MIRIAM - Multiplexed Image Resegmentation of Internal Aberrant Membranes

Matlab code to run cell segmentation on multiplexed imaging data.

This pipeline requires Iltastik for some tasks. Download Ilastik here: https://www.ilastik.org/download.html

See the tutorial for detailed instructions.

Example data contains all files generated in this code except image stacks (too large) that can be re-generated by the user and can be downloaded here: https://www.dropbox.com/sh/s6jz5puinnliby6/AACARYCshwcZr1Cdq7c6j5MTa?dl=0