Making maximum intensity projections not working


I have been trying to make maximum intensity projections from .czi files.

I want to split each file into the 3 color channels and then make a maximum intensity projection out of one of the channels.

Here is my pipeline as I have it so far. I do not see where I am going wrong but whenever I test it the projection is only a 1:1 copy of the image not of the entire z-stack.

Please help.


Markcell profiler pipeline.cpproj (236.6 KB)


That’s the expected behavior in test mode, since it’s only seeing one slice at a time; only when you run it over many cycles (as analysis mode will) do you get a maximum projection.

Haha wow sometimes its the most obvious things you dont think about. thankyou.

Another question. When I now run this I want to identify primary and secondary objects. What happens is that the z-stack is created gradually so lets say I have 15 z-slices.

it will analyse slice 1 and identify primary and secondary objects. then it will make stack 1+2 and identify primary and secondary then it makes stack 1+2+3 and so on.

I only need to identify objects once the entire z-stack has been created but do not see how to make this command.

Please let me know if this is possible.



(updated current protocol is attached)cell profiler pipeline.cpproj (142.5 KB)

You have to do the projection in a separate pipeline, CP has no way internally to let you say “run all these to the end, then run all these”. I’ve copied the relevant section from the MakeProjection module help. Sorry for the confusion!

Keep in mind that the projection image is not immediately available in subsequent modules because the output of this module is not complete until all image processing cycles have completed. Therefore, the projection should be created with a dedicated pipeline.