I have a Pipeline that normally works fine, but has problems with one specific image in the “IdentifyObjectsInGrid” module (see below). The DefineGrid Display looks perfect (see attached file). I even tried to fill the empty spots to see if the problem is due to the empty spots, but that did not work either.

Any Idea what to change in order to let it work?

Error Dialog
There was a problem running the analysis module IdentifyObjectsInGrid which is number 08. Error using ==> IdentifyObjectsInGrid at 168
Image processing was canceled in the IdentifyObjectsInGrid module because the grid you have designed is not working, please check the pipeline.

IdentifyObjectsInGrid in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/Modules/IdentifyObjectsInGrid.m (168)
AnalyzeImagesButton_Callback in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/CellProfiler/CellProfiler.m (9409)
gui_mainfcn in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/CellProfiler/CellProfiler.m (11138)
CellProfiler in /Applications/CellProfiler/CompiledCP/CellProfiler_mcr/CellProfiler/CellProfiler.m (55)

Module #8: IdentifyObjectsInGrid revision - 2
What did you call the grid you defined? GridBlue
What do you want to call the objects identified by this module? NaturalSpots
Would you like the objects to be rectangles that fill the entire grid, circles within the grid at forced locations, circles within the grid at their natural locations, or objects that retain their natural shape (these last two options are based on objects you have already identified in a previous module)? Natural Shape
For NATURAL SHAPE, CIRCLE NATURAL LOCATION, or any CIRCLE option with an automatically calculated diameter (see next question), what did you call the objects that you previously identified? Prespots
For CIRCLE options, enter the diameter of each object in pixels or type Automatic to automatically calculate the diameter based on the average diameter of objects that you previously identified Automatic
What do you want to call the outlines of the identified objects (optional)? NaturalOutlines
If the grid fails, would you like to use a previous grid that worked? Any Previous



I think the problem you’re running into is that what qualifies as a “proper” grid include the condition that the grid lines cannot fall outside the field-of-view. Based on the picture, it seems that the top-most and bottom-most grid lines both do so, and so CellProfiler reports a problem. In your case, it definitely seems that these constraints are too strict and probably need to be relaxed.

But to confirm my guess, would you be able to upload the image you used to create this grid, plus your pipeline?



Hi Mark,
thanks for the fast reply!
You are right, I retried with an input picture which has more space between colonies and border and it works fine now.
Or is there a possibility to change the pipeline in a way that it does not care about the grid border outside the image?

regards, Stefan

P.S. I attached the files.

any96AgarplatePIPE_3.mat (1.59 KB)


Hi Stefan,

If you are using the Developers version of CellProfiler (which requires the full licensed version of MATLAB to run), I can show which lines in the source code need to altered to make it work. Otherwise, I don’t think there is a workaround currently available, other than insuring that you leave some extra space around the perimeter of the colonies when you acquire the images.



We have a MATLAB license in our lab, however, now that I know the problem it is easy to get around it.

Thanks again, Stefan


Do you know if/how I can avoid to get a memory error, if I try to process more than one image in a row (I have to restart after each image)?



Hi Stefan,

There are a few things you can do to address memory issues, most of which are listed in Help (in the menubar at top) > General Help > MemoryAndSpeed. Please let us know which (if any) of these options work for you, or if you have continued problems.



sorry, but in my version there is no “MemoryAndSpeed” under General Help (see attached screen shot).



Ah, I see you’re using an older version! If you go to the CellProfiler website, you’ll see that have a newer version available for download. Your original problem will still remain, but you might find some of the newer features helpful nonetheless.



I installed a newer version of CellProfiler and it seems that I can not load a previous pipeline with this version (error: modules can not be found).
Do I have to remake the pipeline?


No, you should not need to remake the pipeline, and we have made efforts to ensure that, if possible, all settings are migrated for module upgrades. Check that your preferences are set to the new modules’ location with File -> Set Preferences.



you were right, thanks a lot!