Tracking objects



Dear Team members
I am trying to segment some vesicles from the sequence of images and trying to track them. I am using following pipeline

  1. Load images (frames of movies)
  2. Identify primary automatic (as per setting which detects my vesicles relibly)
  3. Track objects
    But the program terminates after first cycle of vesicle identification (first frame).
    What are prerequisites of the tracking alogorithm. Do we need to complete segmentation for all the frames first and then track of it will do automatically frame after frame tracking of objects?
    I will wait for your help.


Hi Anil,

It seems like your pipeline is set up correctly in terms of module order. TrackObjects is meant to track objects on a frame-by-frame basis, so you shouldn’t need to identify all the objects in all the frames first.

One bit of clarification: Is the pipeline actually terminating after the first cycle, or do you mean that the objects are only being successfully tracked for one cycle but the pipeline still runs for all the frames in the sequence? And is it terminating with an error?



Hi Mark,
Yah it terminates after primary automatic segmentation of vesicles and this is the error it spits out!

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: Subscript indices must either be real positive integers or logicals. in the TrackObjects module, which is module #03 in the pipeline.

TrackCPlabel2rgb in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\Modules\TrackObjects.m (547)
TrackObjects in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\Modules\TrackObjects.m (216)
AnalyzeImagesButton_Callback in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (10442)
gui_mainfcn in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (12182)
CellProfiler in C:\Program Files\CellProfiler\CompiledCellProfilerXP325811Bugfix\CompiledCellProfiler\CellProfiler_mcr\CellProfiler\CellProfiler.m (57)

Thanks in advance!


Hi Anil,

Thanks for the additional information. It seems that the problem lies with the color assigned to each object as it’s being tracked. This color is assigned randomly and a bug in the program causes the value to occasionally fall outside of the acceptable range. If this is in fact the case, I suspect that it may happen some of the time but not all of the time. Is this the case with you?

In any case, there have been some revisions to TrackObjects (which is still in beta testing) but it is useful to you if are using the Developers version of CellProfiler 5811 (which requires the full licensed MATLAB installation); the compiled version cannot accept edits without recompiling the whole package. However, if you are using the Developers version, I can forward you the edits that would need to be made. Let me know.



Thanks Mark for information,
I tried with several of my movies but it fails.
For the timebeing I do not have access to MATLAB licennce for the timebeing.
I will wait for the fully complied version as soon as possible
Best regards


Hi Anil,

As far as the compiled version goes, I can provide you with the latest compilation of the developers version (which includes the newest TrackObjects). Do you have an FTP client that you can use?