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<!DOCTYPE html>

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              <p class="caption" role="heading"><span class="caption-text">Introduction</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="installation/">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>

</ul>

<p class="caption" role="heading"><span class="caption-text">Developer Notes</span></p>

<ul>

<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>

</ul>

<p class="caption" role="heading"><span class="caption-text">API</span></p>

<ul>

<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>

<li class="toctree-l1"><a class="reference internal" href="model_torch/">slideflow.model.torch</a></li>

<li class="toctree-l1"><a class="reference internal" href="norm/">slideflow.norm</a></li>

<li class="toctree-l1"><a class="reference internal" href="simclr/">slideflow.simclr</a></li>

<li class="toctree-l1"><a class="reference internal" href="slide/">slideflow.slide</a></li>

<li class="toctree-l1"><a class="reference internal" href="slide_qc/">slideflow.slide.qc</a></li>

<li class="toctree-l1"><a class="reference internal" href="stats/">slideflow.stats</a></li>

<li class="toctree-l1"><a class="reference internal" href="util/">slideflow.util</a></li>

<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="slideflow-documentation">

<h1>Slideflow Documentation<a class="headerlink" href="#slideflow-documentation" title="Permalink to this heading"></a></h1>

<p>Slideflow is a Python package that provides a unified API for building and testing deep learning models for histopathology, supporting both Tensorflow/Keras and PyTorch.</p>

<p>Slideflow includes tools for efficient whole-slide image processing, easy and highly customizable model training with uncertainty quantification (UQ), and a number of functional tools to assist with analysis and interpretability, including predictive heatmaps, mosaic maps, GANs, saliency maps, and more. It is built with both <a class="reference external" href="https://www.tensorflow.org/">Tensorflow/Keras</a> and <a class="reference external" href="https://pytorch.org">PyTorch</a> backends, with fully cross-compatible TFRecord data storage.</p>

<p>This documentation starts with a high-level overview of the pipeline and includes examples of how to perform common tasks using the <code class="docutils literal notranslate"><span class="pre">Project</span></code> helper class. We also provide several tutorials with examples of how Slideflow can be used and extended for additional functionality.</p>

<div class="toctree-wrapper compound">

<p class="caption" role="heading"><span class="caption-text">Introduction</span></p>

<ul>

<li class="toctree-l1"><a class="reference internal" href="installation/">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>

</ul>

</div>

<div class="toctree-wrapper compound">

<p class="caption" role="heading"><span class="caption-text">Developer Notes</span></p>

<ul>

<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>

</ul>

</div>

<div class="toctree-wrapper compound">

<p class="caption" role="heading"><span class="caption-text">API</span></p>

<ul>

<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>

<li class="toctree-l1"><a class="reference internal" href="model_torch/">slideflow.model.torch</a></li>

<li class="toctree-l1"><a class="reference internal" href="norm/">slideflow.norm</a></li>

<li class="toctree-l1"><a class="reference internal" href="simclr/">slideflow.simclr</a></li>

<li class="toctree-l1"><a class="reference internal" href="slide/">slideflow.slide</a></li>

<li class="toctree-l1"><a class="reference internal" href="slide_qc/">slideflow.slide.qc</a></li>

<li class="toctree-l1"><a class="reference internal" href="stats/">slideflow.stats</a></li>

<li class="toctree-l1"><a class="reference internal" href="util/">slideflow.util</a></li>

<li class="toctree-l1"><a class="reference internal" href="studio_module/">slideflow.studio</a></li>

</ul>

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<p class="caption" role="heading"><span class="caption-text">Tutorials</span></p>

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<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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