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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>
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<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>
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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>
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<li class="toctree-l1"><a class="reference internal" href="../project/">slideflow.Project</a></li>
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<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>
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<li class="toctree-l1"><a class="reference internal" href="../biscuit/">slideflow.biscuit</a></li>
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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>
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<h1 id="index">Index</h1>

<div class="genindex-jumpbox">
 <a href="#_"><strong>_</strong></a>
 | <a href="#A"><strong>A</strong></a>
 | <a href="#B"><strong>B</strong></a>
 | <a href="#C"><strong>C</strong></a>
 | <a href="#D"><strong>D</strong></a>
 | <a href="#E"><strong>E</strong></a>
 | <a href="#F"><strong>F</strong></a>
 | <a href="#G"><strong>G</strong></a>
 | <a href="#H"><strong>H</strong></a>
 | <a href="#I"><strong>I</strong></a>
 | <a href="#J"><strong>J</strong></a>
 | <a href="#K"><strong>K</strong></a>
 | <a href="#L"><strong>L</strong></a>
 | <a href="#M"><strong>M</strong></a>
 | <a href="#N"><strong>N</strong></a>
 | <a href="#O"><strong>O</strong></a>
 | <a href="#P"><strong>P</strong></a>
 | <a href="#Q"><strong>Q</strong></a>
 | <a href="#R"><strong>R</strong></a>
 | <a href="#S"><strong>S</strong></a>
 | <a href="#T"><strong>T</strong></a>
 | <a href="#U"><strong>U</strong></a>
 | <a href="#V"><strong>V</strong></a>
 | <a href="#W"><strong>W</strong></a>
 | <a href="#X"><strong>X</strong></a>
 | <a href="#Y"><strong>Y</strong></a>
 | <a href="#Z"><strong>Z</strong></a>

</div>
<h2 id="_">_</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../model/#slideflow.model.Features.__call__">__call__() (in module slideflow.model.Features)</a>
</li>
      <li><a href="../util/#slideflow.util.ImgBatchSpeedColumn.__init__">__init__() (ImgBatchSpeedColumn method)</a>

      <ul>
        <li><a href="../util/#slideflow.util.LabeledMofNCompleteColumn.__init__">(LabeledMofNCompleteColumn method)</a>
</li>
        <li><a href="../util/#slideflow.util.MultiprocessProgress.__init__">(MultiprocessProgress method)</a>
</li>
        <li><a href="../util/#slideflow.util.MultiprocessProgressTracker.__init__">(MultiprocessProgressTracker method)</a>
</li>
        <li><a href="../grad/#slideflow.grad.SaliencyMap.__init__">(SaliencyMap method)</a>
</li>
        <li><a href="../studio_module/#slideflow.studio.Sidebar.__init__">(Sidebar method)</a>
</li>
        <li><a href="../studio_module/#slideflow.studio.Studio.__init__">(Studio method)</a>
</li>
        <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.__init__">(StyleGAN2Interpolator method)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="A">A</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slideflow/#slideflow.about">about() (in module slideflow)</a>

      <ul>
        <li><a href="../util/#slideflow.util.about">(in module slideflow.util)</a>
</li>
      </ul></li>
      <li><a href="../slidemap/#slideflow.SlideMap.activations">activations() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.activations_by_category">activations_by_category() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.add_inset">add_inset() (in module slideflow.Heatmap)</a>
</li>
      <li><a href="../project/#slideflow.Project.add_source">add_source() (in module slideflow.Project)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.add_to_render_pipeline">add_to_render_pipeline() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.add_widgets">add_widgets() (Sidebar method)</a>

      <ul>
        <li><a href="../studio_module/#slideflow.studio.Studio.add_widgets">(Studio method)</a>
</li>
      </ul></li>
      <li><a href="../slide/#slideflow.WSI.align_tiles_to">align_tiles_to() (in module slideflow.WSI)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.align_to">align_to() (in module slideflow.WSI)</a>
</li>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.all">all() (SaliencyMap method)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.threshold.apply">apply() (in module slideflow.biscuit.threshold)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slide/#slideflow.WSI.apply_qc_mask">apply_qc_mask() (in module slideflow.WSI)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.apply_rois">apply_rois() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.apply_segmentation">apply_segmentation() (in module slideflow.WSI)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.area">area() (in module slideflow.WSI)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.ask_load_heatmap">ask_load_heatmap() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.ask_load_model">ask_load_model() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.ask_load_project">ask_load_project() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.ask_load_slide">ask_load_slide() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.ask_zoom_to_mpp">ask_zoom_to_mpp() (Studio method)</a>
</li>
      <li><a href="../project/#slideflow.Project.associate_slide_names">associate_slide_names() (in module slideflow.Project)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.auc">auc() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.auc_and_threshold">auc_and_threshold() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.augment">augment() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.autoload">autoload() (Studio method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="B">B</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset.balance">balance() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../util/#slideflow.util.batch">batch() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.batch_generator">batch_generator() (in module slideflow.util)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig.batched_predict">batched_predict() (in module slideflow.mil.MILModelConfig)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.batched_predict">(in module slideflow.mil.TrainerConfig)</a>
</li>
      </ul></li>
      <li><a href="../util/#slideflow.util.bin_values_to_slide_grid">bin_values_to_slide_grid() (in module slideflow.util)</a>
</li>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.blur_integrated_gradients">blur_integrated_gradients() (SaliencyMap method)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.box_plots">box_plots() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.build_fastai_learner">build_fastai_learner() (in module slideflow.mil)</a>
</li>
      <li><a href="../slideflow/#slideflow.build_feature_extractor">build_feature_extractor() (in module slideflow)</a>

      <ul>
        <li><a href="../model/#slideflow.model.build_feature_extractor">(in module slideflow.model)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slide/#slideflow.WSI.build_generator">build_generator() (in module slideflow.WSI)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.build_index">build_index() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig.build_model">build_model() (in module slideflow.mil.MILModelConfig)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.build_model">(in module slideflow.mil.TrainerConfig)</a>
</li>
      </ul></li>
      <li><a href="../slidemap/#slideflow.SlideMap.build_mosaic">build_mosaic() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.build_multimodal_learner">build_multimodal_learner() (in module slideflow.mil)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.TrainerConfig.build_train_dataloader">build_train_dataloader() (in module slideflow.mil.TrainerConfig)</a>
</li>
      <li><a href="../model/#slideflow.model.build_trainer">build_trainer() (in module slideflow.model)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.TrainerConfig.build_val_dataloader">build_val_dataloader() (in module slideflow.mil.TrainerConfig)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="C">C</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../stats/#slideflow.stats.calculate_centroid">calculate_centroid() (in module slideflow.stats)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.calculate_centroids">calculate_centroids() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.calculate_outlines">calculate_outlines() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.cell_segmentation">cell_segmentation() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../project/#slideflow.Project.cell_segmentation">(in module slideflow.Project)</a>
</li>
      </ul></li>
      <li><a href="../studio_module/#slideflow.studio.Studio.center_next_window">center_next_window() (Studio method)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.centroid_to_image">centroid_to_image() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.centroids">centroids() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.check_duplicates">check_duplicates() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.checkpoint_to_tf_model">checkpoint_to_tf_model() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../util/#slideflow.util.choice_input">choice_input() (in module slideflow.util)</a>
</li>
      <li><a href="../mil_module/#slideflow.clam.CLAMModelConfig">CLAMModelConfig (class in slideflow.clam)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.class_interpolate">class_interpolate() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.clear_filters">clear_filters() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.clear_insets">clear_insets() (in module slideflow.Heatmap)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.clear_message">clear_message() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.clear_model_results">clear_model_results() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.clear_overlay">clear_overlay() (Studio method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../studio_module/#slideflow.studio.Studio.clear_result">clear_result() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.clear_status_message">clear_status_message() (Studio method)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.clip">clip() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.close">close() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.close_model">close_model() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.close_slide">close_slide() (Studio method)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.cluster">cluster() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.collapsing_header">collapsing_header() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.collapsing_header2">collapsing_header2() (Studio method)</a>
</li>
      <li><a href="../grad/#slideflow.grad.comparison_plot">comparison_plot() (in module slideflow.grad)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.concat">concat() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.content_width">content_width (Sidebar property)</a>
</li>
      <li><a href="../io/#slideflow.io.convert_dtype">convert_dtype() (in module slideflow.io)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.convert_xml_rois">convert_xml_rois() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../project/#slideflow.Project.create_blank_annotations">create_blank_annotations() (in module slideflow.Project)</a>
</li>
      <li><a href="../project/#slideflow.Project.create_hp_sweep">create_hp_sweep() (in module slideflow.Project)</a>
</li>
      <li><a href="../slideflow/#slideflow.create_project">create_project() (in module slideflow)</a>
</li>
      <li><a href="../util/#slideflow.util.create_triangles">create_triangles() (in module slideflow.util)</a>
</li>
      <li><a href="../gan/#slideflow.gan.utils.crop">crop() (in module slideflow.gan.utils)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="D">D</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset">Dataset (class in slideflow)</a>
</li>
      <li><a href="../project/#slideflow.Project.dataset">dataset() (in module slideflow.Project)</a>
</li>
      <li><a href="../simclr/#slideflow.simclr.DatasetBuilder">DatasetBuilder (class in slideflow.simclr)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures">DatasetFeatures (class in slideflow)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.decode_image">decode_image() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.decrease_tile_zoom">decrease_tile_zoom() (Studio method)</a>
</li>
      <li><a href="../util/#slideflow.util.ValidJSONEncoder.default">default() (ValidJSONEncoder method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.defer_rendering">defer_rendering() (Studio method)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.delong.delong_roc_test">delong_roc_test() (in module slideflow.biscuit.delong)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.delong.delong_roc_variance">delong_roc_variance() (in module slideflow.biscuit.delong)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../biscuit/#slideflow.biscuit.threshold.detect">detect() (in module slideflow.biscuit.threshold)</a>
</li>
      <li><a href="../io/#slideflow.io.detect_tfrecord_format">detect_tfrecord_format() (in module slideflow.io)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.df_from_cv">df_from_cv() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../stats/#slideflow.stats.df_from_pred">df_from_pred() (in module slideflow.stats)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.dim_text">dim_text() (Studio method)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.dim_to_mpp">dim_to_mpp() (in module slideflow.WSI)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.Experiment.display">display() (in module slideflow.biscuit.Experiment)</a>
</li>
      <li><a href="../util/#slideflow.util.download_from_tcga">download_from_tcga() (in module slideflow.util)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.draw">draw() (Sidebar method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.draw_frame">draw_frame() (Studio method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="E">E</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../util/#slideflow.util.EasyDict">EasyDict (class in slideflow.util)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.TrainerConfig.eval">eval() (in module slideflow.mil.TrainerConfig)</a>
</li>
      <li><a href="../stats/#slideflow.stats.eval_dataset">eval_dataset() (in module slideflow.stats)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.eval_exists">eval_exists() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.eval_mil">eval_mil() (in module slideflow.mil)</a>
</li>
      <li><a href="../model/#slideflow.model.Trainer.evaluate">evaluate() (in module slideflow.model.Trainer)</a>

      <ul>
        <li><a href="../project/#slideflow.Project.evaluate">(in module slideflow.Project)</a>
</li>
      </ul></li>
      <li><a href="../project/#slideflow.Project.evaluate_mil">evaluate_mil() (in module slideflow.Project)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.Experiment">Experiment (class in slideflow.biscuit)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slide/#slideflow.WSI.export_rois">export_rois() (in module slideflow.WSI)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.extract_cells">extract_cells() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../project/#slideflow.Project.extract_cells">(in module slideflow.Project)</a>
</li>
        <li><a href="../slide/#slideflow.WSI.extract_cells">(in module slideflow.WSI)</a>
</li>
      </ul></li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.extract_centroids">extract_centroids() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.extract_tiles">extract_tiles() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../io/#slideflow.io.extract_tiles">(in module slideflow.io)</a>
</li>
        <li><a href="../project/#slideflow.Project.extract_tiles">(in module slideflow.Project)</a>
</li>
        <li><a href="../slide/#slideflow.WSI.extract_tiles">(in module slideflow.WSI)</a>
</li>
      </ul></li>
      <li><a href="../dataset/#slideflow.Dataset.extract_tiles_from_tfrecords">extract_tiles_from_tfrecords() (in module slideflow.Dataset)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="F">F</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../biscuit/#slideflow.biscuit.delong.fastDeLong">fastDeLong() (in module slideflow.biscuit.delong)</a>
</li>
      <li><a href="../util/#slideflow.util.FeatureExtractionProgress">FeatureExtractionProgress (class in slideflow.util)</a>
</li>
      <li><a href="../model/#slideflow.model.Features">Features (class in slideflow.model)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.filter">filter() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../slidemap/#slideflow.SlideMap.filter">(in module slideflow.SlideMap)</a>
</li>
      </ul></li>
      <li><a href="../biscuit/#slideflow.biscuit.find_cv">find_cv() (in module slideflow.biscuit)</a>

      <ul>
        <li><a href="../biscuit/#slideflow.biscuit.utils.find_cv">(in module slideflow.biscuit.utils)</a>
</li>
      </ul></li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.find_cv_early_stop">find_cv_early_stop() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.find_eval">find_eval() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.find_model">find_model() (in module slideflow.biscuit.utils)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset.find_slide">find_slide() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.find_tfrecord">find_tfrecord() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.fit">fit() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../model_tensorflow/#slideflow.model.tensorflow.flatten">flatten() (in module slideflow.model.tensorflow)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.threshold.from_cv">from_cv() (in module slideflow.biscuit.threshold)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.from_df">from_df() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../model/#slideflow.model.Features.from_model">from_model() (in module slideflow.model.Features)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.full_button">full_button() (Sidebar method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.full_button2">full_button2() (Sidebar method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.full_width">full_width (Sidebar property)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="G">G</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../project/#slideflow.Project.gan_generate">gan_generate() (in module slideflow.Project)</a>
</li>
      <li><a href="../project/#slideflow.Project.gan_train">gan_train() (in module slideflow.Project)</a>
</li>
      <li><a href="../slide_qc/#slideflow.slide.qc.Gaussian">Gaussian (class in slideflow.slide.qc)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.generate">generate() (in module slideflow.Heatmap)</a>

      <ul>
        <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate">(StyleGAN2Interpolator method)</a>
</li>
      </ul></li>
      <li><a href="../mil_module/#slideflow.mil.generate_attention_heatmaps">generate_attention_heatmaps() (in module slideflow.mil)</a>
</li>
      <li><a href="../io/#slideflow.io.preservedsite.generate_crossfolds">generate_crossfolds() (in module slideflow.io.preservedsite)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_end">generate_end() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.generate_feature_bags">generate_feature_bags() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../project/#slideflow.Project.generate_feature_bags">(in module slideflow.Project)</a>
</li>
      </ul></li>
      <li><a href="../project/#slideflow.Project.generate_features">generate_features() (in module slideflow.Project)</a>
</li>
      <li><a href="../mosaic/#slideflow.Mosaic.generate_grid">generate_grid() (in module slideflow.Mosaic)</a>
</li>
      <li><a href="../project/#slideflow.Project.generate_heatmaps">generate_heatmaps() (in module slideflow.Project)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.generate_mil_features">generate_mil_features() (in module slideflow.mil)</a>
</li>
      <li><a href="../project/#slideflow.Project.generate_mosaic">generate_mosaic() (in module slideflow.Project)</a>
</li>
      <li><a href="../project/#slideflow.Project.generate_mosaic_from_annotations">generate_mosaic_from_annotations() (in module slideflow.Project)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_np_end">generate_np_end() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_np_from_embedding">generate_np_from_embedding() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_np_start">generate_np_start() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_start">generate_start() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_tf_end">generate_tf_end() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_tf_from_embedding">generate_tf_from_embedding() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.generate_tf_start">generate_tf_start() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../project/#slideflow.Project.generate_tfrecord_heatmap">generate_tfrecord_heatmap() (in module slideflow.Project)</a>
</li>
      <li><a href="../simclr/#slideflow.simclr.get_args">get_args() (in module slideflow.simclr)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.get_bags">get_bags() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../stats/#slideflow.stats.get_centroid_index">get_centroid_index() (in module slideflow.stats)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.get_default_widgets">get_default_widgets() (Studio static method)</a>
</li>
      <li><a href="../util/#slideflow.util.get_ensemble_model_config">get_ensemble_model_config() (in module slideflow.util)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.get_eval_results">get_eval_results() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.get_extension">get_extension() (Studio method)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.get_fit">get_fit() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../util/#slideflow.util.get_gan_config">get_gan_config() (in module slideflow.util)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../io/#slideflow.io.get_locations_from_tfrecord">get_locations_from_tfrecord() (in module slideflow.io)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.TrainerConfig.get_metrics">get_metrics() (in module slideflow.mil.TrainerConfig)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.get_mil_tile_predictions">get_mil_tile_predictions() (in module slideflow.mil)</a>
</li>
      <li><a href="../util/#slideflow.util.get_model_config">get_model_config() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.get_model_normalizer">get_model_normalizer() (in module slideflow.util)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.get_model_results">get_model_results() (in module slideflow.biscuit)</a>

      <ul>
        <li><a href="../biscuit/#slideflow.biscuit.utils.get_model_results">(in module slideflow.biscuit.utils)</a>
</li>
      </ul></li>
      <li><a href="../model_params/#slideflow.ModelParams.get_normalizer">get_normalizer() (in module slideflow.ModelParams)</a>
</li>
      <li><a href="../util/#slideflow.util.get_preprocess_fn">get_preprocess_fn() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.get_relative_tfrecord_paths">get_relative_tfrecord_paths() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.FeatureExtractionProgress.get_renderables">get_renderables() (FeatureExtractionProgress method)</a>

      <ul>
        <li><a href="../util/#slideflow.util.TileExtractionProgress.get_renderables">(TileExtractionProgress method)</a>
</li>
      </ul></li>
      <li><a href="../studio_module/#slideflow.studio.Studio.get_renderer">get_renderer() (Studio method)</a>
</li>
      <li><a href="../util/#slideflow.util.get_slide_paths">get_slide_paths() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.get_slides_from_model_manifest">get_slides_from_model_manifest() (in module slideflow.util)</a>
</li>
      <li><a href="../io/#slideflow.io.get_tfrecord_by_index">get_tfrecord_by_index() (in module slideflow.io)</a>
</li>
      <li><a href="../io/#slideflow.io.get_tfrecord_by_location">get_tfrecord_by_location() (in module slideflow.io)</a>
</li>
      <li><a href="../io/#slideflow.io.get_tfrecord_length">get_tfrecord_length() (in module slideflow.io)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.get_tfrecord_locations">get_tfrecord_locations() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../io/#slideflow.io.get_tfrecord_parser">get_tfrecord_parser() (in module slideflow.io)</a>

      <ul>
        <li><a href="../io_tensorflow/#slideflow.io.tensorflow.get_tfrecord_parser">(in module slideflow.io.tensorflow)</a>
</li>
      </ul></li>
      <li><a href="../dataset/#slideflow.Dataset.get_tile_dataframe">get_tile_dataframe() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../slide/#slideflow.WSI.get_tile_dataframe">(in module slideflow.WSI)</a>
</li>
      </ul></li>
      <li><a href="../slide/#slideflow.WSI.get_tile_mask">get_tile_mask() (in module slideflow.WSI)</a>
</li>
      <li><a href="../util/#slideflow.util.get_valid_model_dir">get_valid_model_dir() (in module slideflow.util)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.get_widget">get_widget() (Studio method)</a>
</li>
      <li><a href="../slideflow/#slideflow.getLoggingLevel">getLoggingLevel() (in module slideflow)</a>

      <ul>
        <li><a href="../util/#slideflow.util.getLoggingLevel">(in module slideflow.util)</a>
</li>
      </ul></li>
      <li><a href="../util/#slideflow.util.global_path">global_path() (in module slideflow.util)</a>
</li>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.gradcam">gradcam() (SaliencyMap method)</a>
</li>
      <li><a href="../grad/#slideflow.grad.grayscale">grayscale() (in module slideflow.grad)</a>
</li>
      <li><a href="../stats/#slideflow.stats.group_reduce">group_reduce() (in module slideflow.stats)</a>
</li>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.guided_integrated_gradients">guided_integrated_gradients() (SaliencyMap method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="H">H</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset.harmonize_labels">harmonize_labels() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.has_live_viewer">has_live_viewer() (Studio method)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.has_rois">has_rois() (in module slideflow.WSI)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.has_uq">has_uq() (Studio method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../studio_module/#slideflow.studio.Studio.header">header() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.header_with_buttons">header_with_buttons() (Studio method)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap">Heatmap (class in slideflow)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.highlighted">highlighted() (Studio method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="I">I</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../util/#slideflow.util.ImgBatchSpeedColumn">ImgBatchSpeedColumn (class in slideflow.util)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.increase_tile_zoom">increase_tile_zoom() (Studio method)</a>
</li>
      <li><a href="../io_torch/#slideflow.io.torch.IndexedInterleaver">IndexedInterleaver (class in slideflow.io.torch)</a>
</li>
      <li><a href="../util/#slideflow.util.infer_stride">infer_stride() (in module slideflow.util)</a>
</li>
      <li><a href="../grad/#slideflow.grad.inferno">inferno() (in module slideflow.grad)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig.inspect_batch">inspect_batch() (in module slideflow.mil.MILModelConfig)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.inspect_batch">(in module slideflow.mil.TrainerConfig)</a>
</li>
      </ul></li>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.integrated_gradients">integrated_gradients() (SaliencyMap method)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.interleave">interleave() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../io_torch/#slideflow.io.torch.InterleaveIterator">InterleaveIterator (class in slideflow.io.torch)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.interpolate_and_predict">interpolate_and_predict() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig.is_classification">is_classification() (in module slideflow.mil.MILModelConfig)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.is_classification">(in module slideflow.mil.TrainerConfig)</a>
</li>
      </ul></li>
      <li><a href="../dataset/#slideflow.Dataset.is_float">is_float() (in module slideflow.Dataset)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../util/#slideflow.util.is_model">is_model() (in module slideflow.util)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.is_mouse_down">is_mouse_down() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.is_mouse_released">is_mouse_released() (Studio method)</a>
</li>
      <li><a href="../util/#slideflow.util.is_project">is_project() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.is_simclr_model_path">is_simclr_model_path() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.is_slide">is_slide() (in module slideflow.util)</a>
</li>
      <li><a href="../model/#slideflow.model.is_tensorflow_model">is_tensorflow_model() (in module slideflow.model)</a>
</li>
      <li><a href="../util/#slideflow.util.is_tensorflow_model_path">is_tensorflow_model_path() (in module slideflow.util)</a>
</li>
      <li><a href="../model/#slideflow.model.is_tensorflow_tensor">is_tensorflow_tensor() (in module slideflow.model)</a>
</li>
      <li><a href="../util/#slideflow.util.is_tile_size_compatible">is_tile_size_compatible() (in module slideflow.util)</a>
</li>
      <li><a href="../model/#slideflow.model.is_torch_model">is_torch_model() (in module slideflow.model)</a>
</li>
      <li><a href="../util/#slideflow.util.is_torch_model_path">is_torch_model_path() (in module slideflow.util)</a>
</li>
      <li><a href="../model/#slideflow.model.is_torch_tensor">is_torch_tensor() (in module slideflow.model)</a>
</li>
      <li><a href="../util/#slideflow.util.is_uq_model">is_uq_model() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.isnumeric">isnumeric() (in module slideflow.util)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="J">J</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.join_tfrecord">join_tfrecord() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.jpeg_to_jpeg">jpeg_to_jpeg() (in module slideflow.norm.StainNormalizer)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.jpeg_to_rgb">jpeg_to_rgb() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.TrainerConfig.json_dump">json_dump() (in module slideflow.mil.TrainerConfig)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="K">K</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset.kfold_split">kfold_split() (in module slideflow.Dataset)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="L">L</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slidemap/#slideflow.SlideMap.label">label() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.label_by_preds">label_by_preds() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.label_by_slide">label_by_slide() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.label_by_uncertainty">label_by_uncertainty() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../util/#slideflow.util.LabeledMofNCompleteColumn">LabeledMofNCompleteColumn (class in slideflow.util)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.labels">labels() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.large_image_button">large_image_button() (Sidebar method)</a>
</li>
      <li><a href="../model_torch/#slideflow.model.torch.lazy_load_pretrained">lazy_load_pretrained() (in module slideflow.model.torch)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.linear_interpolate">linear_interpolate() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../model/#slideflow.model.list_extractors">list_extractors() (in module slideflow.model)</a>
</li>
      <li><a href="../slide_qc/#slideflow.slide.qc.Load">Load (class in slideflow.slide.qc)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.load">load() (in module slideflow.Heatmap)</a>

      <ul>
        <li><a href="../model/#slideflow.model.load">(in module slideflow.model)</a>
</li>
        <li><a href="../model_tensorflow/#slideflow.model.tensorflow.load">(in module slideflow.model.tensorflow)</a>
</li>
        <li><a href="../model_torch/#slideflow.model.torch.load">(in module slideflow.model.torch)</a>
</li>
        <li><a href="../model/#slideflow.model.Trainer.load">(in module slideflow.model.Trainer)</a>
</li>
        <li><a href="../simclr/#slideflow.simclr.load">(in module slideflow.simclr)</a>
</li>
        <li><a href="../slidemap/#slideflow.SlideMap.load">(in module slideflow.SlideMap)</a>
</li>
      </ul></li>
      <li><a href="../dataset/#slideflow.Dataset.load_annotations">load_annotations() (in module slideflow.Dataset)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.load_cache">load_cache() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.load_coordinates">load_coordinates() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.load_csv_roi">load_csv_roi() (in module slideflow.WSI)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.load_heatmap">load_heatmap() (Studio method)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.load_indices">load_indices() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../util/#slideflow.util.load_json">load_json() (in module slideflow.util)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.load_json_roi">load_json_roi() (in module slideflow.WSI)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.load_model">load_model() (Studio method)</a>
</li>
      <li><a href="../simclr/#slideflow.simclr.load_model_args">load_model_args() (in module slideflow.simclr)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.load_npz">load_npz() (in module slideflow.Heatmap)</a>
</li>
      <li><a href="../util/#slideflow.util.load_predictions">load_predictions() (in module slideflow.util)</a>
</li>
      <li><a href="../slideflow/#slideflow.load_project">load_project() (in module slideflow)</a>

      <ul>
        <li><a href="../studio_module/#slideflow.studio.Studio.load_project">(Studio method)</a>
</li>
      </ul></li>
      <li><a href="../slide/#slideflow.WSI.load_roi_array">load_roi_array() (in module slideflow.WSI)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.load_slide">load_slide() (Studio method)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.load_umap">load_umap() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../util/#slideflow.util.location_heatmap">location_heatmap() (in module slideflow.util)</a>
</li>
      <li><a href="../model_tensorflow/#slideflow.model.tensorflow.log_manifest">log_manifest() (in module slideflow.model.tensorflow)</a>

      <ul>
        <li><a href="../model_torch/#slideflow.model.torch.log_manifest">(in module slideflow.model.torch)</a>
</li>
        <li><a href="../util/#slideflow.util.log_manifest">(in module slideflow.util)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="M">M</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../util/#slideflow.util.make_dir">make_dir() (in module slideflow.util)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.manifest">manifest() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.manifest_histogram">manifest_histogram() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.map_activations">map_activations() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.map_predictions">map_predictions() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../util/#slideflow.util.map_values_to_slide_grid">map_values_to_slide_grid() (in module slideflow.util)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.mask_to_image">mask_to_image() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../util/#slideflow.util.md5">md5() (in module slideflow.util)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.merge">merge() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../stats/#slideflow.stats.metrics_from_dataset">metrics_from_dataset() (in module slideflow.stats)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.mil_config">mil_config() (in module slideflow.mil)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig">MILModelConfig (class in slideflow.mil)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.model">model (Studio property)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.model_exists">model_exists() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../model_params/#slideflow.ModelParams.model_type">model_type() (in module slideflow.ModelParams)</a>
</li>
      <li><a href="../model_params/#slideflow.ModelParams">ModelParams (class in slideflow)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li>
    module

      <ul>
        <li><a href="../gan/#module-slideflow.gan">slideflow.gan</a>
</li>
        <li><a href="../gan/#module-slideflow.gan.utils">slideflow.gan.utils</a>
</li>
        <li><a href="../grad/#module-slideflow.grad">slideflow.grad</a>
</li>
        <li><a href="../io_tensorflow/#module-slideflow.io.tensorflow">slideflow.io.tensorflow</a>
</li>
        <li><a href="../io_torch/#module-slideflow.io.torch">slideflow.io.torch</a>
</li>
        <li><a href="../studio_module/#module-slideflow.studio">slideflow.studio</a>
</li>
        <li><a href="../util/#module-slideflow.util">slideflow.util</a>
</li>
      </ul></li>
      <li><a href="../mosaic/#slideflow.Mosaic">Mosaic (class in slideflow)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.mouse_input_is_suspended">mouse_input_is_suspended() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.mouse_is_over_viewer">mouse_is_over_viewer (Studio property)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.mpp_to_dim">mpp_to_dim() (in module slideflow.WSI)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.multi_image_example">multi_image_example() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../grad/#slideflow.grad.multi_plot">multi_plot() (in module slideflow.grad)</a>
</li>
      <li><a href="../util/#slideflow.util.multi_warn">multi_warn() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.MultiprocessProgress">MultiprocessProgress (class in slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.MultiprocessProgressTracker">MultiprocessProgressTracker (class in slideflow.util)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="N">N</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../stats/#slideflow.stats.name_columns">name_columns() (in module slideflow.stats)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.hp.nature2022">nature2022() (in module slideflow.biscuit.hp)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slidemap/#slideflow.SlideMap.neighbors">neighbors() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../gan/#slideflow.gan.utils.noise_tensor">noise_tensor() (in module slideflow.gan.utils)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="O">O</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../studio_module/#slideflow.studio.Studio.offset_x">offset_x (Studio property)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.offset_x_pixels">offset_x_pixels (Studio property)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.offset_y">offset_y (Studio property)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.offset_y_pixels">offset_y_pixels (Studio property)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../grad/#slideflow.grad.oranges">oranges() (in module slideflow.grad)</a>
</li>
      <li><a href="../slide_qc/#slideflow.slide.qc.Otsu">Otsu (class in slideflow.slide.qc)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.outline_to_image">outline_to_image() (in module slideflow.cellseg.Segmentation)</a>
</li>
      <li><a href="../grad/#slideflow.grad.overlay">overlay() (in module slideflow.grad)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="P">P</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../studio_module/#slideflow.studio.Studio.P">P (Studio property)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.parser_from_labels">parser_from_labels() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../util/#slideflow.util.path_input">path_input() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.path_to_ext">path_to_ext() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.path_to_name">path_to_name() (in module slideflow.util)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.patients">patients() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.plot">plot() (in module slideflow.Heatmap)</a>

      <ul>
        <li><a href="../mosaic/#slideflow.Mosaic.plot">(in module slideflow.Mosaic)</a>
</li>
        <li><a href="../slidemap/#slideflow.SlideMap.plot">(in module slideflow.SlideMap)</a>
</li>
      </ul></li>
      <li><a href="../slidemap/#slideflow.SlideMap.plot_3d">plot_3d() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.plot_comparison">plot_comparison() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.plot_thumbnail">plot_thumbnail() (in module slideflow.Heatmap)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.threshold.plot_uncertainty">plot_uncertainty() (in module slideflow.biscuit.threshold)</a>

      <ul>
        <li><a href="../heatmap/#slideflow.Heatmap.plot_uncertainty">(in module slideflow.Heatmap)</a>
</li>
      </ul></li>
      <li><a href="../biscuit/#slideflow.biscuit.Experiment.plot_uq_calibration">plot_uq_calibration() (in module slideflow.biscuit.Experiment)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.plot_with_logit_cmap">plot_with_logit_cmap() (in module slideflow.Heatmap)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.png_to_png">png_to_png() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.png_to_rgb">png_to_rgb() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../mosaic/#slideflow.Mosaic.points_at_grid_index">points_at_grid_index() (in module slideflow.Mosaic)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig.predict">predict() (in module slideflow.mil.MILModelConfig)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.predict">(in module slideflow.mil.TrainerConfig)</a>
</li>
        <li><a href="../model/#slideflow.model.Trainer.predict">(in module slideflow.model.Trainer)</a>
</li>
        <li><a href="../project/#slideflow.Project.predict">(in module slideflow.Project)</a>
</li>
        <li><a href="../slide/#slideflow.slide.predict">(in module slideflow.slide)</a>
</li>
        <li><a href="../slide/#slideflow.WSI.predict">(in module slideflow.WSI)</a>
</li>
      </ul></li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../stats/#slideflow.stats.predict_dataset">predict_dataset() (in module slideflow.stats)</a>
</li>
      <li><a href="../project/#slideflow.Project.predict_ensemble">predict_ensemble() (in module slideflow.Project)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.predict_from_bags">predict_from_bags() (in module slideflow.mil)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.predict_from_multimodal_bags">predict_from_multimodal_bags() (in module slideflow.mil)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.predict_mil">predict_mil() (in module slideflow.mil)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.predict_multimodal_mil">predict_multimodal_mil() (in module slideflow.mil)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.predict_slide">predict_slide() (in module slideflow.mil)</a>
</li>
      <li><a href="../project/#slideflow.Project.predict_wsi">predict_wsi() (in module slideflow.Project)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.prediction_metrics">prediction_metrics() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.TrainerConfig.prepare_training">prepare_training() (in module slideflow.mil.TrainerConfig)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.preprocess_uint8">preprocess_uint8() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.preview">preview() (in module slideflow.WSI)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.print_error">print_error() (Studio method)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.print_tfrecord">print_tfrecord() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.threshold.process_group_predictions">process_group_predictions() (in module slideflow.biscuit.threshold)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.process_image">process_image() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.process_rois">process_rois() (in module slideflow.WSI)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.threshold.process_tile_predictions">process_tile_predictions() (in module slideflow.biscuit.threshold)</a>
</li>
      <li><a href="../project/#slideflow.Project">Project (class in slideflow)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Q">Q</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slide/#slideflow.WSI.qc">qc() (in module slideflow.WSI)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="R">R</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../io/#slideflow.io.read_and_return_record">read_and_return_record() (in module slideflow.io)</a>

      <ul>
        <li><a href="../io_tensorflow/#slideflow.io.tensorflow.read_and_return_record">(in module slideflow.io.tensorflow)</a>
</li>
      </ul></li>
      <li><a href="../util/#slideflow.util.read_annotations">read_annotations() (in module slideflow.util)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.read_group_predictions">read_group_predictions() (in module slideflow.biscuit.utils)</a>
</li>
      <li><a href="../model/#slideflow.model.read_hp_sweep">read_hp_sweep() (in module slideflow.model)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.read_tfrecord_by_location">read_tfrecord_by_location() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../model/#slideflow.model.rebuild_extractor">rebuild_extractor() (in module slideflow.model)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.rebuild_index">rebuild_index() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../model/#slideflow.model.RegressionTrainer">RegressionTrainer (class in slideflow.model)</a>
</li>
      <li><a href="../util/#slideflow.util.relative_path">relative_path() (in module slideflow.util)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.reload_model">reload_model() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.reload_viewer">reload_viewer() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.reload_wsi">reload_wsi() (Studio method)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.remove_filter">remove_filter() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.remove_from_render_pipeline">remove_from_render_pipeline() (Studio method)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.remove_qc">remove_qc() (in module slideflow.WSI)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.remove_roi">remove_roi() (in module slideflow.WSI)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.remove_slide">remove_slide() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.remove_widget">remove_widget() (Sidebar method)</a>

      <ul>
        <li><a href="../studio_module/#slideflow.studio.Studio.remove_widget">(Studio method)</a>
</li>
      </ul></li>
      <li><a href="../util/#slideflow.util.ImgBatchSpeedColumn.render">render() (ImgBatchSpeedColumn method)</a>

      <ul>
        <li><a href="../util/#slideflow.util.LabeledMofNCompleteColumn.render">(LabeledMofNCompleteColumn method)</a>
</li>
        <li><a href="../util/#slideflow.util.TileExtractionSpeedColumn.render">(TileExtractionSpeedColumn method)</a>
</li>
      </ul></li>
      <li><a href="../studio_module/#slideflow.studio.Studio.reset_background">reset_background() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.reset_tile_zoom">reset_tile_zoom() (Studio method)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.resize_tfrecords">resize_tfrecords() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.Experiment.results">results() (in module slideflow.biscuit.Experiment)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.resume_keyboard_input">resume_keyboard_input() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.resume_mouse_input_handling">resume_mouse_input_handling() (Studio method)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.rgb_to_rgb">rgb_to_rgb() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.rois">rois() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig.run_metrics">run_metrics() (in module slideflow.mil.MILModelConfig)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.run_metrics">(in module slideflow.mil.TrainerConfig)</a>
</li>
      </ul></li>
      <li><a href="../simclr/#slideflow.simclr.run_simclr">run_simclr() (in module slideflow.simclr)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="S">S</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../grad/#slideflow.grad.saliency_map_comparison">saliency_map_comparison() (in module slideflow.grad)</a>
</li>
      <li><a href="../grad/#slideflow.grad.SaliencyMap">SaliencyMap (class in slideflow.grad)</a>
</li>
      <li><a href="../slide_qc/#slideflow.slide.qc.Save">Save (class in slideflow.slide.qc)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation.save">save() (in module slideflow.cellseg.Segmentation)</a>

      <ul>
        <li><a href="../heatmap/#slideflow.Heatmap.save">(in module slideflow.Heatmap)</a>
</li>
        <li><a href="../mosaic/#slideflow.Mosaic.save">(in module slideflow.Mosaic)</a>
</li>
        <li><a href="../project/#slideflow.Project.save">(in module slideflow.Project)</a>
</li>
        <li><a href="../slidemap/#slideflow.SlideMap.save">(in module slideflow.SlideMap)</a>
</li>
      </ul></li>
      <li><a href="../slidemap/#slideflow.SlideMap.save_3d">save_3d() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.save_cache">save_cache() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.save_coordinates">save_coordinates() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.save_encoder">save_encoder() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.save_example_tiles">save_example_tiles() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.save_npz">save_npz() (in module slideflow.Heatmap)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.save_plot">save_plot() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../mosaic/#slideflow.Mosaic.save_report">save_report() (in module slideflow.Mosaic)</a>
</li>
      <li><a href="../slidemap/#slideflow.SlideMap.save_umap">save_umap() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.seed_search">seed_search() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.segment_slide">segment_slide() (in module slideflow.cellseg)</a>
</li>
      <li><a href="../slideflow_cellseg/#slideflow.cellseg.Segmentation">Segmentation (class in slideflow.cellseg)</a>
</li>
      <li><a href="../io/#slideflow.io.serialized_record">serialized_record() (in module slideflow.io)</a>

      <ul>
        <li><a href="../io_tensorflow/#slideflow.io.tensorflow.serialized_record">(in module slideflow.io.tensorflow)</a>
</li>
      </ul></li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.set_classifier">set_classifier() (StyleGAN2Interpolator method)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.set_fit">set_fit() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.set_grid_overlay">set_grid_overlay() (Studio method)</a>
</li>
      <li><a href="../util/#slideflow.util.set_ignore_sigint">set_ignore_sigint() (in module slideflow.util)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.set_message">set_message() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.set_overlay">set_overlay() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.set_prediction_message">set_prediction_message() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.set_status_message">set_status_message() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.set_viewer">set_viewer() (Studio method)</a>
</li>
      <li><a href="../slideflow/#slideflow.setLoggingLevel">setLoggingLevel() (in module slideflow)</a>

      <ul>
        <li><a href="../util/#slideflow.util.setLoggingLevel">(in module slideflow.util)</a>
</li>
      </ul></li>
      <li><a href="../slide/#slideflow.WSI.show_alignment">show_alignment() (in module slideflow.WSI)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.show_overlay">show_overlay (Studio property)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.shuffle_tfrecord">shuffle_tfrecord() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.shuffle_tfrecords_by_dir">shuffle_tfrecords_by_dir() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar">Sidebar (class in slideflow.studio)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../simclr/#slideflow.simclr.SimCLR">SimCLR (class in slideflow.simclr)</a>
</li>
      <li><a href="../simclr/#slideflow.simclr.SimCLR_Args">SimCLR_Args (class in slideflow.simclr)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.slide_manifest">slide_manifest() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.slide_paths">slide_paths() (in module slideflow.Dataset)</a>
</li>
      <li>
    slideflow.gan

      <ul>
        <li><a href="../gan/#module-slideflow.gan">module</a>
</li>
      </ul></li>
      <li>
    slideflow.gan.utils

      <ul>
        <li><a href="../gan/#module-slideflow.gan.utils">module</a>
</li>
      </ul></li>
      <li>
    slideflow.grad

      <ul>
        <li><a href="../grad/#module-slideflow.grad">module</a>
</li>
      </ul></li>
      <li>
    slideflow.io.tensorflow

      <ul>
        <li><a href="../io_tensorflow/#module-slideflow.io.tensorflow">module</a>
</li>
      </ul></li>
      <li>
    slideflow.io.torch

      <ul>
        <li><a href="../io_torch/#module-slideflow.io.torch">module</a>
</li>
      </ul></li>
      <li>
    slideflow.studio

      <ul>
        <li><a href="../studio_module/#module-slideflow.studio">module</a>
</li>
      </ul></li>
      <li>
    slideflow.util

      <ul>
        <li><a href="../util/#module-slideflow.util">module</a>
</li>
      </ul></li>
      <li><a href="../slidemap/#slideflow.SlideMap">SlideMap (class in slideflow)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.slides">slides() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../project/#slideflow.Project.smac_search">smac_search() (in module slideflow.Project)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.small_button">small_button() (Sidebar method)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.softmax_mean">softmax_mean() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.softmax_percent">softmax_percent() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.softmax_predict">softmax_predict() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.split">split() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../util/#slideflow.util.split_list">split_list() (in module slideflow.util)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.split_tfrecord">split_tfrecord() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.split_tfrecords_by_roi">split_tfrecords_by_roi() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.square_thumb">square_thumb() (in module slideflow.WSI)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer">StainNormalizer (class in slideflow.norm)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.stats">stats() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../slide_qc/#slideflow.slide.qc.StridedDL">StridedDL (class in slideflow.slide.qc)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio">Studio (class in slideflow.studio)</a>
</li>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator">StyleGAN2Interpolator (class in slideflow.gan)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.summary">summary() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../model/#slideflow.model.SurvivalTrainer">SurvivalTrainer (class in slideflow.model)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.suspend_keyboard_input">suspend_keyboard_input() (Studio method)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.suspend_mouse_input_handling">suspend_mouse_input_handling() (Studio method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="T">T</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset.tensorflow">tensorflow() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../slide/#slideflow.WSI.tensorflow">(in module slideflow.WSI)</a>
</li>
      </ul></li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.tf_to_rgb">tf_to_rgb() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.tf_to_tf">tf_to_tf() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.tfrecord_example">tfrecord_example() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../io/#slideflow.io.tfrecord_has_locations">tfrecord_has_locations() (in module slideflow.io)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.tfrecord_heatmap">tfrecord_heatmap() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../util/#slideflow.util.tfrecord_heatmap">(in module slideflow.util)</a>
</li>
      </ul></li>
      <li><a href="../dataset/#slideflow.Dataset.tfrecord_report">tfrecord_report() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.tfrecords">tfrecords() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.tfrecords_by_subfolder">tfrecords_by_subfolder() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.tfrecords_folders">tfrecords_folders() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.tfrecords_from_tiles">tfrecords_from_tiles() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.tfrecords_have_locations">tfrecords_have_locations() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Sidebar.theme">theme (Sidebar property)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.Experiment.thresholds_from_nested_cv">thresholds_from_nested_cv() (in module slideflow.biscuit.Experiment)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.thumb">thumb() (in module slideflow.WSI)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.thumbnails">thumbnails() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../studio_module/#slideflow.studio.Studio.tile_preview_enabled">tile_preview_enabled (Studio property)</a>
</li>
      <li><a href="../util/#slideflow.util.tile_size_label">tile_size_label() (in module slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.TileExtractionProgress">TileExtractionProgress (class in slideflow.util)</a>
</li>
      <li><a href="../util/#slideflow.util.TileExtractionSpeedColumn">TileExtractionSpeedColumn (class in slideflow.util)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.to_csv">to_csv() (in module slideflow.DatasetFeatures)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.to_df">to_df() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.MILModelConfig.to_dict">to_dict() (in module slideflow.mil.MILModelConfig)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.to_dict">(in module slideflow.mil.TrainerConfig)</a>
</li>
        <li><a href="../model_params/#slideflow.ModelParams.to_dict">(in module slideflow.ModelParams)</a>
</li>
      </ul></li>
      <li><a href="../util/#slideflow.util.to_onehot">to_onehot() (in module slideflow.util)</a>
</li>
      <li><a href="../dataset_features/#slideflow.DatasetFeatures.to_torch">to_torch() (in module slideflow.DatasetFeatures)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.torch">torch() (in module slideflow.Dataset)</a>

      <ul>
        <li><a href="../slide/#slideflow.WSI.torch">(in module slideflow.WSI)</a>
</li>
      </ul></li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.torch_to_torch">torch_to_torch() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.Experiment.train">train() (in module slideflow.biscuit.Experiment)</a>

      <ul>
        <li><a href="../mil_module/#slideflow.mil.TrainerConfig.train">(in module slideflow.mil.TrainerConfig)</a>
</li>
        <li><a href="../model/#slideflow.model.Trainer.train">(in module slideflow.model.Trainer)</a>
</li>
        <li><a href="../project/#slideflow.Project.train">(in module slideflow.Project)</a>
</li>
      </ul></li>
      <li><a href="../project/#slideflow.Project.train_ensemble">train_ensemble() (in module slideflow.Project)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.train_mil">train_mil() (in module slideflow.mil)</a>

      <ul>
        <li><a href="../project/#slideflow.Project.train_mil">(in module slideflow.Project)</a>
</li>
      </ul></li>
      <li><a href="../biscuit/#slideflow.biscuit.Experiment.train_nested_cv">train_nested_cv() (in module slideflow.biscuit.Experiment)</a>
</li>
      <li><a href="../project/#slideflow.Project.train_simclr">train_simclr() (in module slideflow.Project)</a>
</li>
      <li><a href="../model/#slideflow.model.Trainer">Trainer (class in slideflow.model)</a>
</li>
      <li><a href="../mil_module/#slideflow.mil.TrainerConfig">TrainerConfig (class in slideflow.mil)</a>
</li>
      <li><a href="../norm/#slideflow.norm.StainNormalizer.transform">transform() (in module slideflow.norm.StainNormalizer)</a>
</li>
      <li><a href="../io_tensorflow/#slideflow.io.tensorflow.transform_tfrecord">transform_tfrecord() (in module slideflow.io.tensorflow)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.transform_tfrecords">transform_tfrecords() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../biscuit/#slideflow.biscuit.utils.truncate_colormap">truncate_colormap() (in module slideflow.biscuit.utils)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="U">U</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../slidemap/#slideflow.SlideMap.umap_transform">umap_transform() (in module slideflow.SlideMap)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.unclip">unclip() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../model_tensorflow/#slideflow.model.tensorflow.unwrap">unwrap() (in module slideflow.model.tensorflow)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset.update_annotations_with_slidenames">update_annotations_with_slidenames() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.update_manifest">update_manifest() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../io/#slideflow.io.update_manifest_at_dir">update_manifest_at_dir() (in module slideflow.io)</a>
</li>
      <li><a href="../util/#slideflow.util.update_results_log">update_results_log() (in module slideflow.util)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="V">V</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../model_params/#slideflow.ModelParams.validate">validate() (in module slideflow.ModelParams)</a>
</li>
      <li><a href="../util/#slideflow.util.ValidJSONEncoder">ValidJSONEncoder (class in slideflow.util)</a>
</li>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.vanilla">vanilla() (SaliencyMap method)</a>
</li>
      <li><a href="../slide/#slideflow.WSI.verify_alignment">verify_alignment() (in module slideflow.WSI)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.verify_annotations_slides">verify_annotations_slides() (in module slideflow.Dataset)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../dataset/#slideflow.Dataset.verify_img_format">verify_img_format() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../dataset/#slideflow.Dataset.verify_slide_names">verify_slide_names() (in module slideflow.Dataset)</a>
</li>
      <li><a href="../heatmap/#slideflow.Heatmap.view">view() (in module slideflow.Heatmap)</a>

      <ul>
        <li><a href="../mosaic/#slideflow.Mosaic.view">(in module slideflow.Mosaic)</a>
</li>
        <li><a href="../slide/#slideflow.WSI.view">(in module slideflow.WSI)</a>
</li>
      </ul></li>
  </ul></td>
</tr></table>

<h2 id="W">W</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../util/#slideflow.util.write_json">write_json() (in module slideflow.util)</a>
</li>
      <li><a href="../io/#slideflow.io.write_tfrecords_merge">write_tfrecords_merge() (in module slideflow.io)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../io/#slideflow.io.write_tfrecords_multi">write_tfrecords_multi() (in module slideflow.io)</a>
</li>
      <li><a href="../io/#slideflow.io.write_tfrecords_single">write_tfrecords_single() (in module slideflow.io)</a>
</li>
      <li><a href="../slide/#slideflow.slide.WSI">WSI (class in slideflow.slide)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="X">X</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.xrai">xrai() (SaliencyMap method)</a>
</li>
  </ul></td>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../grad/#slideflow.grad.SaliencyMap.xrai_fast">xrai_fast() (SaliencyMap method)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Y">Y</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../util/#slideflow.util.yes_no_input">yes_no_input() (in module slideflow.util)</a>
</li>
  </ul></td>
</tr></table>

<h2 id="Z">Z</h2>
<table style="width: 100%" class="indextable genindextable"><tr>
  <td style="width: 33%; vertical-align: top;"><ul>
      <li><a href="../gan/#slideflow.gan.StyleGAN2Interpolator.z">z() (StyleGAN2Interpolator method)</a>
</li>
  </ul></td>
</tr></table>



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