How do I load images with a large number of channels?


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-

  1. Do it by pointing/clicking/typing in NamesAndTypes as usual - this is tedious particularly on Windows (due to refresh bugs), but it will work.
  2. Open the pipeline file in a text editor and edit it directly by following the pattern.
  3. Create a CSV and use LoadData.

(ideas stolen from @bcimini)