I’m trying to find a way to interactively detect spots using the beautiful user interface in TrackMate, but then take a given
SpotCollection and do some downstream processing using scripting, such as running a segmentation, plotting intensity distributions etc.
Ideally, I want to avoid having to display or save the list of spots, but just:
- browse through the hyperstack displayer that’s showing my spots and tracks as overlay
- go forth and back changing parameters until I’m satisfied
- run a script that takes the current
TrackMateinstance, or some other way to get at the given
I was looking at
TrackMateRunner_, the class that starts TrackMate from the UI, but it doesn’t have any method that would return the
TrackMate object it starts. All the scripts on the Scripting TrackMate wiki page actually work the opposite way: they create a
TrackMate programmatically and set all the parameters in the script, thereby taking away the interactivity (because they’re intended for automation).
The best way I see to accomplish this is replicating these lines from
… and then keeping that instance of
TrackMate for later processing (likely using a
WaitForUserDialog or some such).
Is there a better way, @tinevez? If not, would it make sense to add some code to retrieve a currently running (i.e. displayed) TrackMate instance?
Does anybody have similar use cases?