When I update the module metadata I have a column C (not SizeC, just C). What is this number? In my case I have the number 0 when the channel is Alexa Fluor 488 and 1 when the channel is DAPI. This number is like a index attributed to each channel? Thanks
Yup, that’s exactly it! CellProfiler is realizing that your images have multiple channels and then giving each one an index so that if you wanted to use that in, for example, NamesAndTypes to define channels, you could.