Pathology Python Packages

histolab

Library for Digital Pathology Image Processing

13K 457 66

slideflow

Powerful, open-source AI tools for digital pathology.

2K 361 64

eozin

A Rust library to read digital pathology images

2K 5 1

deepliif

DeepLIIF: Deep-Learning Inferred Multiplex Immunofluorescence for Immunohistochemical Image Quantification

1K 250 90

kaiko-eva

Evaluation framework for oncology foundation models (FMs)

1K 156 38

pathopatch

PathoPatch - Accelerating Artificial Intelligence Based Whole Slide Image Analysis with an Optimized Preprocessing Pipeline

996 11 8

pathml

Tools for computational pathology

748 452 89

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

wsinfer

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

544 85 14

vitaminp

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

523 8 1

spatiomic

A python toolbox for spatial omics analysis.

412 17 0

pyslide

Digital Pathology Whole Slide Image Analysis Toolbox

335 53 8

panoptes-he

A multi-resolution CNN to predict cancer histopathologic features

313 2 0

histocartography

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

308 269 65

digipathos

No description available

293 44 9

answer

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

245 44 9

bio2bel-adeptus

Convert differential gene expression signatures for diseases from ADEPTUS to BEL

142 1 0

tissueloc

Whole Slide Digital Pathology Image Tissue Localization

121 45 12

trident-test

A package for preprocessing whole-slide images.

67 553 118

pymut

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

47 6 4