Problem during segmentation


#1

Hello!
First of all thanks for nice software for HCS data analysis.
I am new to forum and have started using Cell profiler recently. I have one problem. I am trying to segment mitochondria and while setting up primary automatic segmentation, if I am setting

  1. Try to mergee small objects with the nearby large object= Yes
    Its giving some kind of error which is shown in C:\ prompt cell profiler.exe
    It stops and does not segments then further? If I do not allow merging it can segment.
    Secondly sometimes I have issues with memory (though my laptop has 2 GB RAM).
    Can you advise me what should I do?
    Thanks and regards
    Anil

#2

Hi Anil,

Thanks for giving CellProfiler a try! I’ll address your questions in order:

[quote=“htscdri”] I am trying to segment mitochondria and while setting up primary automatic segmentation, if I am setting

  1. Try to mergee small objects with the nearby large object= Yes
    Its giving some kind of error which is shown in C:\ prompt cell profiler.exe
    It stops and does not segments then further? If I do not allow merging it can segment.[/quote]

This parameter should be used with caution since you may run into a situation where the module is trying to split objects apart (de-clumping) and then trying to merge them back together. This may be part of the reason you don’t see any further segmentation. The help for IdentifyPrimAutomatic has some further explanation on the use of this parameter, but in general you probably want to set it to ‘no’ and make sure that your other settings work well.

In addition, if you are able to cut-and-paste the error and post it on the forum, that would also be helpful.

.
There are a few things you can do to address the memory issue, 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.

Regards,
-Mark