Short Description

Track manager plug-in measuring motion statistics in 2D/3D, including min/max/avg/total displacement (absolute & relative to origin), and displacement profiles along all spatial axes.

Documentation

"Motion Profiler" is a plug-in for the Track Manager that computes motion statistics and informative graphs describing the displacement of objects in the field. This plug-in also lets you filter selected tracks based on these statistics.

Computing & plotting statistics

Statistics and graphs are displayed either in pixel/frame units or in real units (in the latter case, make sure that the sequence on which the tracks are displayed has correct pixel size and time interval values).

They are presented in 3 (or 4) separate tabs containing one global summary plus specific statistics for each spatial direction X, Y (and Z if applicable). Such direction-specific information is particularly useful for directed migration experiments (e.g. chemotaxis), where one spatial direction is usually privileged over the others.

The following statistics are computed:

  • Duration: the length of a track, i.e. its number of detections minus one (NB: tracks with only onw time point will not appear as they have no duration; a track with two consecutive time points will have a duration of 1, etc.)
  • Total displacement: the sum of all consecutive displacements in each track, which corresponds to the total distance travelled by the object
  • Relative displacement: the distance between the starting and ending position of each track. It basically indicates if the object has returned to its initial position at the end of its path.
  • Min/Max/Avg displacement: the minimum/maximum/average displacement between any two consecutive time points throughout each track. NB: an option lets you display speed here instead of displacement.

These statistics can be exported as a .xls file for further processing in your favorite spreadsheet software.

In addition to quantitative statistics, this plug-in also plots a graph per sheet describing the displacement profiles over time. In the global case, the graph plots all tracks centered on the origin, which allows to visualise their degree (and direction) of spread. In each "directional" sheet, the tracks are not centered to the origin, and display the evolution of each spatial coordinate for each track over time. Note that the raw data for each graph is also available (click on the "table" icon on top of each graph to view and export them).

Filtering tracks

One of the great powers of the Track Manager is the ability to stack processors one after the other, in order to modify and/or filter tracks to build a powerful pipeline. "Motion Profiler" lets you do this as well: an option called "Filter tracks..." will basically replace the default statistics view by a filter view, where you can select on which criterion to filter, the operation and the threshold value (e.g. "Keep tracks where the duration is greater than 5 frames").

And because these processors can be stacked to infinity (or almost), you can add as many "Motion Profiler" instances to filter the right tracks and compute just the statistics you need. It's that simple.

Acknowledgments

The library used to create the graphs in 2D and 3D is called "jmathplot", it is written by Yann Richet and is released under a BSD license (available here).

Resources needing this

4 reviews on “Motion Profiler

  1. Fantastic update. Can retrieve datas from the tracks crossing a ROI !!!! Units are displayed !!!!
  2. IcyLyd
    update (2014-Jun22th): Now you deserve the 5 stars: We can add many layers of filtering and export the results. The filtering is just ... perfect ! :) Great update (2014-Jun20th): the available switch between displacement and speed is really usefull. Excel file export is clear and the scale is taken into account. I would love an update with filtering or sorting of the tracks inside the processor ! :)
  3. I use it often and it is very helpful to analyze our data. Thank you!

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Changelog

  • Version 4.1.2.1 • Released on: 2019-02-21 14:03:54
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    Description:

    minor tweak to cache file cleanup

  • Version 4.1.2.0 • Released on: 2019-02-21 13:58:23
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    Description:

    Clean temporary files

  • Version 4.1.1.0 • Released on: 2018-07-27 10:16:31
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    Description:

    fixed empty XLS export regression.

  • Version 4.1.0.0 • Released on: 2018-07-19 10:02:16
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    Description:

    - major performance improvement
    - statistics can now be done on partially filtered tracks (using time clipper for instance).
    - filtering is now taking care of partially filtered tracks as well.

  • Version 4.0.0.0 • Released on: 2018-04-13 11:56:27
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    Description:

    Major rewrite (separated in several files) :
    - separated filtering / statistics track processors
    - fixed some issues with filtering using real unit
    - fixed some GUI issues
    - others minors fixes and tweaks
    - now compatible with protocols (filter tracks and motion profiler) !

  • Version 3.2.0.1 • Released on: 2017-08-11 18:02:29
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    Description:

    Revert to Java 1.6

  • Version 3.2.0.0 • Released on: 2017-06-29 10:56:57
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    Description:

    * Code cleaning (requires Java 1.8)
    * New criteria:
    - start time
    - end time
    - current time (filter only)

  • Version 3.1.4.0 • Released on: 2016-10-19 12:13:38
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    Description:

    Track index is now zero-based (matches the track manager panel)

  • Version 3.1.3.0 • Released on: 2016-03-17 20:22:06
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    Description:

    Moved internal plotting code to standalone libraries (see the JMathIO and JMathPlot plugins)

  • Version 3.1.2.0 • Released on: 2016-02-04 20:00:44
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    Description:

    Minor adjustment on the plot panel to have an equal X to Y scale ratio (warning: not optimal)

  • Version 3.1.1.0 • Released on: 2015-12-11 11:34:56
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    Description:

    Fixed an issue with negative coordinates

  • Version 3.1.0.0 • Released on: 2015-05-21 18:47:03
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    Description:

    * New criterion: extent (maximum distance between any 2 detections of a track)
    * Renamed "tortuosity" to "linearity"
    * New: ability to filter tracks by linearity and extent

  • Version 3.0.5.0 • Released on: 2014-11-27 11:09:45
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    Description:

    The 3D motion graph had disappeared from the previous update...

  • Version 3.0.4.0 • Released on: 2014-11-18 16:55:17
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    Description:

    The export folder is now automatically saved in the plugin preferences

  • Version 3.0.3.0 • Released on: 2014-08-21 17:02:11
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    Description:

    * Renamed "Relative" to "net" displacement
    * New "tortuosity" measure (ratio of net to total displacement"

  • Version 3.0.2.0 • Released on: 2014-07-21 18:43:42
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    Description:

    Improved track filtering performance

  • Version 3.0.1.0 • Released on: 2014-07-21 15:23:50
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    Description:

    - Moved the "export" button on the upper interface panel
    - Fixed the "Filter tracks" option which wasn't working
    - The statistics table now includes the name of each group and the track's ID within the group

  • Version 3.0.0.1 • Released on: 2014-06-20 16:41:22
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    Description:

    Re-uploaded JAR file (rolled back class path to initial one)

  • Version 3.0.0.0 • Released on: 2014-06-20 16:24:45
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    Description:

    New feature: tracks can now be filtered based on the available motion statistics

  • Version 2.0.0.4 • Released on: 2014-06-19 17:00:55
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    Description:

    Fixing the JAR file (again)

  • Version 2.0.0.3 • Released on: 2014-06-19 16:54:58
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    Description:

    Regression from version 2.0.0.1

  • Version 2.0.0.2 • Released on: 2014-06-19 16:53:50
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    Description:

    Re-uploading the correct JAR file

  • Version 2.0.0.1 • Released on: 2014-06-19 16:51:31
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    Description:

    Regression from version 1.0.1.0

  • Version 2.0.0.0 • Released on: 2014-06-19 16:49:56
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    Description:

    Rewrote plug-in from scratch. New interface, faster calculations, new display for plots & graphs, and export functionalities

  • Version 1.0.1.0 • Released on: 2013-07-02 16:09:58
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    Description:

    Fixed display issue in the track manager

  • Version 1.0.0.0 • Released on: 2012-08-08 16:13:07
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    Description:

    - Fixed error when setting the display sequence to null
    - Graphical layout adjusted

  • Version 0.0.1.0 • Released on: 2012-08-08 15:44:29
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