Error when exporting cells to Excel

cellprofiler

#1

Hi,

I’ve been having a problem when processing multiple pictures and exporting the cell information into Excel. Restarting CellProfiler doesn’t work. Oddly, I only have this problem after 2 or 3 processing cycles, and only when I indicate to manually distinguish clumped objects in the IdentifyPrimary module. I do not have the output problem when I process single images, nor when I chose to use another method to distinguish clumped objects.
Here are the error messages:

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: Attempted to access NumberSignIndex(1); index out of bounds because numel(NumberSignIndex)=0. in the ExportToExcel module, which is module #06 in the pipeline.

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 ExportToExcel module, which is module #06 in the pipeline.

I cannot figure out what is wrong, it would be great if I could get some help, thanks!

Lili


#2

Hi Lili,

It is likely that Export is failing when there are zero objects in an image/cycle. Is this the case for you? This bug will be fixed in the next release. See this page for a discussion: ExportData chokes on fields with zero identified objects . You can also try exporting only object data, since the bug is only seen when exporting Image data.

If this is not the case (i.e. all your images have >0 objects), then we will have to look into this further.

Hope this helps,
David


#3

Hi,

Thanks! However, all my images have >0 objects, which are recognized but somehow not properly transported to Excel…

Best,
Lili


#4

Hi Lili,

I also see the error now in IdentifyPrimAutomatic, with Manual as the option chosen for declumping objects. Just to confirm, does your error message say the problem is in CPupdatefigurecycle.m (right under the “Stack:” line)?

David


#5

Hi Lili,

It turns out that the problem is with the handling of the manual identification in IDPrimAuto; CellProfiler is losing track of the figure window in which you do the selection, and errors when it tries to re-use it in a subsequent cycle.

I’ve fixed the bug in the code. However, if you are using the compiled version of CellProfiler, you won’t be able to take advantage of the fix until the next release (which should hopefully be in the next few weeks).

Regards,
-Mark


#6

Hi,

thanks! I am indeed using the compiled version… But I’ve found out that if I chose to only export Cells to Excel and not also Image, it gives the same error message but there is an Excel-file made, and it looks normal. Anyway, great that you found out where the problem was en fixed the bug, I think I can manage now, it’s not perfect but it will do, and I’m ofcourse looking forward for the next release!

Lili


#7

OK great, glad to hear that it’s working well enough for now. Just be careful that the output is really OK when an error appears.

The Image exporting problem is another one that we’re aware of and will be fixed in the next release, in addition to the manual declumping error you found, detailed above.

Best,
David