Histopathology Python Packages

torchstain

Stain normalization tools for histological analysis and computational pathology

9K 191 30

tiatoolbox

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

3K 557 113

lazyslide

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

2K 328 32

wholeslidedata

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

2K 119 31

slideflow

Powerful, open-source AI tools for digital pathology.

768 376 66

pathml

Tools for computational pathology

633 465 87

openpatchminer

OpenSlide Patch Manager

601 4 6

moozy

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

481 32 2

wsiprocess

Whole Slide Image (WSI) Processing Library for Histopathological / Cytopathological Machine Learning Tasks

222 25 3

aestetik

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

215 28 4

imzdesk

WSI-MSI Workbench

213 0 0

stainx

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

204 26 0

deeperhistreg

DeeperHistReg - Source Code

171 109 18

raw2features

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

152 4 2

prismtoolbox

Toolbox for histopathology image analysis

145 7 0

spinpath

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

78 7 1

harpipe

Repository for Histopathological Artifact Restoration Pipeline

74 9 0

wsinfer-mil

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

62 7 1