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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.