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

deepspotm

Multimodal foundation model predicting transcriptome-wide virtual spatial transcriptomics from histology.

histoseg

Python toolkit for H&E image analysis, spatial contour analysis, and 3D contour reconstruction.

histopia

Histology Spatial Topology for Omics Profiling and Inter-section Alignment

partial-aligner

Partial-Aligner is a napari plugin used for manual registration and histology slide repair

trident-test

Toolkit for large-scale whole-slide image processing.