Hello, hope you are doing well. I have another question. We are thinking on running nf-core/mcmicro directly from the MACSima/Prepared results instead of RawData. Since MACSima preprocesses and stiches the data for every ROI on the machine. This results in B and S tif files for every marker like:
C-006_S-000_S_DAPI_R-01_W-B01_ROI-01_A-DAPI.tif
C-006_S-000_B_DAPI_R-01_W-B01_ROI-01_A-DAPI.tif
C-006_S-000_S_Vio-B515_R-01_W-B01_ROI-01_A-S100A4_C-REAL1572.tif
C-006_S-000_B_Vio-B515_R-01_W-B01_ROI-01_A-S100A4_C-REAL1572.tif
For running nf-core/mcmicro the docs specify to use ome.tif and a per cycle samplesheet, or per sample directory. But shouldn't the input be ometifs? What would you recommend to do make these files per cycle?
Also should this be done for every B and S separately, and if so how is the B and S specified in the samplesheet?