Copy/Paste spots in TrackMate TrackScheme

Hi @tinevez,

Do you think it would be usefull to add copy/paste features of spots inside TrackScheme ? If you do, how hard would it be to implement it in your opinion ? (I can eventually have a look).

I am asking that because I am trying to export TrackMate xml files in Python (https://github.com/hadim/spindle_tracker/blob/master/spindle_tracker/io/trackmate.py) with split and merge events and the thing is each Track objects inside the XML contain in fact severals tracks when there is split and merge events.

An algorithm to “duplicates” these Track into multiple tracks and taking into account all the possible combinaisons is making me crazy :smile:

This is why I was thinking about duplicates theses tracks directly in TrackMate.

Let me know what do you think !

Hi @hadim!

I am sorry but I was unable to understand what you want to do (copy/paste features??!) and why. Can you help me a bit?

Sorry if I wasn’t clear. The idea would be to select a set of spots inside TrackScheme and be able to duplicates them in order to duplicate an entire trajectory.

About the XML TrackMate import algorithm, I created a question on stackoverflow : http://stackoverflow.com/questions/34043582/find-all-possible-paths-in-a-graph-with-a-time-constraint

Ok I get it better now.

So for your questions:

  1. No. And it won’t be interesting for you nor anyone. Because:

  2. What you are trying to do is to split a track into branches. I define a branch as the longest segment in a track without any split or merge events. At the core of your problem is the individualization of these branches. Then you want to build your combinations on branches themselves, rather than on spot.

I did something for branches on TrackMate because I had projects for which I needed to extract branch feature (for instance, the duration of a cell cycle between two cell divisions is the duration of a branch). Maybe you would find it interesting?

Check this:

and an application of this here:

It is also used in the Icy export or import, because Icy tracks are built on branches linked between them.

Tell me if it helps.
Best
jy

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Thank you @tinevez. I better understand why the XML is structured this way now.

So the most elegant way to resolve my issue is to find an algorithm to “reconstruct” all the possible tracks from the TrackMate XML.

I finally find a way using graph theory : http://stackoverflow.com/questions/34043582/find-all-possible-paths-in-a-graph-with-a-time-constraint/34045612#34045612

Hope it can help someone in the future.

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