Histopathology 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.

openpatchminer

A patch miner for large histopathology images

pathml

Tools for computational pathology

wholeslidedata

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

wsiprocess

Whole Slide Image (WSI) Processing Library

aestetik

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

prismtoolbox

Toolbox for histopathology image analysis

stainx

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

deeperhistreg

DeeperHistReg - Source Code

harpipe

Repository for Histopathological Artifact Restoration Pipeline

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.

wsinfer-mil

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

spinpath

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

torchunmix

Automatic stain unmixing and augmentation for histopathology images in PyTorch