Escape response data
====================

This is the "escape response" dataset from:

   Broekmans, Onno, Rodgers, Jarlath, Ryu, William, and Stephens, Greg,
   Resolving coiled shapes reveals new reorientation behaviors in C. elegans.

Corresponding author:

   Greg J. Stephens <g.j.stephens@vu.nl>


About the data
--------------

Data were produced in the lab of William S. Ryu by Jarlath B. Rodgers.

Data is included for 98 individual worms, each recorded for 600 seconds at 20
Hz, on a food-filled agar plate. An infrared laser impulse is applied at
t = 10 s.

Each sequence has images for 10 seconds pre-zap, and 20 seconds post-zap.

Worms 6, 13, 17, 30, 42, 88 were not part of the manuscript analysis, as they
were hardly moving.


Archive contents
----------------

This archive contains one subdirectory per worm, for 98 worms in total. In each
subdirectory, the following files can be found:

 - *.jpg

   Video frames, taken at a 20 Hz framerate.


 - Notes.txt

   Contains additional metadata on the video sequence, in the following format:

      apr8_long_follow_worm1      : recording name
      4/8/2014                    : date of recording
      Laser Current (mA): 75      : laser current of IR laser
      Laser Duration (ms): 100    : duration of laser pulse
      Laser Start: 199            : at which frame does the pulse occur?
      galvo x: 8.186000e+002      : position of the galvo mirror (X)
      galvo y: 6.284000e+002      : position of the galvo mirror (Y)
      Vulvar Orientation: L       : vulvar orientation of the worm (L/R)
      FPS: 20                     : frame rate (Hz / frames per second)

   Note that fields such as laser current, duration, start and FPS are
   consistent across all video sequences.

   Movies for which the vulvar orientation, as recorded in the "Notes.txt"
   metadata file, is disputed, have had their "Notes.txt" amended to reflect
   this. A question mark has been added to the "Notes.txt" contents, like so:

      Vulvar Orientation: R?

 - tracking.txt

   Our tracking results for each frame, as a tab-separated text file. Each
   column is an eigenmode value, with a1 in the first column, a2 in the second,
   etc. The 6th column is the overall orientation <theta>, as described in the
   paper. To reconstitute full centerlines, you will also need the eigenworms;
   see the 'eigenworms.txt' file below.


Other files in this archive are:

 - eigenworms.txt

   Tab-separated text file containing a matrix with the eigenworms from the
   original 'eigenworms' paper [1]. Each column is an eigenworm, with one
   backbone tangent angle per row.


Additional notes
----------------

Original root folder name in the Ryu Lab:
   single_stimulus_75mA_100ms


References
----------

 1. Stephens et al., Dimensionality and dynamics in the behavior of C. elegans,
    PLoS Computational Biology, e1000028 (2008).
    doi:10.1371/journal.pcbi.1000028