This project was done in collaboration with the LSENS laboratory, EPFL. The LSENS correlates frame-by-frame mouse behavior videos with a second set of videos showing the cortex activity. The mice are deprived from all their whiskers but one.

The LSENS quantifies whisker movements by pointing three pixels on each frame: one along the whisker, one at the beginning of the whisker and one on the nose tip. They use these three coordinates to compute the angle of the whisker with the snout. The project consisted in developing a plugin for ImageJ able to automate the process of tracking these three points.

The plugin uses three filters already developed by the BIG: the edge detector, steerable ridge detector, and LoG.

On the image above we can see that the manual tracking consisted in linearly interpolating the movement by recording the coordinates on a few frames. As the plugin goes through every single frame its result is much more accurate.

The animated gif shows the plugin tracking over 20 frames. For the sake of better display the image here has been scaled, compressed and cropped.