TrackObjects memory error

Hi everyone,
I’m trying to run the following pipeline on 200 images and upon reaching the last image with TrackObjects, the computer freezes while the physical memory is being overloaded (until a memory error is being thrown by CellProfiler).
The error I receive is:
Traceback (most recent call last):
File “cellprofiler\pipeline.pyc”, line 1376, in post_group
File “cellprofiler\modules\trackobjects.pyc”, line 1276, in post_group
File “numpy\lib\index_tricks.pyc”, line 236, in getitem
MemoryError

Attached are the pipeline and a screenshot of the memory usage (out of 8GB) while freezing.

Thanks in advance,
Hilla
DefaultOUT__226.mat (961 KB)


Hi Hilla,

It is very likely the second phase of the LAP tracking method that is the culprit. You can test this by unchecking the “Run the second phase…?” box in TrackObjects. However you likely want to use the second phase, so other suggestions to save RAM are listed here (though not all apply for you).

  • The simplest thing to do to save RAM is “Window->Hide All Windows on Run”
  • Break up your run into smaller batches, if possible. But of course you at least need to have each whole movie in a single batch.

Have you gotten it to run in the meantime?
David