Bug in relating many SecondaryObjects to PrimaryObjects

Hello all,

There seems to be a bug when many SecondaryObjects have to be related to PrimaryObjects. I wanted to use the Nuclear Translocation Example Pipeline from the website to detect Smad Translocation into the nucleus. The thing is that I have many many nuclei in each image. The following error is produced:

Traceback (most recent call last): File "cellprofiler\pipeline.pyc", line 309, in run File "cellprofiler\modules\identifysecondaryobjects.pyc", line 640, in run File "cellprofiler\objects.pyc", line 314, in relate_children File "cellprofiler\objects.pyc", line 399, in relate_labels File "numpy\core\fromnumeric.pyc", line 718, in argmax MemoryError

I attached the pipeline and the images. 0001.tif is the Smad channel, 0003.tif is DAPI. Is there a workaround for this bug? I really need to quantify all those…

Thanks a lot!

Till




AE_NucTransloc.cp (12.5 KB)

Hi Till,

The pipeline/set of images runs IdentifySecondary successfully on my machine; however, it’s a 64-bit computer with 4GB of RAM. What are the specs on your computer, and do you have the option of using a 64-bit machine?

Regards,
-Mark