Companion Data Page
MARGO (Massively Automated Real-time GUI for Object-tracking),
a platform for high-throughput ethology
Zach Werkhoven,
Chuan Qin, Christian Rohrsen,
Björn Brembs, and
Benjamin de Bivort
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138, USA.
Institut für Zoologie - Neurogenetik, Universität Regensburg, Regensburg, Germany
** Corresponding author: debivort@oeb.harvard.edu
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Data files (MATLAB 2016a)
Download a .zip of all these data files. |
| noise_injection_error_data.mat |
Contains two data arrays from tracking following manual noise injection. Cen_error is a number
of frames by number of noise levels matrix of frame to frame error. Noise_level is an ordered one by number of
noise levels array of probabilities of converting any given pixel of the threshold image to TRUE. Columns of
cen_error are organised by increasing noise level. Data can be visualized with plot_mean_injection_error.m.
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| reference_shift_simulation_data.mat |
Contains data from the background reference shifting simulation. Summary of items:
- raw_cen - x,y trace data from ground truth
- shift_cen - x,y trace data from background shifting
- shift_int - interval between shift events (frames)
- shift_idx - frame indices of shift events
- ifi - mean interframe interval (seconds)
Data can be visualized with reference_shift_triggered_averaging.m.
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| margo_ctrax_comparison_centroids.mat |
Contains tracking data from the same video tracked in both Ctrax and MARGO. Summary of items:
- ctrax_x - (1 x nFlies) cell array of x-centroid data obtained with Ctrax
- ctrax_y - (1 x nFlies) cell array of y-centroid data obtained with Ctrax
- margo_x - (1 x nFlies) cell array of x-centroid data obtained with MARGO
- margo_y - (1 x nFlies) cell array of y-centroid data obtained with MARGO
Data can be visualized with calculate_margo_to_ctrax_error.m.
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| LED_ymaze_individual_trial_data.mat |
Contains individual phototaxis and handedness biases grouped by whether the light stimulus occured to the
right or left of the maze choice point. Summary of items:
- nTrials - (1 x nFlies) number of trials for each fly
- p_LR - (1 x nFlies) probabilities p(light_choice|light_on_right)
- p_LL - (1 x nFlies) probabilities p(light_choice|light_on_left)
- p_RL - (1 x nFlies) probabilities p(right_choice|light_on_right)
- p_RD - (1 x nFlies) probabilities p(right_choice|light_on_left)
- side_mat - (nTrials x nFlies) matrix of lit side relative to the starting point.
Right = 1, Left = -1, No turn = 0
Data can be visualized with LED_ymaze_plot_pairdots.m.
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| optomotor_individual_data.mat |
Contains individual trial triggered averages of optomotor data. Summary of items:
- numTrials - (1 x nExperiments) cell array of arrays w/ individual trial numbers for each experiment
- delta_ang - (1 x nExperiments) cell array of arrays w/ individual trial triggered average change in body angle for a single experiment
- delta_rad - (1 x nExperiments) cell array of arrays w/ individual trial triggered average change in normalize radial position for a single experiment
- trial_t - (1 x nExperiments) cell array of trial-relative time stamps of for each experiment
Data can be visualized with plot_trial_triggered_averages_opotomotor.m.
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| optomotor_bootstrap_data.mat |
Contains individual trial triggered averages of optomotor data. Summary of items:
- numTrials - (1 x nExperiments) cell array of arrays w/ individual trial numbers for each experiment
- raw_delta - (1 x nExperiments) cell array of arrays of total angular distance traveled in each trial
- stim_delta - (1 x nExperiments) cell array of arrays of total angular distance traveled in the direction of stimulus rotation in each trial
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| single_roi_sample |
Sample video of a single roi at low resolution (31 x 31 pixel). Note: this sample was used in conjuction with
tile_single_roi_vid.m to generate a sample video with thousands of ROIs for frame rate.
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| optogenetic_speed_distributions |
Contains a struct of individual mean speed data distributions split by condition and time blocks from the
optogenetic speed reinforcement paradigm. Summary of items:
- by_time_block - struct of speed data split by time block
- data - (1 x nBlocks) cell array individual mean speeds per experimental group and time block
- labels - (1 x nBlocks) cell array of condition/time block labels for columns in data
- by_condition - struct of speed data split by reinforcement condition
- data - (1 x nBlocks) cell array individual mean speeds per experimental group and condition
- labels - (1 x nBlocks) cell array of condition/group labels for columns in data
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| optogenetic_speed_traces |
Contains a struct of speed trace data from the
optogenetic speed reinforcement paradigm. Summary of items:
- data - (nGenotypes x 1) cell array of individual speed traces (nFrames x nFlies)
- frame_labels - (nGenotypes x 1) cell array of frame labels by reinforcement paradigm (nFrames x 1)
- labels - (nGenotypes x 1) cell array of genotype labels
- frame_label_key - (nParadigms x 1) lookup table for frame to frame labels by reinforcement paradigm
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| optogenetic_ymaze_data |
Contains structs of ymaze distributions from the
optogenetic Y-maze reinforcement paradigm. Summary of items:
- occ_int_gr66 - struct of Gr66a occupancy distributions and labels split by stimulation intensity
- occ_freq_gr66 - struct of Gr66a occupancy distributions and labels split by stimulation frequency
- occ_norpa_gr66 - struct of NorpA+Gr28bd occupancy distributions and labels split by ATR(-/+)
- ent_int_gr66 - struct of Gr66a arm entry distributions and labels split by stimulation intensity
- ent_freq_gr66 - struct of Gr66a arm entry distributions and labels split by stimulation frequency
- ent_norpa_gr66 - struct of NorpA+Gr28bdarm entry distributions and labels split by ATR(-/+)
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| 960_fly_meta_data |
Contains the ExperimentData object from the 960 high-throughput tracking demonstration. Summary of items:
- expmt - ExperimentData object. See MARGO documentation for details.
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| raw_data_960_fly |
Contains binary raw data for centroids and time stamps from the 960 high-throughput tracking demonstration . Summary of items:
- centroids.bin - (nFlies x [x,y] x nFrames) raw centroid coordinates in single floating point precision
- time.bin - (nFrames x 1) raw time stamps formatted as inter-frame interval (in seconds) in single floating point precision
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Analysis, simulation, and visualization functions and scripts (MATLAB 2016a)
Download a .zip of all these scripts and functions. |
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inject_image_noise.m
plot_mean_injection_error.m |
Function: inject_image_noise.m
Description: converts each pixel of a binary image to TRUE at a uniform probabilty
Inputs:
- thresh_im - binary threshold image for foreground segementation (foreground = TRUE)
- noise_level - probability of converting any given pixel (0-1)
Outputs:
- noise_im - binary threshold image with added noise
Script: plot_mean_injection_error.m
Description: plots total mean centroid error relative to a ground truth sample
Data: noise_injection_error_data.mat
Additional details in the top line comments |
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shift_reference.m
reference_shift_triggered_averaging.m |
Function: shift_reference.m
Description: shifts the background reference image 2 pixels in a random direction
Inputs:
- trackDat - Frame to frame tracking data (including bg reference)
- expmt - MARGO ExperimentData meta data container
Outputs:
- shifted bg reference (trackDat.ref.im)
- time since reference shift (expmt.shift.t)
- updated list of indices of frame shifts (expmt.shift.idx)
Script: reference_shift_triggered_averaging.m
Description: calculates and plots average tracking error triggered in a short (2s) window around the
the reference shift. Error is calculated relative to a ground truth sample with the reference unshifted
Data: reference_shift_simulation_data.mat
Additional details in the top line comments |
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calculate_margo_to_ctrax_error.m |
Script: calculate_margo_to_ctrax_error.m
Description: calculates and aggregates the error between centroid coordinates obtained with MARGO and Ctrax.
Plots a density estimate of the total error between the two samples.
Data: margo_ctrax_comparison_centroids.mat
Additional details in the top line comments |
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tile_single_roi_vid.m
| Function: tile_single_roi_vid.m
Description: replicates an sample video of a single ROI up to an M x N tiling
Inputs:
- vid_path - file path to a single ROI sample video to tile. A sample is provided in (sample_roi_vid.avi)
- ntiles - (1 x 2) array of M rows and N columns to tile the sample
Outputs:
- saves the tiled video under the current directory in "tiled_roi_sample.avi"
Additional details in the top line comments |
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LED_ymaze_plot_pairdots.m
| Function: LED_ymaze_plot_pairdots.m
Description: plots LED Y-maze individual animal averages grouped by whether the light
appeared to the right or left of the choice point
Data: LED_ymaze_individual_trial_data.mat
Additional details in the top line comments |
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generate_optomotor_null_model.m
| Script: generate_optomotor_null_model.m
Description: Creates an identical individuals null model distribution by bootstrapping
all individual trial data
Data: optomotor_bootstrap_data.mat
Function: opto_bootstrap_all.m
Description: bootstrap resamples individual optomotor trial data up to the number
of individuals in the observed data set (with randomly sampled observed trial numbers for each individual)
Inputs:
- all_stim_delta - (nFlies) cell array of arrays of total angular distance traveled in the direction of stimulus rotation in each trial
- all_raw_delta - (nFlies) cell array of arrays of total angular distance traveled in each trial
Outputs:
- null_data - individual average optomotor indices from bootstrapped data
- obs_data - individual average optomotor indices from observed data
Additional details in the top line comments |
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kde_plots_960_fly.m |
Script: kde_plots_960_fly.m
Description: Generate log speed kernel density estimates for individual flies
process the speed data to regenerate the raw speed data and extract speed
bouts.
Data: meta_data_960_fly.mat, raw_data_960_fly.zip
Additional details in the top line comments |
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raw_speed_plot_960_fly.m |
Script: raw_speed_plot_960_fly.m
Description: Generates summary representations from the raw speed data
from the complete raw data found in '960_fly_raw_data.zip'.
Data: meta_data_960_fly.mat, raw_data_960_fly.zip
Additional details in the top line comments |