Keisuke Sehara cde18baf20 describe analysis		2 år sedan
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datareader	33073240d8 add analysis	2 år sedan
01_asymmetry.ipynb	33073240d8 add analysis	2 år sedan
02a_prediction-analysis-ROC.ipynb	cde18baf20 describe analysis	2 år sedan
02b_prediction-analysis-perceptron.ipynb	33073240d8 add analysis	2 år sedan
03_saccades.ipynb	33073240d8 add analysis	2 år sedan
README.md	cde18baf20 describe analysis	2 år sedan
ROC.py	33073240d8 add analysis	2 år sedan
epoch_analysis.py	33073240d8 add analysis	2 år sedan
kw_dunn.py	33073240d8 add analysis	2 år sedan
saccades.py	33073240d8 add analysis	2 år sedan
trial_envelope.py	33073240d8 add analysis	2 år sedan

Analysis

The analysis code used in the study.

01_asymmetry: Plots and statistical analysis on whisker asymmetry and pupil positions under different behavioral states.
02a_prediction-analysis-ROC: ROC analysis of whisker asymmetry and pupil positions during the backward-running epoch.
02b_prediction-analysis-perceptron: Perceptron analysis of whisker asymmetry and pupil positions during the backward-running epoch.
03_saccades: Analysis of whisker asymmetry around saccades.

Dependencies

You will need Python ≥ 3.4 to run the code.

Package	Version used in the paper
`numpy`	1.18.1
`scipy`	1.4.1
`matplotlib`	3.1.3
`statsmodels` (used to run `kw_dunn.py`)	0.13.0
`pandas`	1.0.1
`scikit-learn` (only for 02b)	0.22.1
`sliding1d`	1.0

You can install all the packages via pip (assuming you have an appropriate version of python):

$ pip install numpy scipy matplotlib statsmodels pandas scikit-learn sliding1d

In case anything does not work, consider upgrading/downgrading the package that generates the error.

License

kw_dunn.py is based on the one being shared at https://gist.github.com/alimuldal/fbb19b73fa25423f02e8 . The authors of this repository do not claim any copyright.
For the other parts of the code (including packages and modules stored in this directory): so long as you cite {{the paper}} or this repository, you are free to reuse, remix, and/or redistribute for any purposes.

datacite.yml
Title	Data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack)
Authors	Bergmann,Ronny;Institut für Biologie, Humboldt Universität zu Berlin, Berlin, 10117 Germany. Sehara,Keisuke;Institut für Biologie, Humboldt Universität zu Berlin, Berlin, 10117 Germany.;ORCID:0000-0003-4368-8143 Dominiak,Sina E.;Institut für Biologie, Humboldt Universität zu Berlin, Berlin, 10117 Germany. Colomb,Julien;Institut für Biologie, Humboldt Universität zu Berlin, Berlin, 10117 Germany.;ORCID:0000-0002-3127-5520 Kremkow,Jens;Charité–Universitätsmedizin Berlin, Berlin, 10117 Germany.;ORCID:0000-0001-7077-4528 Larkum,Matthew E.;Institut für Biologie, Humboldt Universität zu Berlin, Berlin, 10117 Germany.;ORCID:0000-0001-9799-2656 Sachdev,Robert N.S.;Institut für Biologie, Humboldt Universität zu Berlin, Berlin, 10117 Germany.;ORCID:0000-0002-6627-0199
Description	Navigation through complex environments requires motor planning, motor preparation and the coordination between multiple sensory–motor modalities. For example, the stepping motion when we walk is coordinated with motion of the torso, arms, head and eyes. In rodents, movement of the animal through the environment is coordinated with whisking. Even head fixed mice navigating a plus maze position their whiskers asymmetrically with the bilateral asymmetry signifying the upcoming turn direction. Here we report that, in addition to moving their whiskers, on every trial mice also move their eyes conjugately in the direction of the upcoming turn. Not only do mice move their eyes, but they coordinate saccadic eye movement with the asymmetric positioning of the whiskers. Our analysis shows that asymmetric positioning of whiskers predicted the turn direction that mice will make at an earlier stage than eye movement. Consistent with these results, our observations also revealed that whisker asymmetry increases before saccadic eye movement. Importantly, this work shows that when rodents plan for active behavior, their motor plans can involve both eye and whisker movement. We conclude that, when mice are engaged in and moving through complex real-world environments, their behavioral state can be read out in the movement of both their whiskers and eyes.
License	Creative Commons 4.0 Attribution (https://creativecommons.org/licenses/by/4.0/)
References	Bergmann R, Sehara K, Dominiak SE, Kremkow J, Larkum ME, Sachdev RNS (2022) Coordination between eye movement and whisking in head fixed mice navigating a plus-maze. [] (IsSupplementTo)
Funding	EU, EU.670118 EU, EU.327654276 EU, EU.720270 EU, EU.785907 EU, EU.945539 DFG, DFG.250048060 DFG, DFG.246731133 DFG, DFG.267823436
Keywords	Neuroscience Behavioral tracking Motor coordination Whiskers Pupil tracking Airtrack
Resource Type	Dataset

README.md

Analysis

Dependencies

License