Histology Python Packages

histomicstk

A Python toolkit for pathology image analysis algorithms.

histomicsui

A Girder plugin for pathology image annotations and analysis.

axondeepseg

Axon/Myelin segmentation using Deep Learning

deepslice

A python package which aligns histology to the Allen Brain Atlas and Waxholm rat atlas using deep learning.

slideflow

Powerful, open-source AI tools for digital pathology.

myoquant

MyoQuant🔬: a tool to automatically quantify pathological features in muscle fiber histology images. Demo version deployed at: https://huggingface.co/spaces/corentinm7/MyoQuant

histoseg

Python toolkit for H&E image analysis and spatial contour analysis.

partial-aligner

A napari plugin for manual registration of (a part of) an image

trident-test

Toolkit for large-scale whole-slide image processing.

ads-base

Axon/Myelin segmentation using Deep Learning