Companion Data Page

Recovery of locomotion after injury in Drosophila melanogaster depends on proprioception

Alexander Isakov1,2,*, Sean M. Buchanan3,*, Brian Sullivan2,4, Akshitha Ramachandran2,4, Joshua K. S. Chapman3, Edward S. Lu2,4, L. Mahadevan1,2,4,5,** and Benjamin de Bivort2,3,4,**

1 Department of Physics, Harvard University, Cambridge, MA 02138, USA.
2 Center for Brain Science, Harvard University, Cambridge, MA 02138, USA.
3 Rowland Institute at Harvard, Cambridge, MA 02142, USA.
4 Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
5 School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138, USA.
* These authors contributed equally.
** Corresponding authors: debivort@oeb.harvard.edu, lm@seas.harvard.edu

Data files (MATLAB 2014b and R format)

Download a .zip of all these data files.
Fly_Data.RData Contains three data frames. Columns V1, V2, V3, V4, V5, V6 correspond to legs labeled as in Figure 1 in the main text (after amputation, V4 is all zeros). Column day corresponds to experimentation day (-1 is pre-amputation, 0 is immediately post-amputation, 1-3 are days 1-3 post-amputation). The column strain can take on the values "cs", "iav", "nan", corresponding to wild type, inactive, and nanchung mutants in the paper. The column flynum is a unique individual identifier for the flies.
  • Data frame "df.leg.to.centroid.all.data" (distance from leg endpoint to center of body)
  • Data frame "df.all.dist.data": non-binarized leg distances
  • Data frame "df.thresholded.data": binarized distances (method described in paper).
    • HMM_Data.RData Contains one data frame, "df.hmm.data". Columns that share names with "Fly Data.RData" have the same description. Columns of the form [Gait]To[Number], where Gait can take the values {"Wave", "Tetrapod", "Tripod"} and Number can take the values {0,1,2,3} represent emission probabilities. Columns of the form [Gait]To[Gait] are transition probabilities. See paper for description. The column HiddenState represents the likeliest hidden state given the corresponding emission and transition probability matrix. The column NumLegsMoving is the observed "ground truth" number of legs moving (after binarizing leg motion).
    allPlastData.mat Individual fly theta-delta histograms from arena circling experiments. Columns in cell array respectively indicate arena position number in 3x3 arena array, experiment ID, experimenter ID, imaging rig ID, experimental group, theta-d histogram values (cols 7-31). This file contains the binning used for figures in the manuscript.
    allPlastDataStatusSummary.mat Contains a struct with two objects, respectively containing (in cols 4-16) the mean or standard deviation of the individual theta-d histogram values for flies belonging to the experimental groups indicated in column 1, with sample sizes indicated in column 2 and the mean mu score (or standard error of the mean of the mu score) in column 3.

    Analysis and simulation functions and scripts (MATLAB 2014b)

    Download a .zip of all these scripts and functions.
    automated movie annotation
    Main_Movie_Correction_Script.m Instructions, including input and output, are in the files. A schematic of logic flow is in the paper. In brief, this script runs, cell by cell, the functions: RemoveBeginningFramesByTimeFunction (cropping by time), RemoveFramesFunction (cropping by frame-by-frame), AutomaticTrackingFunction (auto-tracker), ErrorCorrectionFunction (hand-by-hand leg endpoint correction), MotionDetectionFunction (to detect how far leg moved), and ShowFinalMovieFunction (to see the final output of movies in one place).
    Important Note: Some of the files listed below (such as cropping) overwrite the original movie. The script default is set to look at all movie files in the prescribed folder. Please put a copy of the originals in a separate folder.
    Important Note: If the script is run as a batch on a large number of movies, a large number of output files can be generated in the folder. Outputs (including file types) are given in top-line comments in each cell of this script.
    RemoveBeginningFramesByTimeFunction.m, RemoveFramesFunction.m, AutomaticTrackingFunction.m, ErrorCorrectionFunction.m, MotionDetectionFunction.m, ShowFinalMovieFunction.m Functions for cropping movies, tracking leg motion, and showing output. A schematic of logic flow is provided in the paper. Functions have numerous inputs, including some that switch between algorithms (with set defaults). All descriptions, including inputs and outputs, are given in top-level comments within each function.
    walking simulation
    ArenaPathsSim.m Simulation of fly body movement in arena for calibration (see: calibration curve description in Materials and methods section in paper). Inputs: numSims (number of simulations to run), numSteps (number of steps in one simulation – reasonable default is 10,000), headingDrift (heading drift – described in paper), bias (described in paper), visualizationFlag (can take value 0 or 1, with 0 meaning no visualization and 1 meaning show final theta-delta histogram and plot arena paths). Several parameters can be set inside the function (e.g. body length, arena radius), with defaults provided.
    walking_diff_eq_function.m Function for simulating fly walking. A number of parameters are set and explained via comments in the code. Inputs: numStrides (number of strides to take -- 3 or more is reasonable, as described in paper), h (solver time-step, 0.001 is reasonable), deltaVec, phiVec, omega, (leg parameter vectors, as described in paper -- reasonable values for canonical tripod gait are delta = [.5,.5,.5,.5,.5,.5], omega = 1, phi = [0,.5,0,.5,0,.5]), p (sets maximum/minimum leg stretch), c_2_vec (forces), visualization_flag (1 displays movie after solving, 0 does not).
    energy_function.m Energy calculation for simulated annealing optimization algorithm. Takes output of walking_diff_eq_function (theta_vector = body angle vector, centroid_vector = centroid vector; both at each time-step in the differential equation solver), h (number of time- steps used in equation solver), omega (step frequency), numStrides (number of strides used in equation solver), targetabsoluteBias (the observed bias in experiment to try to match). Descriptions of inner workings are in function comments.