Short Description

Mice Profiler tracks multiple mice from a top view video.

Computerized video analysis of social interactions in mice. Nature Methods 2012: http://www.nature.com/nmeth/journal/v9/n4/full/nmeth.1924.html
Source code: https://gitlab.pasteur.fr/bia/mice-profiler-tracker

Documentation

The version of MiceProfiler provided by Nature methods does not contain the automatic updater. If you downloaded MiceProfiler from Nature methods, you are running an old version. Please uninstall and reinstall the plugin to get the last version.

For test purposes, you can use this video file.

Tutorial about this software:

Here is another example showing the supervised tracking:

With the corresponding results extracted from the plugins VideoLabelMaker and Label Analyser (for the temporal graph)

As a number of people had trouble loading video sequences because of the codec and 32 bit stuff. I had release by the 15 May 2012 a new version with a completely new video file loader called xuggler, that is faster, and able to work in 64bits. Please look at the xuggler website for supported video codecs (basically FFMPEG). If you have trouble with your video please use the following softwares to convert it:

  • http://www.freemake.com/free_video_converter/ (use custom install to avoid toolbars and advert-stuff)
  • SUPER (but I highly don’t recommend it since it installs a lot of adware that you can’t avoid on you computer.)
  • The software you like (send me the link I will add it to this list !)

Last note about video: do not use HD video. The software has originaly been designed for 384×288 video. Still it’s ok to use 640×480 videos but you should not exceed this. Else the loader will be slow and the tracking will be impacted. The day I find a proper frame-per-frame loader in java I will update to support HD file, even 4K if needed ! (If anybody knows a proper lib, contact me !)

New: shortcuts: (thanks to Sibah)

Resources needing this

5 reviews on “Mice Profiler Tracker”

  1. v
    vkumar
    Software looks really promising. However I have had issues installing. Sorry in advance if this is not the right forum for reporting bugs. On Mac I cannot load video - I'll wait for the new loader on May 15.
  2. J
    Very Nice work, improved by a very reactive programer's team! However, some little thing could be adds: - Shortcut's keyboard for exemple....
  3. a
    Hi, this is a really nice work, at least in the video test, because I cannot load mine, encoded in MPG. I could not find any information about this format in xuggler website, do you know any software to convert videos in a good format ?? Thank you in advance for any help
  4. j
    This is a great piece of software from a competent, reactive, and helpful developer. It offers the potential to combine a rich ethological approach with a semi-automated and efficient one, to study subtle aspects of animal social behavior that are impossible to study reliably with human hand-scoring. They accomplish this by implementing sophisticated techniques that solve the main problem inherent in multiple animal-tracking, disambiguating animals once they've made physical contact. In addition, the user is able to make manual corrections when the program goes off course. I especially appreciate the ability to track multiple animals without having to tag or label the animals in a way that may influence their behavior. And I'm particularly excited to study the very 'social' things that occur outside of physical contact; this opens a big, new door in the study of social behavior in animals. Overall, a very important advance. A couple suggested additions: - Ability to parse data by ROI. This would be useful in social preference paradigms, for ex, in which different animals are confined to different compartments in a single test apparatus. (although running a session in each ROI will accomplish this, I believe) - Ability to report the 'distance traveled'. This would be useful since we often have to consider whether changes in general arousal or activity account for effects we label as 'social'.
  5. M
    Maria Gulinello
    This looks like it would be amazing but I can also not load any videos. In any format. Not the test video provided and not any other of the 640 x 480 in avi or mp4 format

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Changelog

  • Version 7.1.4.0 • Released on: 2021-12-07 15:30:00
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    Description:

    Small fix for graph label export

  • Version 7.1.3.0 • Released on: 2021-12-06 16:00:00
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    Description:

    Updated from maven project, minors fixes for Icy 2.4.0

  • Version 7.1.1.0 • Released on: 2020-03-11 17:30:00
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    Description:

    Included Phys2d library into the JAR file as it's used only in this plugin so it an be removed from Icy lib folder (finally) - Stephane

  • Version 7.1.0.22 • Released on: 2017-04-14 15:26:40
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    Description:

    XML Fix
    Custom code removed. Switch to kernel code.

  • Version 7.1.0.21 • Released on: 2017-04-14 15:10:04
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    Description:

    Fix XML no file exists error

  • Version 7.1.0.20 • Released on: 2017-04-14 14:27:25
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    Description:

    Fix a problem with XML export due to new version of lib in java8

  • Version 7.1.0.19 • Released on: 2015-11-25 15:03:05
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    Description:

    fix load error of new XML format

  • Version 7.1.0.18 • Released on: 2015-11-25 14:50:23
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    Description:

    XML now save base of the neck position

  • Version 7.1.0.17 • Released on: 2014-09-02 11:06:17
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    Description:

    - Fix the tracking of white mice.

  • Version 7.1.0.16 • Released on: 2014-07-08 17:36:27
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    Description:

    Updated to fit with new features added in the video label maker.

  • Version 7.1.0.15 • Released on: 2014-04-03 18:37:16
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    Description:

    - Fix an error in a label

  • Version 7.1.0.14 • Released on: 2014-04-03 18:28:26
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    Description:

    - World E removed
    - Add: button to switch identity of tracks from t to the end of the records
    - Lock scroll ( key e )
    - Video name is in the title of the sequence
    - Seeking moves the initialization ROIs
    - Model size can now be changed anytime (not before video load)
    - Head of mouse can be tracked manually using the 1 and 2 keys.

  • Version 7.1.0.13 • Released on: 2013-12-05 10:56:19
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    Description:

    Dependencies update for Video Label Maker

  • Version 7.1.0.12 • Released on: 2013-12-04 15:03:03
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    Description:

    Fix dependencies from the VideoLabelMaker

  • Version 7.1.0.11 • Released on: 2013-10-31 11:36:13
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    Description:

    Better video file support

  • Version 7.1.0.10 • Released on: 2013-10-31 11:14:34
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    Description:

    Compatibility fixes for version 1.4.0.0

  • Version 7.1.0.9 • Released on: 2013-09-17 17:56:16
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    Description:

    New shortcuts (asked by sibah). See in the doc page for a ready-to-print document.

  • Version 7.1.0.8 • Released on: 2013-09-04 11:31:20
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    Description:

    end of debugging

  • Version 7.1.0.7 • Released on: 2013-09-04 11:26:38
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    Description:

    - debugging

  • Version 7.1.0.6 • Released on: 2013-09-04 11:19:29
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    Description:

    - Debug info added for video decompression

  • Version 7.1.0.5 • Released on: 2013-07-05 16:20:42
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    Description:

    - Add support for vision graph export

  • Version 7.1.0.4 • Released on: 2013-07-03 15:39:54
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    Description:

    - Now tracks white mice

  • Version 7.1.0.3 • Released on: 2013-05-23 10:58:50
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    Description:

    The read position from line ROI button is now disabled while tracking. This button should be used only while tracking is stopped

  • Version 7.1.0.2 • Released on: 2013-01-31 16:53:04
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    Description:

    Fix a problem to access video files

  • Version 7.1.0.1 • Released on: 2013-01-31 14:05:14
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    Description:

    very minor fix

  • Version 7.1.0.0 • Released on: 2012-11-07 14:51:19
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    Description:

    Fix : If big scales are used, such as 1.3, the models blew out ! This is now fixed.

  • Version 7.0.1.2 • Released on: 2012-07-06 13:21:28
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    Description:

    Fixed a minor error on display

  • Version 7.0.1.1 • Released on: 2012-06-26 14:58:46
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    Description:

    - The speed of the tracking can be too fast for human supervision :) so I added a 'slow down tracking to 15fps' option.

  • Version 7.0.1.0 • Released on: 2012-05-21 11:50:43
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    Description:

    removed debug log.
    Fix an error if the user close the sequence while tracking.

  • Version 7.0.0.0 • Released on: 2012-05-16 13:37:25
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    Description:

    Fix: prevent crash if the user switch to a 3D viewer.
    Fix: VideoLabelMaker image compilation: fix a bug when no file is found.
    Fix: The video reader is now based on xuggler. Video can now be read by x64 architecture, Win, Mac and Linux
    New: Video management improved.
    Improved display speed of edge and binary maps
    t-Cursor of sequence can now be used
    VideoLabelMaker display fixed.
    + a number of minor updates

  • Version 6.1.1.6 • Released on: 2012-03-13 11:56:46
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  • Version 6.1.1.5 • Released on: 2012-03-13 11:54:41
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  • Version 6.1.1.4 • Released on: 2012-03-13 11:43:09
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  • Version 6.1.1.3 • Released on: 2012-03-13 11:25:38
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  • Version 6.1.1.2 • Released on: 2012-03-13 11:23:27
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    Description:

    Fix automatic scale of painters

  • Version 0.6.1.1 • Released on: 2012-03-13 11:10:59
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    Description:

    Memory ghost position fixed.

  • Version 0.0.1.0 • Released on: 2012-03-05 14:21:09
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