https://github.com/histocartography/histocartography
Tip revision: cb9c35f8fa5397c438c2eeb44c00f3eb73b9613f authored by Deployment Bot (from Travis CI) on 20 May 2021, 08:40:43 UTC
Deploy histocartography/histocartography to github.com/histocartography/histocartography.git:gh-pages
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<li class="toctree-l1"><a class="reference internal" href="api/histocartography.html">histocartography package</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>
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| <a href="#G"><strong>G</strong></a>
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| <a href="#U"><strong>U</strong></a>
| <a href="#V"><strong>V</strong></a>
| <a href="#W"><strong>W</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="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.AugmentedDeepFeatureExtractor.__init__">__init__() (AugmentedDeepFeatureExtractor method)</a>
<ul>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.BaseCAM.__init__">(BaseCAM method)</a>
</li>
<li><a href="api/histocartography.interpretability.base_explainer.html#histocartography.interpretability.base_explainer.BaseExplainer.__init__">(BaseExplainer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.BaseGraphBuilder.__init__">(BaseGraphBuilder method)</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.BaseGraphGradCAMExplainer.__init__">(BaseGraphGradCAMExplainer method)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseGraphVisualization.__init__">(BaseGraphVisualization method)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseImageVisualization.__init__">(BaseImageVisualization method)</a>
</li>
<li><a href="api/histocartography.ml.models.base_model.html#histocartography.ml.models.base_model.BaseModel.__init__">(BaseModel method)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.BatchPipelineRunner.__init__">(BatchPipelineRunner method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.BNReLU.__init__">(BNReLU method)</a>
</li>
<li><a href="api/histocartography.ml.models.cell_graph_model.html#histocartography.ml.models.cell_graph_model.CellGraphModel.__init__">(CellGraphModel method)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.ColorMergedSuperpixelExtractor.__init__">(ColorMergedSuperpixelExtractor method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Conv2dWithActivation.__init__">(Conv2dWithActivation method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Decoder.__init__">(Decoder method)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.DeepFeatureExtractor.__init__">(DeepFeatureExtractor method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.DenseBlock.__init__">(DenseBlock method)</a>
</li>
<li><a href="api/histocartography.ml.layers.dense_gin_layer.html#histocartography.ml.layers.dense_gin_layer.DenseGINLayer.__init__">(DenseGINLayer method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Encoder.__init__">(Encoder method)</a>
</li>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.ExplainerModel.__init__">(ExplainerModel method)</a>
</li>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#histocartography.preprocessing.tissue_mask.GaussianTissueMask.__init__">(GaussianTissueMask method)</a>
</li>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer.__init__">(GINLayer method)</a>
</li>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.GraphPruningExplainer.__init__">(GraphPruningExplainer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.GridAugmentedDeepFeatureExtractor.__init__">(GridAugmentedDeepFeatureExtractor method)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.GridDeepFeatureExtractor.__init__">(GridDeepFeatureExtractor method)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.GridPatchDataset.__init__">(GridPatchDataset method)</a>
</li>
<li><a href="api/histocartography.ml.models.hact_model.html#histocartography.ml.models.hact_model.HACTModel.__init__">(HACTModel method)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.HACTVisualization.__init__">(HACTVisualization method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.HoverNet.__init__">(HoverNet method)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#histocartography.preprocessing.nuclei_extraction.ImageToPatchDataset.__init__">(ImageToPatchDataset method)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.InstanceMapPatchDataset.__init__">(InstanceMapPatchDataset method)</a>
</li>
<li><a href="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.KNNGraphBuilder.__init__">(KNNGraphBuilder method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.MacenkoStainNormalizer.__init__">(MacenkoStainNormalizer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.MergedSuperpixelExtractor.__init__">(MergedSuperpixelExtractor method)</a>
</li>
<li><a href="api/histocartography.ml.layers.mlp.html#histocartography.ml.layers.mlp.MLP.__init__">(MLP method)</a>
</li>
<li><a href="api/histocartography.ml.layers.multi_layer_gnn.html#histocartography.ml.layers.multi_layer_gnn.MultiLayerGNN.__init__">(MultiLayerGNN method)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_concept_extraction.html#histocartography.preprocessing.nuclei_concept_extraction.NucleiConceptExtractor.__init__">(NucleiConceptExtractor method)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#histocartography.preprocessing.nuclei_extraction.NucleiExtractor.__init__">(NucleiExtractor method)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.OverlayGraphVisualization.__init__">(OverlayGraphVisualization method)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.PatchFeatureExtractor.__init__">(PatchFeatureExtractor method)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineRunner.__init__">(PipelineRunner method)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineStep.__init__">(PipelineStep method)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNALayer.__init__">(PNALayer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.RAGGraphBuilder.__init__">(RAGGraphBuilder method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.ResidualBlock.__init__">(ResidualBlock method)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.SLICSuperpixelExtractor.__init__">(SLICSuperpixelExtractor method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.StainNormalizer.__init__">(StainNormalizer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.SuperpixelExtractor.__init__">(SuperpixelExtractor method)</a>
</li>
<li><a href="api/histocartography.ml.models.tissue_graph_model.html#histocartography.ml.models.tissue_graph_model.TissueGraphModel.__init__">(TissueGraphModel method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Upsample2x.__init__">(Upsample2x method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.VahadaneStainNormalizer.__init__">(VahadaneStainNormalizer 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="api/histocartography.utils.graph.html#histocartography.utils.graph.adj_to_dgl">adj_to_dgl() (in module histocartography.utils.graph)</a>
</li>
<li><a href="api/histocartography.utils.graph.html#histocartography.utils.graph.adj_to_networkx">adj_to_networkx() (in module histocartography.utils.graph)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.aggregate_max">aggregate_max() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.aggregate_mean">aggregate_mean() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.aggregate_min">aggregate_min() (in module histocartography.ml.layers.constants)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.aggregate_std">aggregate_std() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.aggregate_var">aggregate_var() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#histocartography.preprocessing.tissue_mask.AnnotationPostProcessor">AnnotationPostProcessor (class in histocartography.preprocessing.tissue_mask)</a>
</li>
<li><a href="api/histocartography.preprocessing.assignment_matrix.html#histocartography.preprocessing.assignment_matrix.AssignmnentMatrixBuilder">AssignmnentMatrixBuilder (class in histocartography.preprocessing.assignment_matrix)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.AugmentedDeepFeatureExtractor">AugmentedDeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction)</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="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.BaseCAM">BaseCAM (class in histocartography.interpretability.grad_cam)</a>
</li>
<li><a href="api/histocartography.interpretability.base_explainer.html#histocartography.interpretability.base_explainer.BaseExplainer">BaseExplainer (class in histocartography.interpretability.base_explainer)</a>
</li>
<li><a href="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.BaseGraphBuilder">BaseGraphBuilder (class in histocartography.preprocessing.graph_builders)</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.BaseGraphGradCAMExplainer">BaseGraphGradCAMExplainer (class in histocartography.interpretability.grad_cam)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseGraphVisualization">BaseGraphVisualization (class in histocartography.visualization.visualization)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseImageVisualization">BaseImageVisualization (class in histocartography.visualization.visualization)</a>
</li>
<li><a href="api/histocartography.ml.models.base_model.html#histocartography.ml.models.base_model.BaseModel">BaseModel (class in histocartography.ml.models.base_model)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.BatchPipelineRunner">BatchPipelineRunner (class in histocartography.pipeline)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.BNReLU">BNReLU (class in histocartography.ml.models.hovernet)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.buffer_plot_and_get">buffer_plot_and_get() (in module histocartography.utils.io)</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="api/histocartography.ml.models.cell_graph_model.html#histocartography.ml.models.cell_graph_model.CellGraphModel">CellGraphModel (class in histocartography.ml.models.cell_graph_model)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.check_for_dir">check_for_dir() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.BaseCAM.clear_hooks">clear_hooks() (BaseCAM method)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.ColorMergedSuperpixelExtractor">ColorMergedSuperpixelExtractor (class in histocartography.preprocessing.superpixel)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.ConfusionMatrixMetric">ConfusionMatrixMetric (class in histocartography.metrics.metrics)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Conv2dWithActivation">Conv2dWithActivation (class in histocartography.ml.models.hovernet)</a>
</li>
<li><a href="api/histocartography.utils.graph.html#histocartography.utils.graph.copy_graph">copy_graph() (in module histocartography.utils.graph)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.crop_op">crop_op() (in module histocartography.ml.models.hovernet)</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="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Decoder">Decoder (class in histocartography.ml.models.hovernet)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.DeepFeatureExtractor">DeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.DenseBlock">DenseBlock (class in histocartography.ml.models.hovernet)</a>
</li>
<li><a href="api/histocartography.ml.layers.dense_gin_layer.html#histocartography.ml.layers.dense_gin_layer.DenseGINLayer">DenseGINLayer (class in histocartography.ml.layers.dense_gin_layer)</a>
</li>
<li><a href="api/histocartography.preprocessing.io.html#histocartography.preprocessing.io.DGLGraphLoader">DGLGraphLoader (class in histocartography.preprocessing.io)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Dice">Dice (class in histocartography.metrics.metrics)</a>
</li>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.ExplainerModel.distillation_loss">distillation_loss() (ExplainerModel method)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.download_box_link">download_box_link() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.download_example_data">download_example_data() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.download_test_data">download_test_data() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.draw_circle">draw_circle() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseGraphVisualization.draw_edges">draw_edges() (BaseGraphVisualization method)</a>
<ul>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.OverlayGraphVisualization.draw_edges">(OverlayGraphVisualization method)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.draw_ellipse">draw_ellipse() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseGraphVisualization.draw_instances">draw_instances() (BaseGraphVisualization method)</a>
<ul>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseImageVisualization.draw_instances">(BaseImageVisualization method)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.InstanceImageVisualization.draw_instances">(InstanceImageVisualization method)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.OverlayGraphVisualization.draw_instances">(OverlayGraphVisualization method)</a>
</li>
</ul></li>
<li><a href="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.draw_large_circle">draw_large_circle() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.draw_line">draw_line() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseGraphVisualization.draw_nodes">draw_nodes() (BaseGraphVisualization method)</a>
<ul>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.OverlayGraphVisualization.draw_nodes">(OverlayGraphVisualization method)</a>
</li>
</ul></li>
<li><a href="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.draw_poly">draw_poly() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.utils.html#histocartography.utils.dynamic_import_from">dynamic_import_from() (in module histocartography.utils)</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="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Encoder">Encoder (class in histocartography.ml.models.hovernet)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.ExplainerModel">ExplainerModel (class in histocartography.interpretability.graph_pruning_explainer)</a>
</li>
<li><a href="api/histocartography.utils.image.html#histocartography.utils.image.extract_patches_from_image">extract_patches_from_image() (in module histocartography.utils.image)</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="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.fast_confusion_matrix">fast_confusion_matrix() (in module histocartography.metrics.metrics)</a>
</li>
<li><a href="api/histocartography.preprocessing.utils.html#histocartography.preprocessing.utils.fast_histogram">fast_histogram() (in module histocartography.preprocessing.utils)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.FeatureExtractor">FeatureExtractor (class in histocartography.preprocessing.feature_extraction)</a>
</li>
<li><a href="api/histocartography.preprocessing.io.html#histocartography.preprocessing.io.FileLoader">FileLoader (class in histocartography.preprocessing.io)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.MacenkoStainNormalizer.fit">fit() (MacenkoStainNormalizer method)</a>
<ul>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.StainNormalizer.fit">(StainNormalizer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.VahadaneStainNormalizer.fit">(VahadaneStainNormalizer method)</a>
</li>
</ul></li>
<li><a href="api/histocartography.ml.models.base_model.html#histocartography.ml.models.base_model.BaseModel.forward">forward() (BaseModel method)</a>
<ul>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.BNReLU.forward">(BNReLU method)</a>
</li>
<li><a href="api/histocartography.ml.models.cell_graph_model.html#histocartography.ml.models.cell_graph_model.CellGraphModel.forward">(CellGraphModel method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Conv2dWithActivation.forward">(Conv2dWithActivation method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Decoder.forward">(Decoder method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.DenseBlock.forward">(DenseBlock method)</a>
</li>
<li><a href="api/histocartography.ml.layers.dense_gin_layer.html#histocartography.ml.layers.dense_gin_layer.DenseGINLayer.forward">(DenseGINLayer method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Encoder.forward">(Encoder method)</a>
</li>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.ExplainerModel.forward">(ExplainerModel method)</a>
</li>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer.forward">(GINLayer method)</a>
</li>
<li><a href="api/histocartography.ml.models.hact_model.html#histocartography.ml.models.hact_model.HACTModel.forward">(HACTModel method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.HoverNet.forward">(HoverNet method)</a>
</li>
<li><a href="api/histocartography.ml.layers.mlp.html#histocartography.ml.layers.mlp.MLP.forward">(MLP method)</a>
</li>
<li><a href="api/histocartography.ml.layers.multi_layer_gnn.html#histocartography.ml.layers.multi_layer_gnn.MultiLayerGNN.forward">(MultiLayerGNN method)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNALayer.forward">(PNALayer method)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNATower.forward">(PNATower method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.ResidualBlock.forward">(ResidualBlock method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.SamepaddingLayer.forward">(SamepaddingLayer method)</a>
</li>
<li><a href="api/histocartography.ml.models.tissue_graph_model.html#histocartography.ml.models.tissue_graph_model.TissueGraphModel.forward">(TissueGraphModel method)</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Upsample2x.forward">(Upsample2x method)</a>
</li>
</ul></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="api/histocartography.preprocessing.tissue_mask.html#histocartography.preprocessing.tissue_mask.GaussianTissueMask">GaussianTissueMask (class in histocartography.preprocessing.tissue_mask)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.get_filename">get_filename() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.utils.image.html#histocartography.utils.image.get_last_steps">get_last_steps() (in module histocartography.utils.image)</a>
</li>
<li><a href="api/histocartography.ml.models.base_model.html#histocartography.ml.models.base_model.get_number_of_classes">get_number_of_classes() (in module histocartography.ml.models.base_model)</a>
</li>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#histocartography.preprocessing.tissue_mask.get_tissue_mask">get_tissue_mask() (in module histocartography.preprocessing.tissue_mask)</a>
</li>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer">GINLayer (class in histocartography.ml.layers.gin_layer)</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.GradCAM">GradCAM (class in histocartography.interpretability.grad_cam)</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.GradCAMpp">GradCAMpp (class in histocartography.interpretability.grad_cam)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.BaseGraphVisualization.graph_preprocessing">graph_preprocessing() (BaseGraphVisualization method)</a>
<ul>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.OverlayGraphVisualization.graph_preprocessing">(OverlayGraphVisualization method)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.preprocessing.stats.html#histocartography.preprocessing.stats.GraphDiameter">GraphDiameter (class in histocartography.preprocessing.stats)</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.GraphGradCAMExplainer">GraphGradCAMExplainer (class in histocartography.interpretability.grad_cam)</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#histocartography.interpretability.grad_cam.GraphGradCAMPPExplainer">GraphGradCAMPPExplainer (class in histocartography.interpretability.grad_cam)</a>
</li>
<li><a href="api/histocartography.interpretability.lrp_gnn_explainer.html#histocartography.interpretability.lrp_gnn_explainer.GraphLRPExplainer">GraphLRPExplainer (class in histocartography.interpretability.lrp_gnn_explainer)</a>
</li>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.GraphPruningExplainer">GraphPruningExplainer (class in histocartography.interpretability.graph_pruning_explainer)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.GridAugmentedDeepFeatureExtractor">GridAugmentedDeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.GridDeepFeatureExtractor">GridDeepFeatureExtractor (class in histocartography.preprocessing.feature_extraction)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.GridPatchDataset">GridPatchDataset (class in histocartography.preprocessing.feature_extraction)</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="api/histocartography.utils.io.html#histocartography.utils.io.h5_to_numpy">h5_to_numpy() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.h5_to_tensor">h5_to_tensor() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.preprocessing.io.html#histocartography.preprocessing.io.H5Loader">H5Loader (class in histocartography.preprocessing.io)</a>
</li>
<li><a href="api/histocartography.ml.models.hact_model.html#histocartography.ml.models.hact_model.HACTModel">HACTModel (class in histocartography.ml.models.hact_model)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.HACTVisualization">HACTVisualization (class in histocartography.visualization.visualization)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.HandcraftedFeatureExtractor">HandcraftedFeatureExtractor (class in histocartography.preprocessing.feature_extraction)</a>
</li>
<li>
histocartography
<ul>
<li><a href="api/histocartography.html#module-histocartography">module</a>
</li>
</ul></li>
<li>
histocartography.interpretability
<ul>
<li><a href="api/histocartography.interpretability.html#module-histocartography.interpretability">module</a>
</li>
</ul></li>
<li>
histocartography.interpretability.base_explainer
<ul>
<li><a href="api/histocartography.interpretability.base_explainer.html#module-histocartography.interpretability.base_explainer">module</a>
</li>
</ul></li>
<li>
histocartography.interpretability.grad_cam
<ul>
<li><a href="api/histocartography.interpretability.grad_cam.html#module-histocartography.interpretability.grad_cam">module</a>
</li>
</ul></li>
<li>
histocartography.interpretability.graph_pruning_explainer
<ul>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#module-histocartography.interpretability.graph_pruning_explainer">module</a>
</li>
</ul></li>
<li>
histocartography.interpretability.lrp_gnn_explainer
<ul>
<li><a href="api/histocartography.interpretability.lrp_gnn_explainer.html#module-histocartography.interpretability.lrp_gnn_explainer">module</a>
</li>
</ul></li>
<li>
histocartography.metrics
<ul>
<li><a href="api/histocartography.metrics.html#module-histocartography.metrics">module</a>
</li>
</ul></li>
<li>
histocartography.metrics.metrics
<ul>
<li><a href="api/histocartography.metrics.metrics.html#module-histocartography.metrics.metrics">module</a>
</li>
</ul></li>
<li>
histocartography.ml
<ul>
<li><a href="api/histocartography.ml.html#module-histocartography.ml">module</a>
</li>
</ul></li>
<li>
histocartography.ml.layers
<ul>
<li><a href="api/histocartography.ml.layers.html#module-histocartography.ml.layers">module</a>
</li>
</ul></li>
<li>
histocartography.ml.layers.constants
<ul>
<li><a href="api/histocartography.ml.layers.constants.html#module-histocartography.ml.layers.constants">module</a>
</li>
</ul></li>
<li>
histocartography.ml.layers.dense_gin_layer
<ul>
<li><a href="api/histocartography.ml.layers.dense_gin_layer.html#module-histocartography.ml.layers.dense_gin_layer">module</a>
</li>
</ul></li>
<li>
histocartography.ml.layers.gin_layer
<ul>
<li><a href="api/histocartography.ml.layers.gin_layer.html#module-histocartography.ml.layers.gin_layer">module</a>
</li>
</ul></li>
<li>
histocartography.ml.layers.mlp
<ul>
<li><a href="api/histocartography.ml.layers.mlp.html#module-histocartography.ml.layers.mlp">module</a>
</li>
</ul></li>
<li>
histocartography.ml.layers.multi_layer_gnn
<ul>
<li><a href="api/histocartography.ml.layers.multi_layer_gnn.html#module-histocartography.ml.layers.multi_layer_gnn">module</a>
</li>
</ul></li>
<li>
histocartography.ml.layers.pna_layer
<ul>
<li><a href="api/histocartography.ml.layers.pna_layer.html#module-histocartography.ml.layers.pna_layer">module</a>
</li>
</ul></li>
<li>
histocartography.ml.models
<ul>
<li><a href="api/histocartography.ml.models.html#module-histocartography.ml.models">module</a>
</li>
</ul></li>
<li>
histocartography.ml.models.base_model
<ul>
<li><a href="api/histocartography.ml.models.base_model.html#module-histocartography.ml.models.base_model">module</a>
</li>
</ul></li>
<li>
histocartography.ml.models.cell_graph_model
<ul>
<li><a href="api/histocartography.ml.models.cell_graph_model.html#module-histocartography.ml.models.cell_graph_model">module</a>
</li>
</ul></li>
<li>
histocartography.ml.models.hact_model
<ul>
<li><a href="api/histocartography.ml.models.hact_model.html#module-histocartography.ml.models.hact_model">module</a>
</li>
</ul></li>
<li>
histocartography.ml.models.hovernet
<ul>
<li><a href="api/histocartography.ml.models.hovernet.html#module-histocartography.ml.models.hovernet">module</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li>
histocartography.ml.models.tissue_graph_model
<ul>
<li><a href="api/histocartography.ml.models.tissue_graph_model.html#module-histocartography.ml.models.tissue_graph_model">module</a>
</li>
</ul></li>
<li>
histocartography.ml.models.zoo
<ul>
<li><a href="api/histocartography.ml.models.zoo.html#module-histocartography.ml.models.zoo">module</a>
</li>
</ul></li>
<li>
histocartography.pipeline
<ul>
<li><a href="api/histocartography.pipeline.html#module-histocartography.pipeline">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing
<ul>
<li><a href="api/histocartography.preprocessing.html#module-histocartography.preprocessing">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.assignment_matrix
<ul>
<li><a href="api/histocartography.preprocessing.assignment_matrix.html#module-histocartography.preprocessing.assignment_matrix">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.feature_extraction
<ul>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#module-histocartography.preprocessing.feature_extraction">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.graph_builders
<ul>
<li><a href="api/histocartography.preprocessing.graph_builders.html#module-histocartography.preprocessing.graph_builders">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.io
<ul>
<li><a href="api/histocartography.preprocessing.io.html#module-histocartography.preprocessing.io">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.nuclei_concept_extraction
<ul>
<li><a href="api/histocartography.preprocessing.nuclei_concept_extraction.html#module-histocartography.preprocessing.nuclei_concept_extraction">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.nuclei_extraction
<ul>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#module-histocartography.preprocessing.nuclei_extraction">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.stain_normalizers
<ul>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#module-histocartography.preprocessing.stain_normalizers">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.stats
<ul>
<li><a href="api/histocartography.preprocessing.stats.html#module-histocartography.preprocessing.stats">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.superpixel
<ul>
<li><a href="api/histocartography.preprocessing.superpixel.html#module-histocartography.preprocessing.superpixel">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.tissue_mask
<ul>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#module-histocartography.preprocessing.tissue_mask">module</a>
</li>
</ul></li>
<li>
histocartography.preprocessing.utils
<ul>
<li><a href="api/histocartography.preprocessing.utils.html#module-histocartography.preprocessing.utils">module</a>
</li>
</ul></li>
<li>
histocartography.utils
<ul>
<li><a href="api/histocartography.utils.html#module-histocartography.utils">module</a>
</li>
</ul></li>
<li>
histocartography.utils.draw_utils
<ul>
<li><a href="api/histocartography.utils.draw_utils.html#module-histocartography.utils.draw_utils">module</a>
</li>
</ul></li>
<li>
histocartography.utils.graph
<ul>
<li><a href="api/histocartography.utils.graph.html#module-histocartography.utils.graph">module</a>
</li>
</ul></li>
<li>
histocartography.utils.image
<ul>
<li><a href="api/histocartography.utils.image.html#module-histocartography.utils.image">module</a>
</li>
</ul></li>
<li>
histocartography.utils.io
<ul>
<li><a href="api/histocartography.utils.io.html#module-histocartography.utils.io">module</a>
</li>
</ul></li>
<li>
histocartography.utils.torch
<ul>
<li><a href="api/histocartography.utils.torch.html#module-histocartography.utils.torch">module</a>
</li>
</ul></li>
<li>
histocartography.visualization
<ul>
<li><a href="api/histocartography.visualization.html#module-histocartography.visualization">module</a>
</li>
</ul></li>
<li>
histocartography.visualization.visualization
<ul>
<li><a href="api/histocartography.visualization.visualization.html#module-histocartography.visualization.visualization">module</a>
</li>
</ul></li>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.HoverNet">HoverNet (class in histocartography.ml.models.hovernet)</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="api/histocartography.preprocessing.io.html#histocartography.preprocessing.io.ImageLoader">ImageLoader (class in histocartography.preprocessing.io)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#histocartography.preprocessing.nuclei_extraction.ImageToPatchDataset">ImageToPatchDataset (class in histocartography.preprocessing.nuclei_extraction)</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.InstanceImageVisualization">InstanceImageVisualization (class in histocartography.visualization.visualization)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.InstanceMapPatchDataset">InstanceMapPatchDataset (class in histocartography.preprocessing.feature_extraction)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.IoU">IoU (class in histocartography.metrics.metrics)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Dice.is_better">is_better() (Dice static method)</a>
<ul>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.IoU.is_better">(IoU static method)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Metric.is_better">(Metric static method)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.is_box_url">is_box_url() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Dice.is_per_class">is_per_class (Dice property)</a>
<ul>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.IoU.is_per_class">(IoU property)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.MeanDice.is_per_class">(MeanDice property)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.MeanIoU.is_per_class">(MeanIoU property)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Metric.is_per_class">(Metric property)</a>
</li>
</ul></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="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.KNNGraphBuilder">KNNGraphBuilder (class in histocartography.preprocessing.graph_builders)</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="api/histocartography.pipeline.html#histocartography.pipeline.BatchPipelineRunner.link_output">link_output() (BatchPipelineRunner method)</a>
</li>
<li><a href="api/histocartography.preprocessing.utils.html#histocartography.preprocessing.utils.load_image">load_image() (in module histocartography.preprocessing.utils)</a>
</li>
<li><a href="api/histocartography.utils.io.html#histocartography.utils.io.load_json">load_json() (in module histocartography.utils.io)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Dice.logs_model">logs_model (Dice property)</a>
<ul>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.IoU.logs_model">(IoU property)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Metric.logs_model">(Metric property)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.ExplainerModel.loss">loss() (ExplainerModel method)</a>
</li>
<li><a href="api/histocartography.ml.models.cell_graph_model.html#histocartography.ml.models.cell_graph_model.CellGraphModel.lrp">lrp() (CellGraphModel method)</a>
<ul>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer.lrp">(GINLayer method)</a>
</li>
<li><a href="api/histocartography.ml.layers.mlp.html#histocartography.ml.layers.mlp.MLP.lrp">(MLP method)</a>
</li>
<li><a href="api/histocartography.ml.layers.multi_layer_gnn.html#histocartography.ml.layers.multi_layer_gnn.MultiLayerGNN.lrp">(MultiLayerGNN method)</a>
</li>
<li><a href="api/histocartography.ml.models.tissue_graph_model.html#histocartography.ml.models.tissue_graph_model.TissueGraphModel.lrp">(TissueGraphModel method)</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="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.MacenkoStainNormalizer">MacenkoStainNormalizer (class in histocartography.preprocessing.stain_normalizers)</a>
</li>
<li><a href="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.map_value_to_color">map_value_to_color() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.MeanDice">MeanDice (class in histocartography.metrics.metrics)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.MeanIoU">MeanIoU (class in histocartography.metrics.metrics)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.MergedSuperpixelExtractor">MergedSuperpixelExtractor (class in histocartography.preprocessing.superpixel)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNATower.message_func">message_func() (PNATower method)</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#histocartography.metrics.metrics.Metric">Metric (class in histocartography.metrics.metrics)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.min_nodes">min_nodes() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#histocartography.preprocessing.tissue_mask.AnnotationPostProcessor.mkdir">mkdir() (AnnotationPostProcessor method)</a>
<ul>
<li><a href="api/histocartography.preprocessing.io.html#histocartography.preprocessing.io.FileLoader.mkdir">(FileLoader method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stats.html#histocartography.preprocessing.stats.StatsComputer.mkdir">(StatsComputer method)</a>
</li>
</ul></li>
<li><a href="api/histocartography.ml.layers.mlp.html#histocartography.ml.layers.mlp.MLP">MLP (class in histocartography.ml.layers.mlp)</a>
</li>
<li>
module
<ul>
<li><a href="api/histocartography.html#module-histocartography">histocartography</a>
</li>
<li><a href="api/histocartography.interpretability.html#module-histocartography.interpretability">histocartography.interpretability</a>
</li>
<li><a href="api/histocartography.interpretability.base_explainer.html#module-histocartography.interpretability.base_explainer">histocartography.interpretability.base_explainer</a>
</li>
<li><a href="api/histocartography.interpretability.grad_cam.html#module-histocartography.interpretability.grad_cam">histocartography.interpretability.grad_cam</a>
</li>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#module-histocartography.interpretability.graph_pruning_explainer">histocartography.interpretability.graph_pruning_explainer</a>
</li>
<li><a href="api/histocartography.interpretability.lrp_gnn_explainer.html#module-histocartography.interpretability.lrp_gnn_explainer">histocartography.interpretability.lrp_gnn_explainer</a>
</li>
<li><a href="api/histocartography.metrics.html#module-histocartography.metrics">histocartography.metrics</a>
</li>
<li><a href="api/histocartography.metrics.metrics.html#module-histocartography.metrics.metrics">histocartography.metrics.metrics</a>
</li>
<li><a href="api/histocartography.ml.html#module-histocartography.ml">histocartography.ml</a>
</li>
<li><a href="api/histocartography.ml.layers.html#module-histocartography.ml.layers">histocartography.ml.layers</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#module-histocartography.ml.layers.constants">histocartography.ml.layers.constants</a>
</li>
<li><a href="api/histocartography.ml.layers.dense_gin_layer.html#module-histocartography.ml.layers.dense_gin_layer">histocartography.ml.layers.dense_gin_layer</a>
</li>
<li><a href="api/histocartography.ml.layers.gin_layer.html#module-histocartography.ml.layers.gin_layer">histocartography.ml.layers.gin_layer</a>
</li>
<li><a href="api/histocartography.ml.layers.mlp.html#module-histocartography.ml.layers.mlp">histocartography.ml.layers.mlp</a>
</li>
<li><a href="api/histocartography.ml.layers.multi_layer_gnn.html#module-histocartography.ml.layers.multi_layer_gnn">histocartography.ml.layers.multi_layer_gnn</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#module-histocartography.ml.layers.pna_layer">histocartography.ml.layers.pna_layer</a>
</li>
<li><a href="api/histocartography.ml.models.html#module-histocartography.ml.models">histocartography.ml.models</a>
</li>
<li><a href="api/histocartography.ml.models.base_model.html#module-histocartography.ml.models.base_model">histocartography.ml.models.base_model</a>
</li>
<li><a href="api/histocartography.ml.models.cell_graph_model.html#module-histocartography.ml.models.cell_graph_model">histocartography.ml.models.cell_graph_model</a>
</li>
<li><a href="api/histocartography.ml.models.hact_model.html#module-histocartography.ml.models.hact_model">histocartography.ml.models.hact_model</a>
</li>
<li><a href="api/histocartography.ml.models.hovernet.html#module-histocartography.ml.models.hovernet">histocartography.ml.models.hovernet</a>
</li>
<li><a href="api/histocartography.ml.models.tissue_graph_model.html#module-histocartography.ml.models.tissue_graph_model">histocartography.ml.models.tissue_graph_model</a>
</li>
<li><a href="api/histocartography.ml.models.zoo.html#module-histocartography.ml.models.zoo">histocartography.ml.models.zoo</a>
</li>
<li><a href="api/histocartography.pipeline.html#module-histocartography.pipeline">histocartography.pipeline</a>
</li>
<li><a href="api/histocartography.preprocessing.html#module-histocartography.preprocessing">histocartography.preprocessing</a>
</li>
<li><a href="api/histocartography.preprocessing.assignment_matrix.html#module-histocartography.preprocessing.assignment_matrix">histocartography.preprocessing.assignment_matrix</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#module-histocartography.preprocessing.feature_extraction">histocartography.preprocessing.feature_extraction</a>
</li>
<li><a href="api/histocartography.preprocessing.graph_builders.html#module-histocartography.preprocessing.graph_builders">histocartography.preprocessing.graph_builders</a>
</li>
<li><a href="api/histocartography.preprocessing.io.html#module-histocartography.preprocessing.io">histocartography.preprocessing.io</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_concept_extraction.html#module-histocartography.preprocessing.nuclei_concept_extraction">histocartography.preprocessing.nuclei_concept_extraction</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#module-histocartography.preprocessing.nuclei_extraction">histocartography.preprocessing.nuclei_extraction</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#module-histocartography.preprocessing.stain_normalizers">histocartography.preprocessing.stain_normalizers</a>
</li>
<li><a href="api/histocartography.preprocessing.stats.html#module-histocartography.preprocessing.stats">histocartography.preprocessing.stats</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#module-histocartography.preprocessing.superpixel">histocartography.preprocessing.superpixel</a>
</li>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#module-histocartography.preprocessing.tissue_mask">histocartography.preprocessing.tissue_mask</a>
</li>
<li><a href="api/histocartography.preprocessing.utils.html#module-histocartography.preprocessing.utils">histocartography.preprocessing.utils</a>
</li>
<li><a href="api/histocartography.utils.html#module-histocartography.utils">histocartography.utils</a>
</li>
<li><a href="api/histocartography.utils.draw_utils.html#module-histocartography.utils.draw_utils">histocartography.utils.draw_utils</a>
</li>
<li><a href="api/histocartography.utils.graph.html#module-histocartography.utils.graph">histocartography.utils.graph</a>
</li>
<li><a href="api/histocartography.utils.image.html#module-histocartography.utils.image">histocartography.utils.image</a>
</li>
<li><a href="api/histocartography.utils.io.html#module-histocartography.utils.io">histocartography.utils.io</a>
</li>
<li><a href="api/histocartography.utils.torch.html#module-histocartography.utils.torch">histocartography.utils.torch</a>
</li>
<li><a href="api/histocartography.visualization.html#module-histocartography.visualization">histocartography.visualization</a>
</li>
<li><a href="api/histocartography.visualization.visualization.html#module-histocartography.visualization.visualization">histocartography.visualization.visualization</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer.msg_fn">msg_fn() (GINLayer method)</a>
</li>
<li><a href="api/histocartography.ml.layers.multi_layer_gnn.html#histocartography.ml.layers.multi_layer_gnn.MultiLayerGNN">MultiLayerGNN (class in histocartography.ml.layers.multi_layer_gnn)</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="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.name2rgb">name2rgb() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer.node_update_fn">node_update_fn() (GINLayer method)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.preprocessing.nuclei_concept_extraction.html#histocartography.preprocessing.nuclei_concept_extraction.NucleiConceptExtractor">NucleiConceptExtractor (class in histocartography.preprocessing.nuclei_concept_extraction)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#histocartography.preprocessing.nuclei_extraction.NucleiExtractor">NucleiExtractor (class in histocartography.preprocessing.nuclei_extraction)</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="api/histocartography.visualization.visualization.html#histocartography.visualization.visualization.OverlayGraphVisualization">OverlayGraphVisualization (class in histocartography.visualization.visualization)</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="api/histocartography.utils.image.html#histocartography.utils.image.pad_image">pad_image() (in module histocartography.utils.image)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.PatchFeatureExtractor">PatchFeatureExtractor (class in histocartography.preprocessing.feature_extraction)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineRunner">PipelineRunner (class in histocartography.pipeline)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineStep">PipelineStep (class in histocartography.pipeline)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNALayer">PNALayer (class in histocartography.ml.layers.pna_layer)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNATower">PNATower (class in histocartography.ml.layers.pna_layer)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNATower.posttrans_nodes">posttrans_nodes() (PNATower method)</a>
</li>
<li><a href="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.BaseGraphBuilder.precompute">precompute() (BaseGraphBuilder method)</a>
<ul>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.BatchPipelineRunner.precompute">(BatchPipelineRunner method)</a>
</li>
<li><a href="api/histocartography.preprocessing.feature_extraction.html#histocartography.preprocessing.feature_extraction.FeatureExtractor.precompute">(FeatureExtractor method)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#histocartography.preprocessing.nuclei_extraction.NucleiExtractor.precompute">(NucleiExtractor method)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineRunner.precompute">(PipelineRunner method)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineStep.precompute">(PipelineStep method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.StainNormalizer.precompute">(StainNormalizer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stats.html#histocartography.preprocessing.stats.StatsComputer.precompute">(StatsComputer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.SuperpixelExtractor.precompute">(SuperpixelExtractor method)</a>
</li>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#histocartography.preprocessing.tissue_mask.TissueMask.precompute">(TissueMask method)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNATower.pretrans_edges">pretrans_edges() (PNATower method)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineStep.process">process() (PipelineStep method)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.StainNormalizer.process_and_save">process_and_save() (StainNormalizer method)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#histocartography.preprocessing.nuclei_extraction.process_instance">process_instance() (in module histocartography.preprocessing.nuclei_extraction)</a>
</li>
<li><a href="api/histocartography.preprocessing.nuclei_extraction.html#histocartography.preprocessing.nuclei_extraction.process_np_hv_channels">process_np_hv_channels() (in module histocartography.preprocessing.nuclei_extraction)</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="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.RAGGraphBuilder">RAGGraphBuilder (class in histocartography.preprocessing.graph_builders)</a>
</li>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer.reduce_fn">reduce_fn() (GINLayer method)</a>
</li>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNATower.reduce_func">reduce_func() (PNATower method)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.reduce_max">reduce_max() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.reduce_min">reduce_min() (in module histocartography.ml.layers.constants)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.ResidualBlock">ResidualBlock (class in histocartography.ml.models.hovernet)</a>
</li>
<li><a href="api/histocartography.utils.draw_utils.html#histocartography.utils.draw_utils.rgb">rgb() (in module histocartography.utils.draw_utils)</a>
</li>
<li><a href="api/histocartography.ml.models.hact_model.html#histocartography.ml.models.hact_model.HACTModel.rlp">rlp() (HACTModel method)</a>
</li>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.BatchPipelineRunner.run">run() (BatchPipelineRunner method)</a>
<ul>
<li><a href="api/histocartography.pipeline.html#histocartography.pipeline.PipelineRunner.run">(PipelineRunner method)</a>
</li>
</ul></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="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.SamepaddingLayer">SamepaddingLayer (class in histocartography.ml.models.hovernet)</a>
</li>
<li><a href="api/histocartography.preprocessing.utils.html#histocartography.preprocessing.utils.save_image">save_image() (in module histocartography.preprocessing.utils)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.scale_amplification">scale_amplification() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.scale_attenuation">scale_attenuation() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.ml.layers.constants.html#histocartography.ml.layers.constants.scale_identity">scale_identity() (in module histocartography.ml.layers.constants)</a>
</li>
<li><a href="api/histocartography.ml.models.base_model.html#histocartography.ml.models.base_model.BaseModel.set_forward_hook">set_forward_hook() (BaseModel method)</a>
</li>
<li><a href="api/histocartography.utils.graph.html#histocartography.utils.graph.set_graph_on_cpu">set_graph_on_cpu() (in module histocartography.utils.graph)</a>
</li>
<li><a href="api/histocartography.utils.graph.html#histocartography.utils.graph.set_graph_on_cuda">set_graph_on_cuda() (in module histocartography.utils.graph)</a>
</li>
<li><a href="api/histocartography.ml.models.cell_graph_model.html#histocartography.ml.models.cell_graph_model.CellGraphModel.set_lrp">set_lrp() (CellGraphModel method)</a>
<ul>
<li><a href="api/histocartography.ml.layers.gin_layer.html#histocartography.ml.layers.gin_layer.GINLayer.set_lrp">(GINLayer method)</a>
</li>
<li><a href="api/histocartography.ml.layers.mlp.html#histocartography.ml.layers.mlp.MLP.set_lrp">(MLP method)</a>
</li>
<li><a href="api/histocartography.ml.layers.multi_layer_gnn.html#histocartography.ml.layers.multi_layer_gnn.MultiLayerGNN.set_lrp">(MultiLayerGNN method)</a>
</li>
<li><a href="api/histocartography.ml.models.tissue_graph_model.html#histocartography.ml.models.tissue_graph_model.TissueGraphModel.set_lrp">(TissueGraphModel method)</a>
</li>
</ul></li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.ml.models.hact_model.html#histocartography.ml.models.hact_model.HACTModel.set_rlp">set_rlp() (HACTModel method)</a>
<ul>
<li><a href="api/histocartography.ml.layers.pna_layer.html#histocartography.ml.layers.pna_layer.PNALayer.set_rlp">(PNALayer method)</a>
</li>
</ul></li>
<li><a href="api/histocartography.interpretability.graph_pruning_explainer.html#histocartography.interpretability.graph_pruning_explainer.ExplainerModel.sigmoid">sigmoid() (ExplainerModel static method)</a>
</li>
<li><a href="api/histocartography.utils.html#histocartography.utils.signal_last">signal_last() (in module histocartography.utils)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.SLICSuperpixelExtractor">SLICSuperpixelExtractor (class in histocartography.preprocessing.superpixel)</a>
</li>
<li><a href="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.StainNormalizer">StainNormalizer (class in histocartography.preprocessing.stain_normalizers)</a>
</li>
<li><a href="api/histocartography.preprocessing.stats.html#histocartography.preprocessing.stats.StatsComputer">StatsComputer (class in histocartography.preprocessing.stats)</a>
</li>
<li><a href="api/histocartography.preprocessing.stats.html#histocartography.preprocessing.stats.SuperpixelCounter">SuperpixelCounter (class in histocartography.preprocessing.stats)</a>
</li>
<li><a href="api/histocartography.preprocessing.superpixel.html#histocartography.preprocessing.superpixel.SuperpixelExtractor">SuperpixelExtractor (class in histocartography.preprocessing.superpixel)</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="api/histocartography.ml.models.tissue_graph_model.html#histocartography.ml.models.tissue_graph_model.TissueGraphModel">TissueGraphModel (class in histocartography.ml.models.tissue_graph_model)</a>
</li>
<li><a href="api/histocartography.preprocessing.tissue_mask.html#histocartography.preprocessing.tissue_mask.TissueMask">TissueMask (class in histocartography.preprocessing.tissue_mask)</a>
</li>
<li><a href="api/histocartography.utils.graph.html#histocartography.utils.graph.to_cpu">to_cpu() (in module histocartography.utils.graph)</a>
</li>
</ul></td>
<td style="width: 33%; vertical-align: top;"><ul>
<li><a href="api/histocartography.utils.graph.html#histocartography.utils.graph.to_device">to_device() (in module histocartography.utils.graph)</a>
</li>
<li><a href="api/histocartography.utils.torch.html#histocartography.utils.torch.torch_to_numpy">torch_to_numpy() (in module histocartography.utils.torch)</a>
</li>
<li><a href="api/histocartography.preprocessing.graph_builders.html#histocartography.preprocessing.graph_builders.two_hop_neighborhood">two_hop_neighborhood() (in module histocartography.preprocessing.graph_builders)</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="api/histocartography.ml.models.hovernet.html#histocartography.ml.models.hovernet.Upsample2x">Upsample2x (class in histocartography.ml.models.hovernet)</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="api/histocartography.preprocessing.stain_normalizers.html#histocartography.preprocessing.stain_normalizers.VahadaneStainNormalizer">VahadaneStainNormalizer (class in histocartography.preprocessing.stain_normalizers)</a>
</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="api/histocartography.utils.io.html#histocartography.utils.io.write_json">write_json() (in module histocartography.utils.io)</a>
</li>
</ul></td>
</tr></table>
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