Tracking neurons in Hydra vulgaris
The code consists of 3 parts.
- Detection
- Tracking
- Tracklet association
The detection algorithm we use is adapted from u-track, described here: http://lccb.hms.harvard.edu/software.html The detection algorithm itself is the one described in Supplementary Note 2 http://www.nature.com/nmeth/journal/v5/n8/extref/nmeth.1237-S1.pdf
The tracklet association is described here: https://www.robots.ox.ac.uk/~vgg/rg/papers/huang_etal__robust_object__eccv2008.pdf
We use the GPML toolbox (for obtaining motion affinity). Download from here: http://www.gaussianprocess.org/gpml/code/matlab/doc/