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.

lazyslide

Accessible and interoperable whole slide image analysis for digital pathology in Python

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

croma

A distributional robustness margin for pathology foundation models

slideflow

Powerful, open-source AI tools for digital pathology.

pathml

Tools for computational pathology

moozy

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

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

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.

aestetik

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

torch-staintools

GPU-accelerated Stain Normalization and Augmentation in PyTorch

deepspotm

Multimodal foundation model predicting transcriptome-wide virtual spatial transcriptomics from histology.

raw2features

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

oncothresh

Clinical threshold evaluation for oncology AI models

tissueloc

Whole Slide Digital Pathology Image Tissue Localization

compay-syntax

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

histopia

Histology Spatial Topology for Omics Profiling and Inter-section Alignment