Neural mechanisms to incorporate visual counterevidence in self movement estimation
Data files
Oct 30, 2023 version files 13.80 GB
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counterevidence_data_upload.zip
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README.md
Abstract
In selecting appropriate behaviors, animals should weigh sensory evidence both for and against specific beliefs about the world. For instance, animals measure optic flow to estimate and control their own rotation. However, existing models of flow detection can be spuriously triggered by visual motion from external movements. Here, we show that stationary patterns on the retina, which constitute evidence against observer rotation, suppress inappropriate stabilizing rotational behavior in the fruit fly Drosophila. In silico experiments show that artificial neural networks that are optimized to distinguish observer movement from object motion similarly detect stationarity and incorporate negative evidence. Employing neural measurements and genetic manipulations, we identified components of the circuitry for stationary pattern detection, which runs parallel to the fly’s local motion- and optic flow-detectors. Our results show how the fly brain incorporates negative evidence to improve heading stability, exemplifying how a compact brain exploits geometrical constraints of the visual world.
README: Data for: Neural mechanisms to incorporate visual counterevidence in self movement estimation
Folder structure
scripts
The easiest way to explore the data is to run the .m scripts under thescripts
folder. Each script loads .mat files in thedata
holder and replicates plots in the paper showing behavioral and physiological data. The folder contains following scripts, with corresponding figure panels:fig1_01_basic.m
: Figure 1G-Lfig1_02_bar.m
: Figure 1PQfig1_03_orientation.m
: Figure 1ST, S1BCfig1_04_movingwindow.m
: Figure S1EFfig1_05_onset.m
: Figure 1VW, S1G-Jfig3_sweeps.m
: Figure 3 (all panels)fig4_01_T4T5.m
: Figure 4EF, S3ABfig4_02_LPTC.m
: Figure 4GH, S3CDfig5_transfer.m
: Figure 5 (all panels)fig6_01_screen_distplot.m
: Figure 6A, S4Afig6_02_replication.m
: Figure 6B, S4Bfig6_03_NTsplit.m
: Figure S4Dfig7_mi4.m
: Figure 7A-D
The generated figure panels will be automatically saved into
figtada/scripts
.data
Data loaded by the scripts are stored here as .mat file. Each .mat file contains cell arrays typically called "data", corresponding to a single batch of animals went through the identical experimental protocol (i.e., a set of visual stimuli). Each "data" cell array holds "analysis" objects, which is a structure array. If a single "data" cell array contains multiple "analysis" objects, they represent different preprocessing parameters (e.g., averaging mirror symmetric pairs of stimulus conditions or not, or selection for different functionally identified cell types in imaging experiments). An analysis object always has following fields:respMatPlot
: A matrix containing time traces of behavioral and physiological measures, averaged across flies. For behavioral experiments, this will be a 3D matrix of time x stimulus type (epoch) x {turning speed (deg/s), normalized walking speed}. For imaging experiments, this will be a 2D matrix of time x stimulus type (epoch), and the unit is ΔF/F.respMatSemPlot
: A matrix containing standard error of the mean (SEM) associated withrespMatPlot
. The structure of the matrix is the same asrespMatPlot
.timeX
: A vector containing timestamps relative to the stimulus onsets in milliseconds. The length oftimeX
is identical to the size of the first dimension ofrespMatPlot
.indFly
: A cell array containing data from individual flies before averaging. Each cell inindFly
corresponds to individual fly. Each cell has several fields named likepX_
. Under each of thesepX_
field, there is a subfield namedsnipMat
, which is a 2D cell array with the dimension order of stimulus type (epoch) x ROIs. Each cell ofsnipMat
contains a matrix with the dimension order of time x repetitions x data type (data type is either turning or forward walking in behavioral experiment, and ΔF/F in imaging experiment). Most of the preprocessing steps simply averages time traces over different dimensions (e.g., repetitions of the same stimulus, different ROIs) and the size of those averaged dimension will become 1 after that processing step. If you are interested in examining the most raw form of the data, the best way to do so is to look atp1_snipMat.snipMat
underindFly
.> Note that, because our analysis pipeline is set up such that it can perform same analysis on both behavioral and imaging data, some features are only relevant to one but not to the other (for example,"averageRoi" step does nothing for behavioral data, and "normalizedWaling" does nothing for imaging data). Also, some of the preprocessing steps are toggled OFF in some analysis (i.e., the existence of "combinedOpposites" field in indFly cell does not necessarily mean that averaging over mirror symmetric versions of stimuli happened in that particular analysis object).
> In addition to
snipMat
, eachpX_
field containsname
string, which is the name of the corresponding preprocessing step.p1_snipMat
containsflyResp
, which is a matrix of raw time traces before cutting out trial-wise snippets.epochList
is a matrix with the same length asflyResp
, which represents temporal ordering of the stimulus epochs presented.epochDurations
are a vector containing the duration of each epoch (in the unit of frames, which is 60 Hz in behavioral experiments and imaging frame rate in imaging experiments).shiftedEpochStartTimes
is a cell array that contains the starting time points of each trial-wise data snippet insnipMat
.normalizedWalking
contains a fieldwalkRespDuringnterleave
, which is the walking speed during the period immediately preceding the stimulus onset, to which the walking speed during stimulus presentation is normalized to (see Methods in the paper for details).
data
folder contains following .mat files and a folder, which correspond one-to-one to scripts inscripts
folder.
*fig1_01_basic.mat
: Behavioral data from wild type flies presented with rotational and translational version of the "islands of motion" stimuli (Figure 1E, J).
*fig1_02_bar.mat
: Behavioral data from wild type flies presented with fast moving bars over different background patterns (Figure 1Q).
*fig1_03_orientation.mat
: Behavioral data from wild type flies presented with the islands of motion stimuli with either horizontal, vertical, or 2D patterns (Figure 1R, S1A).
*fig1_04_movingwindow.mat
: Behavioral data from wild type flies presented with the islands of motion stimuli with either stationary or moving windows (Figure S1D).
*fig1_05_onset.mat
: Behavioral data from wild type flies presented with the islands of motion stimuli where the onset of rotation of background patterns was delayed. This file contains data from two batches of flies (i.e., two 'data' cell arrays) that were presented with stimuli in Figure 1U and Figure S1I.
*fig3_sweeps.mat
: Behavioral data from wild type flies presented with variants of the islands of motion stimuli for stimulus parameter sweeps. This file contains data from multiple batches of flies (i.e., multiple 'data' cell arrays) corresponding to each of the figure panels (Figure 3A for contrast sweep, Figure 3B for background fraction sweep, Figure 3C for velocity sweep, Figure 3D for frequency sweep, Figure 3E for wavelength sweep, and Figure 3FG for contrast/luminance sweep).
*fig4_01_T4T5.mat
: Calcium imaging data from T4/T5 neurons presented with the modified island of motion stimulus (Figure 4D). Because T4/T5 neurons and their subtypes were labeled by the identical driver Gal4 line, we classified each ROI into specific subtypes based on their response to the probe stimuli (see Table S4). The 'data' cell array in this file has four cells corresponding to T4a, T4b, T5a, T5b subtypes.
*fig4_02_LPTC.mat
: Calcium imaging data from LPTCs presented with the islands of motion stimulus. This file contains five 'data' cell arrays each corresponding to one of five cell types studied (HS, CH, H2, Hx, FD1).
*fig5_transfer.mat
: Behavioral data from wild type flies presented with the "split screen" stimuli to probe inter-ocular transfer of the suppression of the optomotor response by stationary patterns.
*fig6
: This directory contains .mat files containing behavioral data for behavioral-genetic screening experiments in Figure 6 and Figure S4. Each .mat file contains a pair of 'data' cell array corresponding to the Gal4>UAS flies and corresponding Gal4/+ controls. The data files are sorted into three subdirectories (screen
,replication
,r13e12
), each corresponding to Figure 6A (initial screening), 6B (replication), and S4D (R13E12 split Gal4 screening).
*fig7_mi4.mat
: Calcium imaging data from Mi4 neurons presented with full-field checkerboard patterns.> In our imaging experiments, cells / regions of interests were selected based on their consistent or desired responses to the probe stimuli, as detailed in the Method section of the paper. Imaging data .mat files (
fig4
andfig7
) containdata_nonselected
structure (in addition todata
), where this selection process is not performed.utilities
The utility functions for data analysis and visualization used by the scripts are here.
Requirements
The scripts are written in Matlab 2019b, and use functions from Statistics and machine learning toolbox.
Methods
This dataset contains all experimental data necessary to create figures in Tanaka et al. (2023), as well as scripts to analyze them. The scripts are written in Matlab 2019b, and uses some functions from Statistics and Machine Learning Toolbox.