cellmil cellmil cellmil
  • Installation
  • Quick Start
  • Pipeline
    • Patch Extraction Extract patches from whole slide images.
    • Cell Segmentation Segment cells in extracted patches.
    • Graph Creation Create spatial graphs from segmented cells.
    • Feature Extraction Extract morphological and radiomics features.
    • Dataset Creation Create datasets for MIL training.
    • Feature Visualization Visualize and analyze extracted features with statistical descriptors.
  • Explainability
  • API Reference
    • Models Models used in the package.
    • CLI Command-line interface for interacting with the package.
    • Interfaces Interfaces used for configuration.
    • Features Features extracted from at cell level.
    • Data Patch extraction and WSI handling.
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User Guide

  • Installation
  • Quick Start
  • CLI Tools
  • Pipeline
    • Patch Extraction
    • Cell Segmentation
    • Graph Creation
    • Feature Extraction
    • Dataset Creation
    • Feature Visualization
    • MIL Training
      • Overview
      • Model Architectures
      • Data Preparation
      • Training
  • Explainability

API Reference

  • API Reference
    • cellmil.cli
      • cellmil.cli.cell_segmentation
      • cellmil.cli.dataset_creation
      • cellmil.cli.eval_external
      • cellmil.cli.eval_report
      • cellmil.cli.feature_extraction
      • cellmil.cli.graph_creation
      • cellmil.cli.patch_extraction
      • cellmil.cli.stats_print
      • cellmil.cli.visualize_features
    • cellmil.config.python
      • cellmil.config.python.config
    • cellmil.data
      • cellmil.data.cucim_deepzoom
      • cellmil.data.patch_extractor
      • cellmil.data.storage
    • cellmil.datamodels
      • cellmil.datamodels.datasets
        • cellmil.datamodels.datasets.cell_gnn_mil_dataset
        • cellmil.datamodels.datasets.cell_mil_dataset
        • cellmil.datamodels.datasets.celltype_dataset
        • cellmil.datamodels.datasets.gnn_mil_dataset
        • cellmil.datamodels.datasets.mil_dataset
        • cellmil.datamodels.datasets.neoplastic_dataset
        • cellmil.datamodels.datasets.patch_gnn_mil_dataset
        • cellmil.datamodels.datasets.patch_mil_dataset
        • cellmil.datamodels.datasets.utils
      • cellmil.datamodels.model
      • cellmil.datamodels.transforms
        • cellmil.datamodels.transforms.base_label_transform
        • cellmil.datamodels.transforms.base_transform
        • cellmil.datamodels.transforms.correlation_filter
        • cellmil.datamodels.transforms.label_pipeline
        • cellmil.datamodels.transforms.normalization
        • cellmil.datamodels.transforms.pipeline
        • cellmil.datamodels.transforms.time_discretizer
      • cellmil.datamodels.wsi
    • cellmil.dataset
      • cellmil.dataset.dataset_creator
    • cellmil.features
      • cellmil.features.extractor
        • cellmil.features.extractor.embedding
        • cellmil.features.extractor.morphological
        • cellmil.features.extractor.topological
      • cellmil.features.feature_extractor
    • cellmil.interfaces
      • cellmil.interfaces.AttentionExplainerConfig
      • cellmil.interfaces.CellSegmenterConfig
      • cellmil.interfaces.DatasetCreatorConfig
      • cellmil.interfaces.EvaluationExternalValidatorConfig
      • cellmil.interfaces.EvaluationReporterConfig
      • cellmil.interfaces.FeatureExtractorConfig
      • cellmil.interfaces.FeatureVisualizerConfig
      • cellmil.interfaces.GraphCreatorConfig
      • cellmil.interfaces.MIL
      • cellmil.interfaces.MILPredictorConfig
      • cellmil.interfaces.MILTrainerConfig
      • cellmil.interfaces.PatchExtractorConfig
      • cellmil.interfaces.SHAPExplainerConfig
      • cellmil.interfaces.StatsPrinterConfig
      • cellmil.interfaces.TableConfig
    • cellmil.models
      • cellmil.models.mil
        • cellmil.models.mil.attentiondeepmil
        • cellmil.models.mil.cellconv
        • cellmil.models.mil.clam
        • cellmil.models.mil.graphmil
        • cellmil.models.mil.head4type
        • cellmil.models.mil.histobistro
        • cellmil.models.mil.multifocus
        • cellmil.models.mil.standard
        • cellmil.models.mil.transmil
        • cellmil.models.mil.utils
      • cellmil.models.segmentation
        • cellmil.models.segmentation.cellpose
        • cellmil.models.segmentation.cellposeV2
        • cellmil.models.segmentation.cellvit
        • cellmil.models.segmentation.hovernet
    • cellmil.segmentation
      • cellmil.segmentation.cell_segmenter
    • cellmil.graph
      • cellmil.graph.creator
      • cellmil.graph.debug_visualizer
      • cellmil.graph.graph_creator
    • cellmil.utils
      • cellmil.utils.dataset_from_dataset
      • cellmil.utils.stain_normalization
      • cellmil.utils.templates
      • cellmil.utils.tools
      • cellmil.utils.train
        • cellmil.utils.train.callbacks
        • cellmil.utils.train.dataset
        • cellmil.utils.train.evals
        • cellmil.utils.train.losses
        • cellmil.utils.train.metrics
      • cellmil.utils.wandb
    • cellmil.statistics
      • cellmil.statistics.stats_printer
    • cellmil.visualization
      • cellmil.visualization.feature_visualizer

Development

  • Contributing
  • Changelog
  1. cellmil /
  2. API Reference /
  3. cellmil.config.python

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