Computational Pathology Python Packages

tiatoolbox

Computational Pathology Toolbox developed by TIA Centre, University of Warwick.

torchstain

Stain normalization tools for histological analysis and computational pathology

slideflow

Powerful, open-source AI tools for digital pathology.

staintools

Tools for tissue image stain normalisation and augmentation in Python 3

torch-staintools

GPU-accelerated Stain Normalization and Augmentation in PyTorch

pathml

Tools for computational pathology

wsistream

Modular online patch streaming from whole-slide images for training pathology foundation models. No pre-extraction, no disk overhead – patches are sampled, filtered, and augmented on-the-fly.

wholeslidedata

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

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

aestetik

AESTETIK: Convolutional autoencoder for learning spot representations from spatial transcriptomics and morphology data

compay-syntax

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

tissueloc

Whole Slide Digital Pathology Image Tissue Localization

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.