Looking at track data

Data files

Running motr produces several data directories:

The track files are in Results/Tracks and are named with "_tracks.mat" suffix after the name of the video file with which they are associated.

Track file format

The track files are MATLAB .mat files and contain two variables: astrctTrackers and strMovieFileName (which, as the name implies, is a string with the name of the movie file in it).

motr tracks the mice by fitting an ellipse around each mouse. astrctTrackers is a 1 x [number of tracked mice] struct with fields describing the position, size and orientation of the ellipse:

m_afX: x position of the ellipse centroid in pixels
m_afY: y position of the ellipse centroid in pixels
m_afA: length of semi-major axis of ellipse in pixels
m_afB: length of semi-minor axis of ellipse in pixels
m_afTheta: angle of the ellipse in radians

Note: the y coordinate of the ellipse center is `image-style', in other words, it increases as you move towards the bottom of the image. Theta is nevertheless measured in the traditional way, counterclockwise from the (rightward-pointing) x axis.


JAABA (the Janelia Automatic Animal Behavior Annotator) can read in motr tracks. This is a very powerful and flexible tool for analyzing mouse movement trajectories. You can download JAABA and get detailed instructions for using it here: jaaba.sourceforge.net.

Miscellaneous notes

If you would like to express your mouse tracks in meters (or feet or furlongs), you'll need to calculate your pixel-to-meter factor. The easiest way to do this is to just put a ruler onto the floor of the arena, take a picture with the camera, load the picture into MATLAB and use imagesc and ginput to measure the number of pixels in your chosen distance unit.

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