Some parameters in TrackObjects.py

Hi,

I have been working on a program which uses the csv output file produced after the module TrackObjects runs. The program visualizes cell locations and tracks. I am trying to optimize the parameters for TrackObjects when LAP option is chosen after manually correct the tracks in my program. I have looked at the code TrackObjects.py to see how the parameters are calculated, however I did not figure out how the parameters “gap initiation” & “gap termination” parameters are found.

regards,

Tugrul Bayrak

Hi Tugrul,

Thanks for taking a look at the code. It is mostly taken from the Jaqaman, et al. article cited: ncbi.nlm.nih.gov/pmc/articles/PMC2747604/
I’m not sure if this is what you wanted (and by now you probably found this on your own!), but in trackobjects.py these lines refer to the Gap Initiation (Cost) and Gap Termination (Cost), around line 1180:

gap_initiation_cost = (gap_cost + gap_closing_cost) / 2 gap_termination_cost = (gap_cost + gap_closing_cost) / 2
where gap_closing_cost is defined above that as

and the rest are settable parameters.

Cheers,
David