Old modules that aren't exist anymore


I’m thinking about update my CellProfiler version (CP5811) to the June release (7522).
Some modules seem to have disappeared in this new version: InvertIntensity, SmoothKeepingEdges
and Subtract, some of these are used in my pipelines. I can’t find information about that.

I’ve noticed that there is an “Smooth Keeping Edges” option in SmoothOrEnhance module. Have
the other modules been replaced too ? where can I find them ?

Thanks a lot in advance.


Yes, some modules were removed because their functionality already existed in other modules- like you point out, SmoothKeepingEdges was already part of SmoothOrEnhance, so we didn’t need another module.

The version notes for 7522 (cellprofiler.org/linked_files/version.7522.txt) explain exactly which modules changed, but your old pipeline should load, and transfer the settings. If the settings don’t transfer automatically, a window will pop up showing you what your old settings were so you can transfer them manually.


Thanks for your quick answer.

In the version notes, there is no mention about InvertIntensity module. What about it please ?


InvertIntensity is part of ImageMath. You select ‘Invert’ as the operation you would like to be performed.

Thanks a lot.


I’m currently upgrading to CP7522. Most old pipelines are ok with the new version but I’m meeting an little problem:
each time “Combine” module was used, it is now automatically replaced by “Image Math”. I don’t understand why as “Combine” is still
there in the new release. Moreover, I used it to combined 2 images. “ImageMath” is not convenient for me becasue it seems that
the only possibility it proposes is to combine 3 images. So I must manually change to “Combine” every time I load my pipeline (even when I
saved it with the new version “Combine”) !
This is a little bit annoying. Anything to avoid that please ? Thanks


Hi PJ,

I believe the inclusion of Combine despite it’s replacement by ImageMath was an oversight on our part. If you want to use the Combine operation in ImageMath with two images, you can select “Other…” and enter a zero for the third image, or alternately enter “Do not use” which is effectively the same thing.