This question comes up from time to time. There are neat techniques like imaging mass spec and sequential bleaching/staining/imaging that can yield images with 30+ channels.
CellProfiler is happy to process these! It just needs to know the channel names of all of the images it’s going to process. That leaves you with essentially 3 options-
- Do it by pointing/clicking/typing in NamesAndTypes as usual - this is tedious particularly on Windows (due to refresh bugs), but it will work.
- Open the pipeline file in a text editor and edit it directly by following the pattern.
- Create a CSV and use LoadData.
(ideas stolen from @bcimini)