OverlayOutlines can't find images in pipeline



The OverlayOutlines module is failing to find images in the pipeline, dying with the error:

There was a problem running the analysis module OverlayOutlines which is number 08. Error using ==> CPretrieveimage at 57
Image processing was canceled in the OverlayOutlines module because CellProfiler could not find the input image. CellProfiler expected to find an image named “”, but that image has not been created by the pipeline. Please adjust your pipeline to produce the image “” prior to this OverlayOutlines module.

CPretrieveimage in D:\CellProfiler_1.0.5122_XP32\CellProfiler_mcr\CPsubfunctions\CPretrieveimage.m (57)
OverlayOutlines in D:\CellProfiler_1.0.5122_XP32\CellProfiler_mcr\Modules\OverlayOutlines.m (82)
AnalyzeImagesButton_Callback in D:\CellProfiler_1.0.5122_XP32\CellProfiler_mcr\CellProfiler\CellProfiler.m (9409)
gui_mainfcn in D:\CellProfiler_1.0.5122_XP32\CellProfiler_mcr\CellProfiler\CellProfiler.m (11138)
CellProfiler in D:\CellProfiler_1.0.5122_XP32\CellProfiler_mcr\CellProfiler\CellProfiler.m (55)

The module fails whether an image loaded with LoadImages (“OrigGreen”) or created by the pipeline (with ColorToGray – “GrayGreen”) is used as the base image. The filter operation produces a non-null set of objects in the cases I’m debugging with.

The error message is the same in builds 5122 and 4884. The pipeline I’m using is attached as a .mat and .txt file. I’m confused because I swear I’ve used this module successfully with a similar pipeline. Any help you can provide would be much appreciated.

greenpipe.zip.zip (3.94 KB)


Hi Tim,

I tried to replicate this error with the compiled 5122 version and I couldn’t at first (though keep reading!). (Since you didn’t include any images, I substituted some others and named them appropriately, but that’s OK).

But then I noticed in the second setting of OverlayOutlines, there are two choices, “FilteredCellOutlines” and a blank entry. If I set it to the blank entry, I get the same error as you. I’m not certain how that setting got there, but first, I would ensure that FilteredCellOutlines is selected. If you still have an error, I think the safest way would be to reconstruct a new pipeline, using your text output as a template.



Curious – I made doubly sure that FilteredCellOutlines was selected, and never saw a blank option. (I superstitiously pulled down the menu and re-selected FilteredCellOutlines, the only visible option, a couple times just to be sure.)

In any case, when I came in the next morning and built up a new pipeline it was working fine.