Making Z projections without loading stacks in CellProfiler

Dear experts,

I’m wring a pipeline in CellPrifiler to process a dataset which includes more than one z slice. In my set each image is a single slice 16-bit tiff file.

Normally I would run an ImageJ macro to make Z-projection for each channel for each FOV and then use CellProfiler to segment and measure. However I’d like the CP pipeline to work on the raw data directly.

The problem is that I can’t figure out how to tell CP to make math using all Z-slices from each FOV and then use it for segmentation.

Only alternatives I see is:

  1. Make z-stacks using ImageJ macro and then use “MakePrjection” module. This however is same as just making Z-projection in ImageJ
  2. Make extra pipeline for Z-projection first, save images and then go to my original pipeline. This however generates extra data which I would like to avoid.

If this problem is already solved, I would be very happy to know the trick :slight_smile:


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So I think you might be disappointed by this answer because as far as I understand 2. is what’s on offer in CellProfiler. If you go and look at the MakeProjection part of the manual then they explain it quite well (below).

I do tend to just group the slices and have an initial pipeline that has MakeProjection and SaveImages to save the projected Z-Stacks that then go into the next pipeline.


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Thanks Laura,

Seems that I’ll just have to stick with 2 pipelines then.

We ran into the same problem in our group. Would be nice if this worked in a single pipeline.