Code set analyzing flashlight fish video.
data_67500 - used to generate Fig. S2 of paper
data_97200 - used to generate Fig. 3 of paper
*/example_frame.tif - An example frame from the dataset
*/imgMean.mat - mean of all frames to get noise statistics
*/ptCoords.mat - extracted coordinates of all fish in all the frames
*/tracks.mat - tracking data of all fish in all the frames
All frames of dataset data_67500 are available in 10.5281/zenodo.3271649
The main files to plot mSync are:
main_mSync_67500.m - Generates plot used in Fig. S2
main_mSync_97200.m - Generates plot, subset of which is used in Fig. 3
Above files use already extracted tracking data - data_*/tracks.mat
Example processing files:
extractCoords.m - Extracts the coordinates of fish from an example frame
trackFish.m - Tracks the fish IDs from the extracted coordinates - data_*/ptCoords.mat
Support file:
particleTrack.m - more info on http://www.physics.emory.edu/faculty/weeks//idl/
Reference: "Methods of Digital Video Microscopy for Colloidal Studies", John C. Crocker and David G. Grier, J. Colloid Interface Sci. 179, 298 (1996)
ReadMe at Simulator/Boids_ReadMe.txt
Bioluminescent Flashes Drive Nighttime Schooling Behavior and Synchronized Swimming Dynamics in Flashlight Fish
David F. Gruber, Brennan T. Phillips, Rory O’Brien, Vivek Boominathan, Ashok Veeraraghavan, Ganesh Vasan, Peter O’Brien, Vincent A. Pieribone and John S. Sparks
David F. Gruber - Baruch College, City University of New York, Department of Natural Sciences, New York, NY 10010, USA
David F. Gruber - City University of New York The Graduate Center Program in Biology, New York, NY 10016, USA
Brennan T. Phillips - University of Rhode Island, Department of Ocean Engineering, Narragansett, RI 02882, USA
Rory O’Brien, Ganesh Vasan, Peter O’Brien, Vincent A. Pieribone - The John B. Pierce Laboratory Cellular and Molecular Physiology Yale University School of Medicine, New Haven, CT 06519, USA
Vivek Boominathan, Ashok Veeraraghavan - Rice University, Department of Electrical and Computer Engineering, Houston, Texas, USA
John S. Sparks - American Museum of Natural History, Division of Vertebrate Zoology, Department of Ichthyology, New York, NY 10024, USA
Correspondence: David.Gruber@Baruch.cuny.edu