MIBIutils

This repository includes utility functions for working with MIBI data.

Installations

• make sure you have Python (version 3.6 or above) installed. https://www.python.org/downloads/

• Open the terminal from the location you want the project to be downloaded to (e.g. PycharmProjects directory)

• run this line: git clone https://github.com/KerenLab/MIBIutils.git

Add MIBItiff files to the input directory

• put the MIBItiff files in 'data/MIBI' (in the project directory).

Run the script

• open terminal from the project directory, and run this line: bash run.sh

• the script extracts all single-channel images from each MIBItiff file.