Pathology Python Packages

histolab

Library for Digital Pathology Image Processing

slideflow

Powerful, open-source AI tools for digital pathology.

kaiko-eva

Evaluation framework for oncology foundation models (FMs)

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]

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

pathml

Tools for computational pathology

wholeslidedata

No description available

wsinfer

Run patch-based classification on pathology whole slide images.

spatiomic

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

panoptes-he

A multi-resolution CNN package to predict endometrial cancer features

vitaminp

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

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

histocartography

Installable histocartography package.

digipathos

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

answer

No description available

tissueloc

Localize the tissue regions in whole slide pathology images.

bio2bel-adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

trident-test

A package for preprocessing whole-slide images.

pymut

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