OverlayOutline overlays objects on nothing

Hi. The last step of my pipeline is to overlay the objects I’ve filtered before onto a channel image. The OverlayOutline module works perfectly in the upstream 2 times, but when for the 3rd time here, it overlays the objects on nothing. I really don’t know where I did it wrong since in the output window, I can see the image that it tries to overlay on, which is very strange. Could someone help me out on this? Thanks!

My setting

The output window
image
And the SaveImage module right after this really gives me the image on the right, which is overlay on nothing.

Hi @Fijipuff,

You might have to adjust the image contrast a bit in your right image. The other option is in the Outline display mode option choose “Grayscale” instead of color it might work. But the outlines appear only in white.
Hope this helps!!!

Regards,
Lakshmi
Fujifilm Wako Automation (Consultant)
www.wakoautomation.com
For CellProfiler training or optimised pipeline write to,
lakshmi.balasubramanian.contractor@fujifilm.com

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1 Like

I am currently struggling with a similar issue. I have generated both composite and RGB images using GrayToColor, then attempted to OverlayOutlines of the cells & nuclei on top. When I use coloured outlines, the result window shows me the original RGB or composite image but the overlay appears to be on a very dim version of the image (basically black).

I have also tried to OverlayOutlines in grayscale - the intensity of RGB or composite images appears to be comparable to the original image but the RGB/composite images become grayscale (which is not what I want). Adjusting the image normalisation for that individual image helps but I want to save the outputs of my overlay so I can check the segmentation after analysis. How do I show the overlay on the colour image and save it?
colour outline:


greyscale outline:

CytDNA_CellProfilerAnalysis_v2.cpproj (830.8 KB)

@Emilyjt - Have you tried running your background image through a RescaleIntensity module before trying to build the overlay?