mushroom

A workflow for 3D serial section registration and analysis

Under active development

Library installation

Although not always neccessary, we recommend installing into a fresh environment when possible to avoid installation issues.

conda create -n mushroom -c conda-forge -y python=3.11 jupyter
conda activate mushroom
pip install git+https://github.com/ding-lab/mushroom.git

Tutorial

API subject to change...

Registering multi-modal serial section data

Running Mushroom

Output analysis

Manuscript materials

Location of materials for 3D Imaging and Multimodal Spatial Characterization of the Precancer-to-Cancer Transition in Breast and Prostate

H&E protein prediction model training

Serial section registration workflow

3D ROI data generation and quantification

Automated 2D epithelial region detection and quantification

DEG plotting and analyses

Automated region connectivity for HT704B1