="reference internal" href="../tutorial1/">Tutorial 1: Model training (simple)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial2/">Tutorial 2: Model training (advanced)</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial3/">Tutorial 3: Using a custom architecture</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial4/">Tutorial 4: Model evaluation &amp; heatmaps</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial5/">Tutorial 5: Creating a mosaic map</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial6/">Tutorial 6: Custom slide filtering</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial7/">Tutorial 7: Training with custom augmentations</a></li>
<li class="toctree-l1"><a class="reference internal" href="../tutorial8/">Tutorial 8: Multiple-Instance Learning</a></li>
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  <section id="installation">
<h1>Installation<a class="headerlink" href="#installation" title="Permalink to this heading">¶</a></h1>
<figure class="align-default">
<img alt="https://github.com/user-attachments/assets/53d5c1f8-8fbc-4e0f-bd62-db16797492b0" src="https://github.com/user-attachments/assets/53d5c1f8-8fbc-4e0f-bd62-db16797492b0" />
</figure>
<p>Slideflow is tested on <strong>Linux-based systems</strong> (Ubuntu, CentOS, Red Hat, and Raspberry Pi OS) and <strong>macOS</strong> (Intel and Apple). Windows support is experimental.</p>
<section id="requirements">
<h2>Requirements<a class="headerlink" href="#requirements" title="Permalink to this heading">¶</a></h2>
<ul class="simple">
<li><p>Python &gt;= 3.7 (&lt;3.10 if using <a class="reference external" href="https://docs.rapids.ai/api/cucim/stable/">cuCIM</a>)</p></li>
<li><dl class="simple">
<dt><a class="reference external" href="https://pytorch.org/">PyTorch</a> (1.9+) <em>or</em> <a class="reference external" href="https://www.tensorflow.org/">Tensorflow</a> (2.5-2.11)</dt><dd><ul>
<li><p>Core functionality, including tile extraction, data processing, and tile-based model training, is supported for both PyTorch and Tensorflow. Additional advanced tools, such as Multiple-Instance Learning (MIL), GANs, and pretrained foundation models, require PyTorch.</p></li>
</ul>
</dd>
</dl>
</li>
</ul>
<section id="optional">
<h3>Optional<a class="headerlink" href="#optional" title="Permalink to this heading">¶</a></h3>
<ul class="simple">
<li><p><a class="reference external" href="https://libvips.github.io/libvips/">Libvips &gt;= 8.9</a> (alternative slide reader, adds support for *.scn, *.mrxs, *.ndpi, *.vms, and *.vmu files)</p></li>
<li><p>Linear solver (for site-preserved cross-validation):</p>
<ul>
<li><p><a class="reference external" href="https://www.ibm.com/docs/en/icos/12.10.0?topic=v12100-installing-cplex-optimization-studio">CPLEX 20.1.0</a> with <a class="reference external" href="https://www.ibm.com/docs/en/icos/12.10.0?topic=cplex-setting-up-python-api">Python API</a></p></li>
<li><p><em>or</em> <a class="reference external" href="http://www.pyomo.org/installation">Pyomo</a> with <a class="reference external" href="https://anaconda.org/conda-forge/coinbonmin">Bonmin</a> solver</p></li>
</ul>
</li>
</ul>
</section>
</section>
<section id="download-with-pip">
<h2>Download with pip<a class="headerlink" href="#download-with-pip" title="Permalink to this heading">¶</a></h2>
<p>Slideflow can be installed either with PyPI or as a Docker container. To install via pip:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Update to latest pip</span>
pip<span class="w"> </span>install<span class="w"> </span>--upgrade<span class="w"> </span>pip<span class="w"> </span>wheel

<span class="c1"># Current stable release, Tensorflow backend</span>
pip<span class="w"> </span>install<span class="w"> </span>slideflow<span class="o">[</span>tf<span class="o">]</span><span class="w"> </span>cucim<span class="w"> </span>cupy-cuda11x

<span class="c1"># Alternatively, install with PyTorch backend</span>
pip<span class="w"> </span>install<span class="w"> </span>slideflow<span class="o">[</span>torch<span class="o">]</span><span class="w"> </span>cucim<span class="w"> </span>cupy-cuda11x
</pre></div>
</div>
<p>The <code class="docutils literal notranslate"><span class="pre">cupy</span></code> package name depends on the installed CUDA version; <a class="reference external" href="https://docs.cupy.dev/en/stable/install.html#installing-cupy">see here</a> for installation instructions. <code class="docutils literal notranslate"><span class="pre">cucim</span></code> and <code class="docutils literal notranslate"><span class="pre">cupy</span></code> are not required if using Libvips.</p>
</section>
<section id="run-a-docker-container">
<h2>Run a Docker container<a class="headerlink" href="#run-a-docker-container" title="Permalink to this heading">¶</a></h2>
<p>Alternatively, pre-configured <a class="reference external" href="https://hub.docker.com/repository/docker/jamesdolezal/slideflow">docker images</a> are available with cuCIM, Libvips, and either PyTorch 1.11 or Tensorflow 2.9 pre-installed. Using a preconfigured <a class="reference external" href="https://docs.docker.com/install/">Docker</a> container is the easiest way to get started with compatible dependencies and GPU support.</p>
<p>To run a Docker container with the Tensorflow backend:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker<span class="w"> </span>pull<span class="w"> </span>jamesdolezal/slideflow:latest-tf
docker<span class="w"> </span>run<span class="w"> </span>-it<span class="w"> </span>--gpus<span class="w"> </span>all<span class="w"> </span>jamesdolezal/slideflow:latest-tf
</pre></div>
</div>
<p>To run a Docker container with the PyTorch backend:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>docker<span class="w"> </span>pull<span class="w"> </span>jamesdolezal/slideflow:latest-torch
docker<span class="w"> </span>run<span class="w"> </span>-it<span class="w"> </span>--shm-size<span class="o">=</span>2g<span class="w"> </span>--gpus<span class="w"> </span>all<span class="w"> </span>jamesdolezal/slideflow:latest-torch
</pre></div>
</div>
</section>
<section id="build-from-source">
<h2>Build from source<a class="headerlink" href="#build-from-source" title="Permalink to this heading">¶</a></h2>
<p>To build Slideflow from source, clone the repository from the project <a class="reference external" href="https://github.com/slideflow/slideflow">Github page</a>:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>git<span class="w"> </span>clone<span class="w"> </span>https://github.com/slideflow/slideflow
<span class="nb">cd</span><span class="w"> </span>slideflow
conda<span class="w"> </span>env<span class="w"> </span>create<span class="w"> </span>-f<span class="w"> </span>environment.yml
conda<span class="w"> </span>activate<span class="w"> </span>slideflow
python<span class="w"> </span>setup.py<span class="w"> </span>bdist_wheel
pip<span class="w"> </span>install<span class="w"> </span>dist/slideflow*<span class="w"> </span>cupy-cuda11x
</pre></div>
</div>
</section>
<section id="extensions">
<h2>Extensions<a class="headerlink" href="#extensions" title="Permalink to this heading">¶</a></h2>
<p>The core Slideflow package is licensed under the <strong>Apache-2.0</strong> license. Additional functionality, such as pretrained foundation models, are distributed in separate packages according to their licensing terms. Available extensions include:</p>
<ul class="simple">
<li><dl class="simple">
<dt><strong>Slideflow-GPL</strong>: GPL-3.0 licensed extensions (<a class="reference external" href="https://github.com/slideflow/slideflow-gpl">GitHub</a>)</dt><dd><ul>
<li><p>Includes: <a class="reference external" href="https://www.sciencedirect.com/science/article/abs/pii/S1361841522002730">RetCCL</a>, <a class="reference external" href="https://www.sciencedirect.com/science/article/abs/pii/S1361841522002043">CTransPath</a>, and <a class="reference external" href="https://www.nature.com/articles/s41551-020-00682-w">CLAM</a>.</p></li>
</ul>
</dd>
</dl>
</li>
<li><dl class="simple">
<dt><strong>Slideflow-NonCommercial</strong>: CC BY-NC 4.0 licensed extensions for non-commercial use (<a class="reference external" href="https://github.com/slideflow/slideflow-noncommercial">GitHub</a>)</dt><dd><ul>
<li><p>Includes: <a class="reference external" href="https://www.medrxiv.org/content/10.1101/2023.07.21.23292757v2.full.pdf">HistoSSL</a>, <a class="reference external" href="https://www.nature.com/articles/s41591-023-02504-3">PLIP</a>, <a class="reference external" href="https://aka.ms/gigapath">GigaPath</a>, <a class="reference external" href="https://www.nature.com/articles/s41591-024-02857-3">UNI</a>, <a class="reference external" href="https://www.nature.com/articles/s41467-022-34025-x">BISCUIT</a>, and <a class="reference external" href="https://nvlabs-fi-cdn.nvidia.com/stylegan3/stylegan3-paper.pdf">StyleGAN3</a>.</p></li>
</ul>
</dd>
</dl>
</li>
</ul>
<p>These extensions can be installed via pip. The GigaPath feature extractor has additional, more restrictive dependencies that must be installed separately.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># Install Slideflow-GPL and Slideflow-NonCommercial</span>
pip<span class="w"> </span>install<span class="w"> </span>slideflow-gpl<span class="w"> </span>slideflow-noncommercial

<span class="c1"># Install GigaPath dependencies, if desired</span>
pip<span class="w"> </span>install<span class="w"> </span>slideflow-noncommercial<span class="o">[</span>gigapath<span class="o">]</span> git+ssh://git@github.com/prov-gigapath/prov-gigapath
</pre></div>
</div>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>The Slideflow-GPL and Slideflow-NonCommercial extensions are not included in the default Slideflow package due to their licensing terms. Please review the licensing terms of each extension before use.</p>
</div>
</section>
<section id="pytorch-vs-tensorflow">
<h2>PyTorch vs. Tensorflow<a class="headerlink" href="#pytorch-vs-tensorflow" title="Permalink to this heading">¶</a></h2>
<p>Slideflow supports both PyTorch and Tensorflow, with cross-compatible TFRecord storage. Slideflow will default to using PyTorch if both are available, but the backend can be manually specified using the environmental variable <code class="docutils literal notranslate"><span class="pre">SF_BACKEND</span></code>. For example:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">SF_BACKEND</span><span class="o">=</span>tensorflow
</pre></div>
</div>
</section>
<section id="cucim-vs-libvips">
<span id="slide-backend"></span><h2>cuCIM vs. Libvips<a class="headerlink" href="#cucim-vs-libvips" title="Permalink to this heading">¶</a></h2>
<p>By default, Slideflow reads whole-slide images using <a class="reference external" href="https://docs.rapids.ai/api/cucim/stable/">cuCIM</a>. Although much faster than other openslide-based frameworks, it supports fewer slide scanner formats. Slideflow also includes a <a class="reference external" href="https://libvips.github.io/libvips/">Libvips</a> backend, which adds support for *.scn, *.mrxs, *.ndpi, *.vms, and *.vmu files. You can set the active slide backend with the environmental variable <code class="docutils literal notranslate"><span class="pre">SF_SLIDE_BACKEND</span></code>:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">export</span><span class="w"> </span><span class="nv">SF_SLIDE_BACKEND</span><span class="o">=</span>libvips
</pre></div>
</div>
<div class="admonition warning">
<p class="admonition-title">Warning</p>
<p>A bug in the pixman library (version=0.38) will corrupt downsampled slide images, resulting in large black boxes across the slide. We have provided a patch for version 0.38 that has been tested for Ubuntu, which is provided in the project <a class="reference external" href="https://github.com/slideflow/slideflow">Github page</a> (<code class="docutils literal notranslate"><span class="pre">pixman_repair.sh</span></code>), although it may not be suitable for all environments and we make no guarantees regarding its use. The <a class="reference external" href="https://hub.docker.com/repository/docker/slideflow/slideflow">Slideflow docker images</a> already have this applied. If you are installing from source, have pixman version 0.38, and are unable to apply this patch, the use of downsampled image layers must be disabled to avoid corruption (pass <code class="docutils literal notranslate"><span class="pre">enable_downsample=False</span></code> to tile extraction functions).</p>
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