Hello, I have been working with some labs that do MACSima experiments on many different markers, and they would split the experiment across separate runs. I made a nextflow script for appending multiple runs into a single RawData folder that can be then used with the staging script (macsima2mc) and the mcmicro pipeline. Feel free to take any of these and adjust if needed: github.com/StonyBrookRCI/MACSIMA_MCMICRO/tree/main A separate issue we had was that some groups used single FOV experiments which causes errors during the illumination correction step. I also want to improve the staging script to dynamically detect ROIs with a single FOV per cycle to turn off illumination correction, or leave it on when multiple FOVs are present.