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Histopathology Python Packages

Python packages with the GitHub topic histopathology. Sorted by relevance, with stars and monthly downloads.
TissueImageAnalytics
tiatoolbox

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

35K 527 107
EIDOSlab
torchstain

Stain normalization tools for histological analysis and computational pathology

33K 179 30
slideflow
slideflow

Powerful, open-source AI tools for digital pathology.

2K 361 64
CBICA
openpatchminer

A patch miner for large histopathology images

1K 4 6
Dana-Farber-AIOS
pathml

Tools for computational pathology

748 452 89
DIAGNijmegen
wholeslidedata

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

567 114 31
tand826
wsiprocess

Whole Slide Image (WSI) Processing Library

410 25 3
ratschlab
aestetik

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

208 23 5
gustaveroussy
prismtoolbox

Toolbox for histopathology image analysis

201 7 0
rendeirolab
stainx

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

178 6 0
MWod
deeperhistreg

DeeperHistReg - Source Code

152 97 18
MECLabTUDA
harpipe

Repository for Histopathological Artifact Restoration Pipeline

132 9 0
AtlasAnalyticsLab
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.

116 15 0
SBU-BMI
wsinfer-mil

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

83 7 1
SBU-BMI
spinpath

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

80 7 1
abbvie-external
torchunmix

Automatic stain unmixing and augmentation for histopathology images in PyTorch

14 0 1
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