DOI: 10.5061/dryad.wwpzgmsqs
title: How small deviations in kinematics and body form dictate muscle performances in the finely tuned avian downstroke

description: Avian takeoff requires peak pectoralis muscle power to generate sufficient
 aerodynamic force during the downstroke. Subsequently the much smaller
 supracoracoideus recovers the wing during the upstroke. How the pectoralis
 work loop is tuned to power flight is unclear. We integrate
 wingbeat-resolved muscle, kinematic and aerodynamic recordings in
 vivo with a new mathematical model to disentangle how the pectoralis
 muscle overcomes wing inertia and generates aerodynamic force during
 takeoff in doves. Doves reduce the incidence of their wing mid-downstroke
 to efficiently generate aerodynamic force, resulting in an aerodynamic
 power dip, that allows transferring excess pectoralis power into
 tensioning the supracoracoideus tendon to assist the upstroke—improving
 the pectoralis work loop efficiency simultaneously. Integrating extant
 bird data, our model shows how the pectoralis of birds with faster wingtip
 speed need to generate proportionally more power. Finally, birds with
 disproportionally larger wing inertia need to activate the pectoralis
 earlier to tune their downstroke.
description: The experimental setup consisted of three time-synchronized
 systems which imaged the 3D surface of the dove, measured the aerodynamic
 forces produced by the dove, and measured the activation and lengthening
 of the pectoralis muscles of four doves. To image the 3D wing surface of
 each dove at 1000 Hz, we used a structured-light system. We measured the
 vertical and horizontal aerodynamic forces produced by the dove at 2000 Hz
 using an aerodynamic force platform (AFP). Finally, sampling at 10,000 Hz,
 we used electromyography (EMG) to measure the electrical activation of the
 pectoralis and sonomicrometry to measure the strain of the pectoralis. We
 analyzed the second wingbeat after takeoff for four 2-year-old near-white
 Ringneck doves (<em>Streptopelia risoria</em>; 3 males, 1
 female), which were trained to fly between perches (1.6 cm diameter) 0.65
 m apart inside of the AFP. We recorded 5 flights from each dove while
 measuring the muscle activity for a total of 20 flights. To assess the
 effect of surgery and the recording cable on flight behavior, we also
 recorded doves 3 and 4 during five pre-surgery flights, and dove 3 during
 five post-surgery flights, but without the cable needed to measure muscle
 activity attached. The perches were mounted 0.36 m above the bottom plate
 of the AFP, and the residual descent angle between the takeoff and landing
 perch was 2 degrees. Training involved light tapping on the tail to
 initiate a flight to the other perch. Some flights were rejected as
 outliers due to inaccurately eliciting a flight or equipment failure
 (noisy or missing sonomicrometry signal; insufficient suspended cable
 length allotment). All experiments were approved by and in accordance with
 Stanford University’s Institutional Animal Care and Use Committee. Further
 details are provided in the paper.
description: #### Usage notes: * To re-generate all of the plots used to create the
 figures in this paper, run RunAll.m in the folder 9 MuscleModel. The
 resulting figures are in the subfolders 3Figs and 4Videos. * Naming
 conventions are detailed below. One commonly used naming conventions uses
 the names of the four doves: OG (dove 1), OB (dove 2), OP (dove 3), and BB
 (dove 4). * The main folders should all remain in a single folder and are
 labeled with numbers 0-9 with contents detailed below: 0 MATLAB Base
 Folder * This should be set as your MATLAB startup folder
 (https://www.mathworks.com/help/matlab/matlab\_env/matlab-startup-folder.html). 1 Experimental Flights * This is where all of the collected data is located (high-speed videos & calibration files not included to save space). * Subfolders are named according to the following naming convention: Date\_DoveName\_Flight#. For each flight, the aerodynamic forces were saved using the file name: Date\_DoveName\_Flight#\_AeroForces.txt, and for post-surgery flights with wires attached, the sonomicrometry and electromyography data were saved using the file name: Date\_DoveName\_Flight#\_SonoEMG.abf. * Calibration: This folder originally contained various camera calibration files (removed to save space) and also contains baseline pectoralis lengths based on sonomicrometry data collected while each dove was resting on the perch. 2 Dissections * SurfArea: This folder contains images and code used to manually extract the wing length and surface area of the extended wings and tails of the doves. Run SurfAreaClick.m to see the manually clicked surface areas (data saved in SurfAreas.mat) & run WingSpan.m to see the manually clicked wing lengths (data saved in WingSpan.mat). * DataProcessing: This folder contains images and code used to extract in-person measurements made during the dissection. Run DissectClick.m to see the manually clicked muscle angles (data saved in DissectClick.mat). The rest of the data is saved in DissectionRecords.xlsx and saved into DissectData.mat by DissectExcelExport.m. * The other folders with dove names (BB, OB, OG, OP) contain pictures taken from the dissection which we used to quantify pectoralis statistics. 3 Other data * SetupPix: This folder contains pictures taken of the setup. * DotPatterns: This folder contains the dot patterns used for calibrating the cameras. * HashPatterns: This folder contains the hash patterns used for 3D reconstruction. 4 * There was originally a folder here, but the content was not relevant to this manuscript, so to save space, this folder was removed. 5 Calibration * 3Results: This folder contains the results & error plots of the camera calibrations. * MainCalibCode: The contents of this folder have been removed to save space, but are included in the deposited data from Deetjen et. al. 2020 (https://datadryad.org/stash/dataset/doi:10.5061/dryad.15dv41ntr). 6 SLS Reconstruction * 2Intermediate: The manually tracked kinematics and the 3D surface reconstructions are stored here. * Vids: The tracked kinematics are overlaid on top of the 5 camera views collected. * The 3D reconstruction code has been removed to save space, but is included in the deposited data from Deetjen et. al. 2020 (https://datadryad.org/stash/dataset/doi:10.5061/dryad.15dv41ntr). 7 AccuracyXYZ * 1 SphereDrop: The saved files record the direction of gravity (fitted using image processing and optimization). * 2 RodDir: The saved files record the forward direction relative to the AFP (fitted using image processing and optimization). * 4 PerchPos: The saved files record the position of the perches (fitted using image processing and optimization). * XYZ\_KeyVars: Here are stored all of the key variables to transfer between reference frames as determined by the sphere drop, rod direction, and perch position. * The code from this folder has been removed to save space, but is included in the deposited data from Deetjen et. al. 2020 (https://datadryad.org/stash/dataset/doi:10.5061/dryad.15dv41ntr). 8 AFP Sono * WithWires: This folder contains code to extract and pre-process the AFP (Aerodynamic Force Platform) and sonomicrometry measurement data for post-surgery flights when the wires to measure muscle activity were attached. Run AeroSonoEMG.m to generate the saved plots and data. * NoWires: This folder is similar to WithWires except it pre-processes only AFP data for flights when the wires to measure muscle activity were not attached. Run Aero.m to generate the saved plots and data. 9 MuscleModel * This is the primary folder within which all of the pre-processed data is used to model the muscle performance and generate plots used directly in the paper. * Run RunAll.m to re-generate all of the plots used in the paper. The plots are saved into 3Figs in both .png and .fig (Matlab figure) types. Additionally, videos are saved into the 4Videos folder. RunAll.m runs 5 functions in sequence: 1. LoadFilesFolders.m: This saves some relevant folder and file path information into FilesFolders.mat. 2. MuscleModel.m: This function uses the 3D reconstructed surface, the measured aerodynamics, and the measured muscle activity of the doves to model the power and moments of the aerodynamics, inertia, and pectoralis muscle. It saves the relevant output data in the folder 2TestRuns. 3. Paper4Figs2D.m: This function generates plots used in the paper and saves the results in 3Figs. Additionally, the elastic energy storage is modeled within this function and the results are stored in ScalingAnalysis\_Vars.mat. 4. Paper4Figs3D.m: This function generates all of the 3D visualizations of the surface of the dove used in the paper and saves the results in 3Figs. Additionally, videos are saved into the 4Videos folder. 5. Paper4\_ScalingAnalysis.m: This function generates all of the plots pertaining to the scaling analysis of extant birds used in the paper and saves the results in 3Figs. #### Other notes on data inclusion: * To save space, the original high-speed videos and 3D reconstructions are not included. For an example high-speed video and code used to generate 3D reconstructions, see the deposited data from Deetjen et. al. 2020 (https://datadryad.org/stash/dataset/doi:10.5061/dryad.15dv41ntr) M. E. Deetjen, D. D. Chin, and D. Lentink, "The aerodynamic force platform as an ergometer," J. Exp. Biol. jeb.220475 (2020). * The high-speed video of the original flights are compressed and overlaid with manually collected kinematics in the folder: 6 SLS Reconstruction\\Vids\\Kinematics.