Computational Pathology Python Packages

torchstain

Stain normalization tools for histological analysis and computational pathology

tiatoolbox

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

wholeslidedata

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

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

oncothresh

Clinical threshold evaluation for oncology AI models

slideflow

Powerful, open-source AI tools for digital pathology.

raw2features

OME-Zarr whole-slide images to patch- and slide-level foundation-model embeddings - cloud-native, FAIR, model- and backend-agnostic.

aestetik

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

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.

pyslide

Python whole slide image analysis toolkit

compay-syntax

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

moozy

[ECCV 2026] A Patient-First Foundation Model for Computational Pathology

tissueloc

Localize the tissue regions in whole slide pathology images.