Description of the setup - HelmchenLabSoftware/contrast-marker-video-tracker GitHub Wiki

mouse-run-img

The behaving animal (mouse) is running on a wheel. It is illuminated using an infrared light source and imaged using an infrared camera. The animal is unable to see infrared light, which is essential, because visual stimulus may interfere with the experiment. The task of the limb detection algorithm is to identify the positions of the 5 marked spots on the joints of the right front limb of the animal as a function of time. The detection is challenging because of the following reasons

  • Infrared camera is grayscale, and while the markings are easily identifiable by eye in most frames, there is not much difference in contrast between the markings and other unrelated objects such as natural coloring of the animal fur.

  • When the animal grabs the bar, the markings on the front paw joints come very close together, which makes it hard to tell them apart. In addition, some of the markings may hide behind fingers of the paw, or behind the bar.

In order to amplify the contrast of the markers, glue containing retro-reflective beads is applied as marker. Such markers reflect light back under narrow angle. In conjunction with an orthogonal illumination using a semi-transparent mirror it is now possible to significantly increase the contrast of the markings.