Problems with track objects

Hi,

I seem to get consistent problems with TrackObjects when using LAP or Distance methods (Overlap worked with error so far, Measurements worked some of the times, and I can’t reliably reproduce the bug with it). The error pops up when the second image is processed. This might be bad memory management as some of the time the errors are reproducible and sometime less so.

I am attaching .cp file and the relevant images. Running on MacOS 10.6.5 using CellProfiler v. 10415.

-Nir

Sample errors:

Traceback (most recent call last):
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/pipeline.py”, line 309, in run
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/modules/trackobjects.py”, line 513, in run
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/modules/trackobjects.py”, line 607, in run_distance
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/modules/trackobjects.py”, line 1307, in map_objects
ValueError: The first argument of bincount must be non-negative

Traceback (most recent call last):
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/pipeline.py”, line 1348, in post_group
File “/Applications/CellProfiler2.0.app/Contents/Resources/lib/python2.5/cellprofiler/modules/trackobjects.py”, line 852, in post_group
IndexError: list index out of range
TrackObjects.cp (18.4 KB)
SampleImages.tgz (4.54 MB)

Hi Nir,

I’ve been able to replicate this problem with v.10415 but we’ve been making a ton of bugfixes to TrackObjects so when I run the pipeline on our current source code, your pipeline works fine.

So if you’re daring, you can download our latest bleeding-edge build of CellProfiler from here. As the webpage says, this is not a full release, so there are some caveats in using it. It should solve your problems, but let us know if it doesn’t.

Cheers,
-Mark