OverlayOutlines bug: black contours instead of red

I have a small pipeline that I have run in CP 2.1.0 (rev 0c7fb94). There is a strange behaviour in OverlayOutlines that sometimes gives black contours instead of red for some images. I have attached the pipeline, ilastik classifier and two input images, one which gives an ok result and one which gives a strange result.
OverlayOutlineBug.zip (789 KB)

This is an issue which is a consequence of not yet being able to properly normalize images for display in all cases. The release shows this unexpected behavior, but the current trunk build does not, so you could give that a try?

Hi Mark,
Thanks for the reply. I have tried it on rev 89a97e1 and I still get the same behavior.

Hi everyone,

I have the exact same issue. The pipeline has been functional on previous versions (up to 2.0) and the OverlayOutlines module produced the expected outlines in Red/Green etc…
I’ve adapted the pipeline to the new CP 2.1 and it does exactly what it should, with the exception that the OverlayOutlines module only creates black outlines. Be it single or multiple color outlines.
When I select grayscale, it works well. I have tried on the latest build (0c7fb94) as well as on the current bleeding edge (dce57e0) and both display this behavior.

As a workaround I am converting my grayscale images to their respective colors (i.e. DAPI -> blue, FITC-> green etc…) and overlaying the grayscale outlines on the colored images. This allows me to better distinguish the outlines from the image underneath.

Is there a way of manually replacing the OverlayOutlines module with the one from a previous version? And more importantly, would this help at all?

Thanks in advance for any input,

Rui Martins

Unfortuately, no; the modules in the compiled version aren’t “plug-and-play” in this way.

We working on resolving this issue (noted here) as part of the upcoming patch release (due in roughly a month or so). In the meantime, would you mind posting your pipeline and an image that has this problem, so we have another data set to test against?

Please see this thread for more info and a fix: cellprofiler.org/forum/viewt … 879#p11342

Let us know if that helps.

This issue has been resolved with the 2.1.1 release.