Whole Slide Image Python Packages

wsidicom

Python package for reading DICOM WSI file sets.

opentile

Python library for reading tiles from wsi tiff-files.

torchmil

Deep Multiple Instance Learning library for Pytorch

wholeslidedata

A package for working with whole-slide data including a fast batch iterator that can be used to train deep learning models.

cellseg-gsontools

Toolbelt for merging and extracting features from geojson masks.

histoslice

Preprocessing module for large histological images

dogsled

Macenko medical slide normalisation

compay-syntax

:microscope: Syntax - the arrangement of whole-slide-images and their image tiles to create well-formed computational pathology pipelines.

moozy

A patient-first foundation model for computational pathology. Two-stage training (self-supervised slide encoding + supervised case-level alignment) on 77K+ public whole-slide images across 333 clinical tasks.

trident-test

A package for preprocessing whole-slide images.

tmil

Transformer based Multiple Instance Learning