Histopathology 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.

pathml

Tools for computational pathology

slideflow

Powerful, open-source AI tools for digital pathology.

openpatchminer

OpenSlide Patch Manager

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

wsiprocess

Whole Slide Image (WSI) Processing Library

stainx

Enhanced stain normalization for histopathology images with batch processing support. Optimized for CPU, GPU (CUDA), and MPS (Apple Silicon) devices.

prismtoolbox

Toolbox for histopathology image analysis

deeperhistreg

DeeperHistReg - Source Code

moozy

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

harpipe

Histological Artifact Restoration Pipeline

wsinfer-mil

CLI tool to run specimen-level inference on whole slide images

spinpath

Run specimen-level inference on whole slide images.

torchunmix

Automatic stain unmixing and augmentation for histopathology images in PyTorch