TrackObjects LAP - parameter optimization

I’m using TrackObjects LAP, including the second phase. My initial guesses for parameter values, based on the defaults, don’t seem to be performing terribly well. For example, I think there are too many cases where a trajectory splits when I’d prefer a new one be started. I will keep playing around with the parameters, but I’d be happier if there was a systematic way to optimize them. This leads me to these questions:

  1. Will the “Sample” module work for LAP 2nd phase?

  2. Another approach is to use some other script to (a) generate a set of CP pipelines that covers the parameter space and (b) run each of these from the command line. On a Mac, do I need the developer version to run CP from the command line? All I have now is the .app, and my setup does not yet have the CP dependencies installed.

Thanks,
Ben

Hi Ben,

To my knowledge, the Sample/Paramorama plugin only works with IdentifyPrimaryObjects – however my knowledge in the Paramorama domain is just about zero! :neutral_face:
I’m sure you could do the same sort of parameter space exploration using the developer’s version and scripting, however before you do that, my first suggestion is to use only the first phase of LAP in your CP pipeline. Then a much more efficient way to explore the LAP parameter space is to use the TrackObjects DataTool (Menu -> DataTool -> TrackObjects), in which you can change the parameters on data already processed with the first phase of LAP.

You could email Hannes (engineering.leeds.ac.uk/peop … s?pub=full) and he would likely be happy to give you more detail. Our own Mark Bray, another author on this project, is not available for awhile unfortunately.

As for running from the command-line on the Mac, you can, though there is a bug we just discovered running headless (having to do with reading at least TIFFs). You would need a slightly updated version of CP beyond the release. Please take a look at the last post here for details: github.com/CellProfiler/CellPro … ssues/1034

Hope this helps!
David