Animal tracking

Code for ImageJ- and Matlab-based image tracking.

ImageJ based tracking

Functions needed (have entire CIAtah pipeline loaded anyways to ensure all dependencies are met):

  • mm_tracking.ijm is the tracking function for use in ImageJ, place in plugins folder. It is found in the ciapkg\tracking folder of the repository.
  • removeIncorrectObjs() is a function to clean-up the ImageJ output.
  • createTrackingOverlayVideo() is a function that allows users to check the output from the tracking by overlaying the mouse tracker onto the video.

Instructions for ImageJ and Matlab

Run mm_tracking from the Plugins menu of ImageJ. Several settings to check:

  • number of session folders to analyze - this will indicate how many movies you want to analyze. Depending on analyze movies from a list file setting, a GUI will appear asking you to select movies to analyze (preferably AVIs) or a text file with a list of movies.
  • pixel to cm conversion, distance (cm) - Make sure pixel to cm conversion indicates a measurable distance in the video, e.g. from one side of the box to another. The program will ask you to draw this distance to estimate pixels/cm.
  • crop stack? - keep this selected, as allow removal of parts of movie where the animal will not go, improving results.
  • erode and dilate - likely keep this selected, as it essentially makes sure the mouse is a solid object and smooths the tracking.
  • analyze movies from a list file - select this option if you have a text file with the location of each movie to be analyzed on a new line. Use this to analyze many movies in batch.
  • hide loaded movie - uncheck this to be able to visualize as ImageJ completes each step in the processing. Leave checked to improve speed of analysis.

Example screen after running mm_tracking within ImageJ, click to expand.

image

Once ImageJ is finished, within MATLAB run the following code (cleans up the ImageJ tracking by removing small objects and adding NaNs for missing frames along with making a movie to check output). Modify to point toward paths specific for your data. 

% CSV file from imageJ and AVI movie path used in ImageJ
moviePath = 'PATH_TO_AVI_USED_IN_IMAEJ';
csvPath = 'PATH_TO_CSV_OUTPUT_BY_IMAGEJ';
% clean up tracking
[trackingTableFilteredCell] = removeIncorrectObjs(csvPath,'inputMovie',{moviePath});

Example output from animal in open field during miniature microscope imaging

Tracking of an animal over time (green = early in session, red = late in session). image

Tracking video

The tracking video can be used to quickly validate that the animal is being correctly tracked.

% make tracking video
% frames to use as example check
nFrames=1500:2500;
inputMovie = loadMovieList(moviePath,'frameList',nFrames);
[inputTrackingVideo] = createTrackingOverlayVideo(inputMovie,movmean(trackingTableFilteredCell.XM(nFrames),5),movmean(trackingTableFilteredCell.YM(nFrames),5));
playMovie(inputTrackingVideo);

Overlay of tracking (red circle) on the mouse in a specific frame. image