Problem with splitting channels


For some reason Cell profiler does not split my images into channels correctly. I separate the images using ImageJ and then merge them/make a composite picture, but when I upload the merged picture to cell profiler it does not split them (red, blue and far red channel). The pictures of the split channels do differ from each other to some extent (so it’s not 3 times the same picture), but they are not split correctly into the 3 different channels. What could be the problem here?

I then tried to upload the different channels separately by using one image for each channel (again; red, blue and far red). Cell profiler treats each channel as a different picture, but I want to use all 3 in the same pipeline. What settings should I use to analyze these 3 images of each channel in 1 pipeline?

Thank you!


If I understand correctly the second part of your message, you can input 3 images for e.g. :


Then in the module NamesAndTypes >> use “Images matching rules” >> select “Files__Does__Contains__”, >> “channel_1” named as “Red”, “channel_2” named as “Green” etc…

Alternatively, you can use module Metadata and capture the number comes after “channel_” as a metadata “channels”, subsequently in NamesAndTypes >> “Images matching rules” >> “Metadata__Does__Have ChannelNumber matching__”

Hope you get the ideas?

It’s not so convenient doing the first way, i.e. first merge images by ImageJ and use CellProfiler to split them back again.