Short Description

The track manager enables the use of DSP-like trackProcessors. This can affect the display of tracks, selection in time or by ROIs, and also compute some views like the overlaid and animated local flow graph, polar graph.

Documentation

The track manager is divided in two main area:

  • The left view is a graphical representation of the tracks. Each line correspond to a distinct track and each quad symbolize one single detection. The red vertical bar displays the current time point, and can be dragged to navigate in time. Clicking on a track select/unselect it.
  • The right view is composed as follow:
    1. The display result on sequence combo box let you choose on which sequence the final display of tracks should be overlapped.
    2. The Track pool selector are container of tracks. You can select which group of track you wish to enable for this track manager. (You can use as many trackmanager as needed, and set specific processors for each of them.)
    3. The track processor rack is the core of the track manager: by using the combo box you can choose to add any track processor in the rack. The processor will then be fed by the selected track pool, and will process in real time the tracks. The processors can filter track, alter them, clip, remove, sort, add a specific overlay, compute speed, MSD, export to files… their is no real limitation since processors are also plugins. You can add several processors to a rack, each processor will be processed in the vertical order, from top to bottom, and each output of a track processor will be used as the input of the next. The first processor will always be fed with the initial track set.

 

 

Here are some example of what the track manager can perform thanks to the processors:

On the left hand side: the original sequence of images generated by the Particle tracking benchmark generator. On the right: the image with the default view of tracks. Each white dot is a detection. Track are represented in blue. Clicking on a track (close to a detection) select/unselect it. Once selected, a white thick background is displayed behind the track. The display is a layer, so you can set the transparency of the rendering by using the layer menu.

Those image illustrates some processors effects: The left image contains two regions of interest. The ROIGate processor allow to display and analyse only the one having at least one detection into the ROIs. The second image represents a flow view of the tracks: The flow processor creates an overlay display of arrows summarizing the local direction and speed of tracks.

The track manager also deals with sub-pixelic accuracy of tracks.The display of the tracks and its thickness automatically adapt with the current magnification of the viewer.

Track links:

You can create links between track by dragging the cursor from one detection to another. TrackManager will create virtual tracks if the detection are not consecutive in time.

To remove a track link, just perform the same action as if you were creating one.

Track split:

To split a track, just drag from one detection of a track to the next detection.

Resources needing this

4 reviews on “Track Manager

  1. delaney
    Useful, but is it possible to export the polar instant speed vector values to Excel
  2. Nicolas Chenouard
    Super useful plugin. I like the visualization tools and the possibility to easily add my own processors for analysis and display.
  3. I just noticed that the Speed Profiler is gone, will it be available again? This plugin is great and I am grateful for it and for Icy being freely available!
  4. Hi, is this plugin available as a block module in protocols?

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Changelog

  • Version 1.4.5.0 • Released on: 2019-05-21 10:00:00
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    Description:

    fixed bug / tweaked TrackSegment id handling (Stephane)

  • Version 1.4.4.0 • Released on: 2018-10-15 19:14:10
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    Description:

    minor fix on track painter

  • Version 1.4.3.0 • Released on: 2018-09-25 11:47:57
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    Description:

    - fixed some refresh issue due to the last changes
    - should have now better performance on screenshot rendering

  • Version 1.4.2.0 • Released on: 2018-09-19 18:49:59
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    Description:

    Optimized the default track painter

  • Version 1.4.1.0 • Released on: 2018-07-19 11:09:27
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    Description:

    Added TrackManager.setCurrentPositionT(..) method so we can change externally the current time position.

  • Version 1.4.0.5 • Released on: 2014-09-22 15:40:53
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    Description:

    display track manager is now a persistent option.

  • Version 1.4.0.4 • Released on: 2014-06-10 17:59:49
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    Description:

    update on vtkRendering

  • Version 1.4.0.3 • Released on: 2014-06-05 15:23:47
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    Description:

    Added a null test in removeResult method in TrackPool

  • Version 1.4.0.2 • Released on: 2014-06-05 14:20:12
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    Description:

    - Fix a display bug if a link has no end.
    - Fix the OutOfMemory Error: now disable left panel

  • Version 1.4.0.1 • Released on: 2014-05-19 18:08:11
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    Description:

    Fix to fit new VTK lib.

  • Version 1.4.0.0 • Released on: 2014-04-25 11:55:02
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    Description:

    Fix: some links could not be deleted
    Fix: display of links: speed improvement
    Fix: some links were duplicated
    Fix some editing issue in the track editor

  • Version 1.3.0.22 • Released on: 2014-03-31 16:04:09
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    Description:

    Track panel is now a bit faster to draw.

  • Version 1.3.0.21 • Released on: 2014-03-31 15:52:41
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    Description:

    Added: a new option to disable the tracking panel. This should speed up the rendering a bit if many tracks are displayed.

  • Version 1.3.0.20 • Released on: 2014-03-13 18:37:05
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    Description:

    - The xms file does not need anymore to specify a classname for each detection.

  • Version 1.3.0.19 • Released on: 2014-01-24 17:52:37
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    Description:

    Now imports the XML files generated by TrackMate

  • Version 1.3.0.18 • Released on: 2014-01-20 12:14:29
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    Description:

    Minor upgrade: Selector for track processor is smaller.

  • Version 1.3.0.17 • Released on: 2013-08-19 14:39:59
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    Description:

    Fixed a problem that occurred when splitting a track when several group are displayed.

  • Version 1.3.0.16 • Released on: 2013-07-12 17:56:45
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    Description:

    New: Select by track lenght ( in nb of detection )

  • Version 1.3.0.15 • Released on: 2013-07-11 14:14:43
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    Description:

    Fix: Problem with painter.

  • Version 1.3.0.14 • Released on: 2013-07-03 15:24:00
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    Description:

    - Fix: rendering of sequence with camera

  • Version 1.3.0.13 • Released on: 2013-07-01 17:09:17
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    Description:

    Fixed the "fuse all tracks" feature.

  • Version 1.3.0.12 • Released on: 2013-06-25 13:17:05
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    Description:

    - Now call the painter of the detection (if enabled)

  • Version 1.3.0.11 • Released on: 2013-06-15 12:41:02
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    Description:

    Added trackPool access from the trackManager

  • Version 1.3.0.10 • Released on: 2013-06-15 12:25:47
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    Description:

    - add getTrackSegmentWithDetection in track group

  • Version 1.3.0.9 • Released on: 2013-06-15 11:23:57
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    Description:

    log info removed

  • Version 1.3.0.8 • Released on: 2013-06-15 11:05:54
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    Description:

    some changes for dev:

    fix : getTrackSegmentWithDetection now scan all track groups
    new: clearAllTrackSegment in trackGroup

  • Version 1.3.0.7 • Released on: 2013-01-24 14:15:53
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    Description:

    Fix a problem while building the image containing all the track in the left panel. If the dimension w*h > 2 billion then the bitmap can't be created due to java buffer index limitation. I put the limit to 1 Billion. If reached, the left panel is disabled but tracks are still displayed.

  • Version 1.3.0.6 • Released on: 2012-12-10 18:10:20
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    Description:

    minor fixes

  • Version 1.3.0.5 • Released on: 2012-11-15 16:28:21
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    Description:

    - Fix a bug related to the unload of swimming pool objects.

  • Version 1.3.0.4 • Released on: 2012-11-14 17:12:19
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    Description:

    - can remove links (just re create a link over an existing one will remove it)
    - bug fix if no sequence is displayed
    - track unique id added to xml and tracksegment structure
    - now load and saves links
    - Color track processor is loaded by default

    - known problem : loading 2 times the same track file may cause problems (because of this new unique track id)

  • Version 1.3.0.3 • Released on: 2012-10-18 16:50:57
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    Description:

    - Fixed a bug if one select a track and no sequence displays the tracks.
    - Improve "delete selection" speed

  • Version 1.3.0.2 • Released on: 2012-10-11 11:59:36
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    Description:

    Fix: Track load tests added.

  • Version 1.3.0.1 • Released on: 2012-10-07 11:55:58
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    Description:

    Fixed: clean exit of the trackmanager (remove all processors and overlays)

  • Version 1.3.0.0 • Released on: 2012-10-06 17:55:29
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    Description:

    - Now supports child/parent track edition with split and merge.

    - Fixed a problem when the trackmanager closed and tracks were still visible

  • Version 1.2.0.13 • Released on: 2012-02-15 18:04:54
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    Description:

    new Stable

  • Version 1.2.0.12b • Released on: 2012-02-15 17:58:40
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    Description:

    -Tracks are now shifted by 0.5 pix to be centered on pixels
    -You can specify on which sequence the track are displayed
    -3D rendering improved (a lot)
    -Track should now not be displayed anymore while exiting the trackManager

  • Version 1.2.0.11 • Released on: 2011-12-08 11:32:33
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    Description:

    add: link between tracks

  • Version 1.2.0.10 • Released on: 2011-12-07 17:07:59
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    Description:

    Fix: Now manage if a track does not have any detection.

  • Version 1.2.0.9 • Released on: 2011-12-07 16:06:37
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    Description:

    update to fit with new detection data structure

  • Version 1.2.0.8 • Released on: 2011-11-22 16:11:32
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    Description:

    Fix a display bug (black box) on last detection.

  • Version 1.2.0.7 • Released on: 2011-11-22 16:02:20
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    Description:

    Second fix of the Last detection view problem

  • Version 1.2.0.6 • Released on: 2011-11-22 11:06:12
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    Description:

    Fix the display of the detection: the very last detection of a sequence was not displayed properly

  • Version 1.2.0.5 • Released on: 2011-10-27 09:58:39
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  • Version 1.2.0.4 • Released on: 2011-10-06 16:21:14
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    Description:

    test for general debug

  • Version 1.2.0.3 • Released on: 2011-09-23 17:22:52
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    Description:

    - UI change: more space for track processor.
    - UI Change: simplier zoom buttons
    - Group of track can now be selected by the menu.
    - Help online menu
    - File now support virtual detection, selection state and color.

  • Version 1.2.0.2 • Released on: 2011-09-15 17:27:48
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  • Version 1.2.0.1 • Released on: 2011-09-15 17:09:50
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    Description:

    load / save improvements

  • Version 1.2.0.0 • Released on: 2011-09-15 14:20:22
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    Description:

    fix: background of track view could be black with certain magnifications
    fix: trackview's scrollbars were not refreshed after zoom operations.
    add: Track processors can now collapse
    add: XML load and save support.

  • Version 1.1.0.0 • Released on: 2011-09-02 16:09:34
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    Description:

    A lot of fixes
    GUI revised. Should be faster.
    Select track in one click either in the sequence viewer and in the internal track display

  • Version 1.0.0.4 • Released on: 2011-08-30 15:24:43
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    Description:

    Better presentation of the track processor list.

  • Version 1.0.0.3 • Released on: 2011-08-25 16:36:53
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  • Version 1.0.0.2 • Released on: 2011-08-25 16:32:52
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  • Version 1.0.0.1 • Released on: 2011-03-25 11:39:18
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    Description:

    minor bugfix

  • Version 1.0.0.0b • Released on: 2011-03-24 14:25:11
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    Description:

    Beta version