Stytra: An open-source, integrated system for stimulation, tracking and closed-loop behavioral experiments
Fig 3
Head-restrained tail tracking in Stytra.
A) The image is first pre-processed by inverting, down-scaling, blurring and clipping, resulting in the image on the right, where the fish is the only object brighter than the background. Then, tail tracing starts from a user-defined point, and in the direction determined by another user-defined point at the end of the tail at rest. For each segment, a square (outlined in white) in the direction of the previous segment (yellow) is sampled, and the direction for the next segment is chosen as the vector (red) connecting the previous segment end and the center of mass of the sampled square (blue). B) A heatmap showing the angles of the tail segments from the start to the end of the tail during a bout, and a trace representing the cumulative curvature sum from a behaving animal. The total curvature is just the difference in angle between the first and last tail segment (adding up angle differences between all segments, only these two terms remain).