Welcome to Digital Pathology Lab Tools’s documentation!

Contents:

• Package overview
  • Main features
  • Installation
  • Code repository
  • Requirements
  • Conventions
  • Acknowledgements
  • License and copyright
• GenericSlide
  • Basic usage
  • Changing WSI reading library
  • Automated resampling
  • Advanced features
    • Example: missing MPP data
  • Class details
    • GenericSlide
• Masks
  • Polygon based mask
    • WSIPolygonMask
    • Basic usage
    • Class details
  • Tissue based mask
    • WSITissueMask
    • Basic usage
    • Class details
    • Parameter details
  • Parameters common in all mask classes
  • Methods and properties common to all mask classes
    • BaseMask
  • Mask overlay examples
• Patch locations/sampling
  • Random patches on whole images
    • WholeImageRandomPatches
    • Basic usage
    • Class details
  • Poisson disk patches on whole images
    • WholeImagePoissonDiskPatches
    • Basic usage
    • Class details
  • Grid based patches on whole images
    • WholeImageGridPatches
    • Basic usage
    • Class details
  • Inverted random patches on whole images
    • WholeImageInvertedRandomPatches
    • Basic usage
    • Class details
  • Inverted Poisson disk patches on whole images
    • WholeImageInvertedPoissonDiskPatches
    • Basic usage
    • Class details
  • Inverted grid based patches on whole images
    • WholeImageInvertedGridPatches
    • Basic usage
    • Class details
  • Random patches on polygon regions
    • PolygonRegionRandomPatches
    • Basic usage
    • Class details
  • Poisson disk patches on polygon regions
    • PolygonRegionPoissonDiskPatches
    • Basic usage
    • Class details
  • Grid based patches on polygon regions
    • PolygonRegionGridPatches
    • Basic usage
    • Class details
  • Custom patches
    • WholeImageCustomPatches
    • WholeImageInvertedCustomPatches
    • PolygonRegionCustomPatches
    • Example
    • Class details
  • Parameters common in all patch classes
  • Methods and properties common to all patch classes
    • BasePatches
  • “check_polygons” explained
  • Parameters details
  • Expandable parameters
  • Preview image
• Patch Extraction
  • In memory patch extraction
    • Basic usage
    • Class details
  • In memory patch extraction (MRP)
    • Basic usage
    • Class details
  • To disk patch extraction
    • Basic usage
    • Class details
  • To disk patch extraction (MRP)
    • Basic usage
    • Class details
  • Parameters common to disk patch extraction classes
  • Parameters common to all patch extraction classes
• Datasets
  • WSI dataset class
    • WSIDataset
    • Basic usage
    • Class details
  • WSI dataset class (MRP)
    • WSIMultiResDataset
    • Basic usage
    • Class details
  • Parameters common in all WSI dataset classes
  • Methods and properties common to all WSI dataset classes
    • BaseDataset
• Inference
  • Basic usage
  • Full example of inference process
  • Model initialization checklist
    • Classifier initialization
  • Class details
    • WSIInference
  • Additional configuration
• Heatmaps
  • Basic usage
  • Class details
    • WSIHeatmap
  • Examples
  • Custom drawing
• Annotations
  • Sedeen annotations
    • SedeenReader
    • Basic usage
    • Class details
  • ASAP annotations
    • AsapReader
    • Basic usage
    • Class details
  • Parameters, methods and properties of the base reader class
    • BaseReader
  • QuPath annotations
    • Basic usage
    • Class details
  • Integration with patch locations classes
• Pool classes
• Patch locations/sampling pool classes
  • Pool classes for patches on whole images
    • WholeImageRandomPatchesPool
    • WholeImagePoissonDiskPatchesPool
    • WholeImageGridPatchesPool
    • Basic usage
    • Class details
  • Pool classes for inverted patches on whole images
    • WholeImageInvertedRandomPatchesPool
    • WholeImageInvertedPoissonDiskPatchesPool
    • WholeImageInvertedGridPatchesPool
    • Basic usage
    • Class details
  • Pool classes for patches on polygon regions
    • PolygonRegionRandomPatchesPool
    • PolygonRegionPoissonDiskPatchesPool
    • PolygonRegionGridPatchesPool
    • Basic usage
    • Class details
  • patches_args
  • Preview images
  • Expandable parameters
  • Parameters common in all patches pool classes
  • Methods and properties common to all patches pool classes
    • BasePatchesPool
• Patch extraction pool classes
  • In memory patch extraction pool
    • Basic usage
    • Class details
  • In memory patch extraction pool (MRP)
    • Basic usage
    • Class details
  • To disk patch extraction pool
    • Basic usage
    • Class details
  • To disk patch extraction pool (MRP)
    • Basic usage
    • Class details
  • Parameters common to disk patch extraction pool classes
  • Parameters common to all patch extraction pool classes
• Miscellaneous
  • Multi resolution patches (MRP)
  • level_or_mpp
  • level_or_minsize
  • AnnotationPolygon class

Indices and tables

• Index

• Module Index

• Search Page