Problem with 'Distance to Nucleus' in 'Relate' module


#1

Hi,
I am searching for someone that might be able to help me with my problem. When I want to measure ‘distance to nucleus’ in the ‘relate’ module, I always get an unspecific error in that module and the pipeline is crashing.
For a short explanation: The pipeline detects nuclei (primary), then cells (secondary) then objects (primary) and I relate the objects to the cells. I then want to measure distance to nucleus.

Has anyone else got the same problem?
Is it my pipeline or is it a bug?

Best, Daniela


#2

Hi Daniela,

Could you post what error message gets output, so we can diagnose the problem?

Regards,
-Mark


#3

I am receiving the same error, I was not getting it with previous versions of Cell Profiler:

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: Reference to non-existent field ‘Distance’. in the Relate module, which is module #13 in the pipeline.

Stack:
Relate in C:\Program Files\CellProfiler\CellProfiler_mcr\Modules\Relate.m (159)
AnalyzeImagesButton_Callback in C:\Program Files\CellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (10442)
gui_mainfcn in C:\Program Files\CellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (12182)
CellProfiler in C:\Program Files\CellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (57)


#4

Hi appendixboy_94,

What version of CellProfiler are you using, i.e, what do you get when you go to Help > Getting Started?

Regards,
-Mark


#5

Version 1.0.6031


#6

Hmmm, the error you’re getting sounds like a 5811 issue, but’re you’re running the 5811Bugfix version of CP.

It sounds like your preferences may not be set correctly. When you go to File > Set preferences, what do you have for the bottom three boxes?
-Mark


#7

I have
C:\Program Files\CellProfiler
C:\Program Files\CellProfiler
C:\Program Files\CellProfiler\Modules


#8

Do you get this error if you do not calculate Distances? There was a bugfix awhile back (revision 6077) which may be causing your problem in Distance calculations. Have you tried the new version of CP, released this week?

David


#9

I reinstalled the updated Cell Profiler just now and for whatever reason it works. I installed the 7055 version
Thanks for the help!


#10

Hallo, I am running the latest version of CP (branch 7184, which is 1.0.7522.
Since today I get a new error message related to the “Relate module”:

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 #10 in the pipeline.

Stack:
Relate in /Applications/CompiledCellProfiler_branch7184/CellProfiler_mcr/Modules/Relate.m (190)
AnalyzeImagesButton_Callback in /Applications/CompiledCellProfiler_branch7184/CellProfiler_mcr/CellProfiler/CellProfiler.m (10890)
gui_mainfcn in /Applications/CompiledCellProfiler_branch7184/CellProfiler_mcr/CellProfiler/CellProfiler.m (12633)
CellProfiler in /Applications/CompiledCellProfiler_branch7184/CellProfiler_mcr/CellProfiler/CellProfiler.m (57)

It does not complain about the distance anymore through…

Best, Dani


#11

Oh, I forgot to mention that this error is only popping up in the SECOND round (2nd image). Not the first time!


#12

Hi Daniela,

Is your Relate module placed after all measurement modules? If this is the case, as a general rule, the Relate module should always be placed after all modules that make measurements of the children objects. This is because for every measurement that has been made of the children objects upstream in the pipeline, this module calculates the mean value of that measurement over all children and stores it as a measurement for the parent. Since you have a measurement 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.

If the above is not the case, let us know and we’ll go from there.

Regards,
-Mark


#13

Okay, it is working now. Thank you for helping.

Daniela


#14

Great, that’s good to hear!
-Mark