Spatial Transcriptomics Multi-modal Clustering (stMMC)

This is the repo of the code for the paper, "Multi-modal Spatial Clustering for Spatial Transcriptomics Utilizing High-resolution Histology Images"

Envrioment Setting

An enviroment yaml file is provide and the needed enviroment can be created using the following command, which requires conda.

conda env create -f environment.yml

R and mclust package are also needed to run stMMC. Instructions to install R can be found here and to install mclust package run the following command in R.

install.packages('mclust')

Demo on DLPFC Slice 151507

This repo also includes the demo data from DLPFC dataset. To run stMMC on this demo data with all the default settings, you can run the following command to get the clustering results.

conda activate stMMC
python src/main.py