wrMTrck

Author: Jesper Søndergaard Pedersen (jsp@phage.dk)
History: 2008/10/29: First version based on MTrack2, adding automatic counting of body-bends based on changes in angular speeds. Adding a speed histogram facility. Changed input value names to allow wrMTrck to be called from macros.
2008/11/29: Added body bend estimation based on aspect-ratio of animals
2009/03/22: Added maxSizeChange parameter to break tracks if objects change size. Measures Perimeter of object useful to estimate animal length = perimeter/2. Reports object speed in terms of body-lengths per seconds (BLPS)
2009/04/08: Machine independent textfile output by chaninging hard-coded "\n" to dos.newLine(). Changed maxAreaChange to a percentage instead of pixel value
2009/07/07: Added summarize feature. Added body-bend count display on showPositions movie. Added ability to override FPS. Now works with scale calibrated images.
2010/02/01: Corrected spelling mistake in input parameter “minTrackLength”(was “minTrackLenght”) - this may affect scripts using wrMTrck.
2010/04/11: Corrected names in some input fields on the dialog
2010/07/06: Added plotBendTrack option to allow output of thrashing quantification plots for trouble-shooting or quality control purposes.
2010/10/04: Now works on both binary and thresholded movies.
Posibility to enable on the fly deflickering and simple background subtraction based on RB15 on first frame. This means that wrMTrck can now track animals in raw movies and virtual stacks. Hitting the ESC key aborts analysis.
2011/06/17: Added input field to allow adjustment of label font size
2011/06/22: Output of body-bend histogram (number of frames between half-bends) per animal only if bendDetect = 3
2011/10/31: Corrected undocumented raw data output with rawData =6 With rawData <0 headers are suppressed.
(Konstantine Palanski) Summary repors frames with maximum and minimum number of objects and the frame with maximum number of tracked objects
Requires: ImageJ 1.34m or later
Source: wrMTrck_.java
Installation:

Download wrmtrck.zip and unzip all files to the ..ImageJ\plugins folder and restart ImageJ.

Note: Movie files can be very large and require a lot of memory (2GB+ RAM recommended) - see this page for information about how to increase memory available for ImageJ.

Or even better use Fiji that automatically adjusts settings to give maximum memory

Description: wrMTrck plugin is based on Mtrack2 by Nico Stuurman, which is based on MultiTracker by Jeffrey Kuhn, which is based on Object_trackerby Wayne Rasband. wrMTrck will identify the objects in each frame, and then determine which objects in successive frames are closest together. If theses are within a user-defined distance (the maximum velocity of the objects) and have similar area (maxAreaChange) they are assembled into tracks. When multiple objects are within the distance determined by the maximum velocity, the closest object is selected and the object is flagged in the output. wrMTrck adds the following functionality to MTrack2:
  • Processes entire movie even if first frame to contain no objects. (subsequent frames might contain objects).
  • Works with scaled images (use the Analyze -> Set Scale... dialog to set scale). Mtrack2, MultiTracker and CASA all report "Cannot display paths if image is spatially calibrated" error.
  • Automatically reports speeds in units (e.g. Ám/s or pixels/s based on scaling) by reading the FPS or seconds between frames.
  • Summarizes tracking for movies processed, useful for batch processing of large number of movies.
  • All parameters can be set from macros using the Imagej macro recording functions.
  • Breaks tracks if objects change size.
  • Machine independent text format output.
  • Reports average area and perimeter of tracked objects (with standard deviations). The perimeter output may be used to measure the length of elongated objects (such as nematodes): length ≈ perimeter/2
  • Ability to process thresholded in addition to binary images
  • Ability to process virtual stacks on the fly - potentially allowing on-the-fly processing of live video feeds
  • (Optional) Output of speed histograms.
  • (Optional) 5-point moving-average smoothing of x-y position to eliminate digital noise.
  • (Optional) Counting of regular shape changes of objects such as seen for nematodes thrashing in liquid.
  • The included script "wrMTrck_batch.txt" can be used to automatically process a folder (including subfolders) of movies of a given file type.
Citation If you manange to publish work using this plugin feel free to cite the following paper : "Investigating the spreading and toxicity of prion-like proteins using the metazoan model organism C. elegans." by Nussbaum-Krammer CI, Neto MF, Brielmann RM, Pedersen JS, Morimoto RI
See Also:

Object Tracker, Manual Tracking, Multitracker CASA (Computer Assisted Sperm Analyzer), SpotTracker, MTrack2, ParticleTracker and MTrackJ plugins.

Instructions Instructions for usage is available in wrMTrck.pdf and wrMTrck_batch.pdf
Demo files

Demo files are available here: N2.avi Q35.avi G85R.avi - movies are 30s long recorded at 60 pixel/mm scaling of animals at day 3 of adulthood grown at 25°C.

Note: Movies of a variety of dfferent file formats can be loaded into ImageJ using LOCI Bio-Formats plugin or the quicktime plugin for ImageJ to load quicktime movies.

Video tutorial

The video tutorial below demonstrates how to use ImageJ functions to enhance a raw movie and use wrMTrck to measure thrashing rates for swimming C. elegans

The second video tutorial demonstrates how to use the wrMTrck_Batch to completely automate all of the steps involved in the movie enhancement and tracking enabling automated analysis of several movies in a folder.

A video showcasing the some of the improvements included in build 101004, notably processing of thresholded images and virtual stacks

Previous versions

In case new bugs were accidentally included in the most recent build here are some of the older builds:
wrmtrck100706.zip wrmtrck110617.zip

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