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Releases: trackmate-sc/TrackMate

New visualization options, Kalman tracker bugfixes and a bit simpler scripting.

19 Dec 16:49
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Customizable colormap.

This release highlight is the new option system in TrackMate, brewed by @imagejan, that allows for specifying what colormap to use in TrackMate. You find it in Edit > Options > TrackMate... menu item.

Screen Shot 2019-12-19 at 17 44 49

There are 21 LUTs to choose from, most of them coming from the MatplotLib project (https://matplotlib.org/3.1.0/tutorials/colors/colormaps.html).

69351317-68623a00-0c7b-11ea-922b-00bf2fd22671

71093761-1fce6b80-21aa-11ea-9db9-f2703994e5fa

After many hesitations, discussions and a poll, we decided to keep 'Jet' the default colormap, despite its flaws. But feel free to change it at your will.

Kalman tracker bugfixes.

Two long standing bugs were fixed in the Kalman tracker:

  • It ignored the spots in frame 2: #113
  • It stopped tracking after a frame without spots: #141

The results tables are interactive.

Selecting a line in any of the table will add the spot / link / track it corresponds to the selection, and highlight it.

Screen Shot 2019-12-18 at 12 01 27

The capture overlay action can be used in scripts.

In a much more simpler way, especially in scripts.
You can now call a static method like this:

final TrackMate trackmate = ...
final ImagePlus capture = CaptureOverlayAction.capture( trackmate, 15, 25 );
capture.show();