Pathology Python Packages

lazyslide

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

2K 328 32

histolab

Library for Digital Pathology Image Processing

2K 467 67

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

kfbslide

纯 Python KFB（KFBio）数字病理切片读取库，提供与 OpenSlide 完全兼容的 API

1K 16 2

kaiko-eva

Evaluation framework for oncology foundation models (FMs)

1K 172 40

pathopatch

PathoPatcher is a Python project designed for accelerating Whole Slide Image Preprocessing, employing AI-based preprocessing techniques with features like annotation handling, color normalization, and configurable parameters

933 13 9

slideflow

Powerful, open-source AI tools for digital pathology.

768 376 66

pathml

Tools for computational pathology

633 465 87

deepliif

Deep Learning Inferred Multiplex ImmunoFluorescence for IHC Image Quantification (https://deepliif.org) [Nature Machine Intelligence'22, CVPR'22, MICCAI'23, Histopathology'23, MICCAI'24, MICCAI'26]

594 263 90

eozin

A Rust library to read digital pathology images

558 5 1

spatiomic

A Python package for unsupervised analysis of spatial (prote)omics data.

353 19 0

panoptes-he

A multi-resolution CNN package to predict endometrial cancer features

335 2 0

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

296 55 10

wsinfer

🔥 🚀 Blazingly fast pipeline for patch-based classification in whole slide images

290 87 14

histocartography

A standardized Python API with necessary preprocessing, machine learning and explainability tools to facilitate graph-analytics in computational pathology.

235 275 66

digipathos

Brazilian Agricultural Research Corporation (EMBRAPA) fully annotated dataset for plant diseases. Plug and play installation over PiP.

190 47 9

vitaminp

VitaminP: a vision transformer-assisted multimodal integration network for pathology cell segmentation

135 13 2

tissueloc

Whole Slide Digital Pathology Image Tissue Localization

91 45 12

answer

Brazilian Agricultural Research Corporation (EMBRAPA) fully annotated dataset for plant diseases. Plug and play installation over PiP.

91 47 9

bio2bel-adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

69 1 0

trident-test

Toolkit for large-scale whole-slide image processing.

48 644 146

pymut

Machine learning methods for the prediction of pathology in protein mutations, as in the PMut predictor.

37 6 4