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

Previous versions

Location of materials for Tumour evolution and microenvironment interactions in 2D and 3D space

Neighborhood model training

Analysis