mushroom

A computational tool for identification of 3D multi-modal spatial neighborhoods.

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 Spatial clonal evolution and clone-specific microenvironment interactions within three-dimensional tumor structures

Model training

Neighborhood analysis