These MATLAB functions are for discretizing worm behaviour using a series of template postures and then using the posture sequences to discover interesting patterns of behaviour and for comparing worm strains to each other.  Details can be found in the following manuscript (please cite it if you use any of this code for a publication):

Roland F. Schwarz, Robyn Branicky, Laura J. Grundy, William R. Schafer, André E.X. Brown (2015) Changes in postural syntax characterize sensory modulation and natural variation of C. elegans locomotion. PLOS Computational Biology, accepted.
Preprint: http://dx.doi.org/10.1101/017707

The 'demo' subfolder contains scripts organised by figure.  Running these scripts should reproduce most the figures of the paper (up to differences based on random numbers used in the code).  Some pre-processing is required (for example, to extract angle arrays from the feature data and to convert these angle arrays to state sequences using template postures).  There are scripts for these tasks included in the repository.

The data used in this paper are mostly available from this ftp site:
ftp://ftp.mrc-lmb.cam.ac.uk/pub/tjucikas/wormdatabase/results-12-06-08/Laura Grundy/

Please e-mail me for any data not available from that address.  We are still (slowly) working to make an improved database that will include original videos for re-analysis.

If you find any bugs or have any questions, please e-mail me at [email protected] or [email protected].


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