Error while cycling through images




I obtained the following error message (below) when running the attached pipeline script. The pipeline is a very short test example.
I tried to attached the images as well but it would not let me do it because of size quota.
The images are 2 test images containing easily identifiable objects using the IdentifyPrimAutomatic module.
The error appears during the second cycle in the Relate module (so you need at least 2 images to get the error since the pipeline uses only one image per cycle). There is no error during the first cycle. And whatever the order in which the images are treated, the error always appears in the 2nd cycle…
I just can’t figure out what generates the error. I hope you’ll be able to help me.

Best regards,

-----------------Error message I got--------------------
There was a problem running the image analysis. Sorry, it is unclear what the problem is. It would be wise to close the entire CellProfiler program in case something strange has happened to the settings. The output file may be unreliable as well. Matlab says the error is: Index exceeds matrix dimensions. in the Relate module, which is module #05 in the pipeline.

Relate in C:\Program Files\Cell Profiler\CellProfiler_mcr\Modules\Relate.m (183)
AnalyzeImagesButton_Callback in C:\Program Files\Cell Profiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (10424)
gui_mainfcn in C:\Program Files\Cell Profiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (12164)
CellProfiler in C:\Program Files\Cell Profiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (57)

TEST_02_PIPE.mat (929 Bytes)

How to save/export outlines coordinates?

The 2 test images to use with the pipeline I uploaded in my previous post can be downloaded from here:

I installed the latest version of CellProfiler (i.e. 1.0.6031 compiled), and I still obtain the same error.

I hope someone can help me to find what I do wrong.




Hi Vincent,

The problem you’re running into is that the Relate module must be placed after any/all Measurement modules, since it takes an average of the prior measurements on a per-parent basis. Since you had the area/shape module after the Relate, it ended up with an extra measurement it hadn’t seen before by the second cycle. You can take a look at the help for Relate for more details.



ok, thank you, it works now.

I have another question on the Relate module that I posted in another thread.