How to use MCMICRO to process imaging mass cytometry (IMC) data ?

[sanrishiguang]

Hi,
In the article 'MCMICRO: a scalable, modular image-processing pipeline for multiplexed tissue imaging', I noticed that the author also processed publicly availabel imaging mass cytometry (IMC) data. I am wondering how to do it. Can you help me ?

[ArtemSokolov]

Hi @sanrishiguang,

The workflow for processing IMC data doesn't differ that much from workflows for other image modalities. The biggest difference is that IMC images don't require stitching, so you can skip the ASHLAR modules by adding the following to your params.yml:

workflow:
  start-at: segmentation

You may also need to tweak module parameters to get accurate segmentation. See the parameter tuning guide for some tips.

[DenisSch]

Hi @sanrishiguang,

As a quick follow up:
I used the "tif" files as input to MCMICRO, which were created in the MCD viewer. Afterwards, I followed the instructions above starting with segmentation.