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Getting Started

  • Overview
    • License
  • Installation

Preprocessing

  • Loading Images
    • Individual Images
    • Datasets of Images
    • Supported slide types
    • Supported file formats
  • Creating Preprocessing Pipelines
    • What is a Transform?
    • What is a Pipeline?
    • Creating custom Transforms
  • Running Preprocessing Pipelines
    • How it works
    • Preprocessing a single WSI
    • Preprocessing a dataset of WSI
    • Distributed processing
  • HDF5 Integration
    • Overview
    • How it Works
    • About HDF5
    • .h5path File Format
    • Reading and Writing

Datasets

  • Datasets
    • DataModules
    • Using public datasets
    • References

Machine Learning

  • DataLoaders
  • Models
    • References

Examples

  • Loading Images: Quickstart
    • Aperio SVS
    • Generic tiled TIFF
    • Hamamatsu NDPI
    • Hamamatsu VMS
    • Leica SCN
    • MIRAX
    • Olympus VSI
    • Trestle TIFF
    • Ventana BIF
    • Zeiss ZVI
    • DICOM
    • Volumetric + time-series OME-TIFF
    • CODEX spatial proteomics
    • MERFISH spatial gene expression
    • Visium 10x spatial gene expression
  • H&E Stain Deconvolution and Color Normalization
    • References
  • Brightfield Imaging: Quickstart
  • Multiparametric Imaging: Quickstart
    • Defining a Multiparametric Pipeline
    • AnnData Integration and Spatial Single Cell Analysis
    • References
  • Multiparametric Imaging: CODEX
    • Reading the slides
    • Define and run the preprocessing pipeline
    • Extract and concatenate the resulting count matrices
    • Annotate the clusters based on the markers intensity
    • Identification of cellular neighborhoods
  • Training an ML Model (HoVer-Net)
    • Data augmentation
    • Load PanNuke dataset
    • Model Training
      • Training with multi-GPU
      • Main training loop
    • Evaluate Model
    • Examples
    • Conclusion
    • References
    • Session info
  • Preprocessing Transforms Gallery
    • Transforms that modify an image
      • Blurring Transforms
      • Superpixel Interpolation
      • Stain Normalization
    • Transforms that create a mask
      • Binary Threshold
      • Nucleus Detection
    • Transforms that modify a mask
      • Morphological Opening
      • Morphological Closing
      • Foreground Detection
      • Tissue Detection

API Reference

  • Core API
    • SlideData
      • Convenience SlideData Classes
        • HESlide
        • VectraSlide
        • MultiparametricSlide
        • CODEXSlide
    • Slide Types
    • Tile
    • SlideDataset
    • Tiles and Masks helper classes
    • Slide Backends
      • OpenslideBackend
      • BioFormatsBackend
      • DICOMBackend
        • OpenSlideBackend
        • BioFormatsBackend
        • DICOMBackend
    • h5pathManager
      • SlideData
        • counts
        • extract_region
        • generate_tiles
        • plot
        • run
        • shape
        • write
      • SlideType
        • asdict
      • Tile
        • plot
        • shape
      • SlideDataset
        • run
        • write
      • Tiles
        • add
        • keys
        • remove
        • tile_shape
        • update
      • Masks
        • add
        • keys
        • remove
        • slice
      • h5pathManager
        • add_mask
        • add_tile
        • get_mask
        • get_slidetype
        • get_tile
        • remove_mask
        • remove_tile
        • slice_masks
        • update_mask
  • Preprocessing API
    • Pipeline
    • Transforms
      • Pipeline
        • apply
        • save
      • MedianBlur
        • F
        • apply
      • GaussianBlur
        • F
        • apply
      • BoxBlur
        • F
        • apply
      • BinaryThreshold
        • F
        • apply
      • MorphOpen
        • F
        • apply
      • MorphClose
        • F
        • apply
      • ForegroundDetection
        • F
        • apply
      • SuperpixelInterpolation
        • F
        • apply
      • StainNormalizationHE
        • F
        • apply
        • fit_to_reference
      • NucleusDetectionHE
        • F
        • apply
      • TissueDetectionHE
        • F
        • apply
      • LabelArtifactTileHE
        • F
        • apply
      • LabelWhiteSpaceHE
        • F
        • apply
      • SegmentMIF
        • F
        • apply
      • QuantifyMIF
        • F
        • apply
      • CollapseRunsVectra
        • F
        • apply
      • CollapseRunsCODEX
        • F
        • apply
      • RescaleIntensity
        • F
        • apply
      • HistogramEqualization
        • F
        • apply
      • AdaptiveHistogramEqualization
        • F
        • apply
  • Datasets API
    • PanNuke
    • DeepFocus
      • PanNukeDataModule
        • test_dataloader
        • train_dataloader
        • valid_dataloader
      • DeepFocusDataModule
        • test_dataloader
        • train_dataloader
        • valid_dataloader
  • ML API
    • h5path Dataset
    • HoVer-Net
      • Helper functions
      • TileDataset
      • HoVerNet
        • forward
        • compute_hv_map
        • loss_hovernet
        • remove_small_objs
        • post_process_batch_hovernet
  • Utilities API
    • Logging Utils
    • Core Utils
    • Datasets Utils
    • ML Utils
    • Miscellaneous Utils
      • PathMLLogger
        • disable
        • enable
      • readtupleh5
      • writedataframeh5
      • writedicth5
      • writestringh5
      • writetupleh5
      • readcounts
      • writecounts
      • pannuke_multiclass_mask_to_nucleus_mask
      • center_crop_im_batch
      • dice_loss
      • dice_score
      • get_sobel_kernels
      • wrap_transform_multichannel
      • upsample_array
      • pil_to_rgb
      • segmentation_lines
      • plot_mask
      • contour_centroid
      • sort_points_clockwise
      • pad_or_crop
      • RGB_to_HSI
      • RGB_to_OD
      • RGB_to_HSV
      • RGB_to_LAB
      • RGB_to_GREY
      • normalize_matrix_rows
      • normalize_matrix_cols
      • plot_segmentation

Contributing

  • Contributing
    • Submitting a bug report
    • Requesting a new feature
    • For developers
      • Coordinate system conventions
      • Setting up a local development environment
      • Running tests
      • Building documentation locally
      • Checking code coverage
      • How to contribute code, documentation, etc.
      • Versioning and Distributing
      • Code Quality
      • Documentation Standards
      • Testing Standards
    • Thank You!
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© Copyright 2023, Dana-Farber Cancer Institute and Weill Cornell Medicine. Revision 88e806cd.

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