Keisuke Sehara 3f320fe067 update README on the analysis 2 gadi atpakaļ
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02a_prediction-analysis-ROC.ipynb cde18baf20 describe analysis 2 gadi atpakaļ
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03_saccades.ipynb 33073240d8 add analysis 2 gadi atpakaļ
README.md 3f320fe067 update README on the analysis 2 gadi atpakaļ
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epoch_analysis.py 33073240d8 add analysis 2 gadi atpakaļ
kw_dunn.py 33073240d8 add analysis 2 gadi atpakaļ
saccades.py 33073240d8 add analysis 2 gadi atpakaļ
trial_envelope.py 33073240d8 add analysis 2 gadi atpakaļ

README.md

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.;ORCID:0000-0002-1477-7502
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 Data repository for Bergmann R, Sehara K, Dominiak SE, Kremkow J, Larkum ME, Sachdev RNS, 2022 eNeuro "Coordination between eye movement and whisking in head fixed mice navigating a plus-maze". This repository contains the raw and the formatted data, code for generating figures, and some demo code to work with analysis python modules.
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. [https://doi.org/10.1523/ENEURO.0089-22.2022] (IsSupplementTo)
Bergmann R, Sehara K, Dominiak SE, Kremkow J, Larkum ME, Sachdev RNS (2022) Raw data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack) [https://doi.org/10.12751/g-node.g8f1jc] (HasPart)
Bergmann R, Sehara K, Dominiak SE, Kremkow J, Larkum ME, Sachdev RNS (2022) Whisker-tracking data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack) [https://doi.org/10.12751/g-node.s62hni] (HasPart)
Bergmann R, Sehara K, Dominiak SE, Kremkow J, Larkum ME, Sachdev RNS (2022) Eye-tracking data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack) [https://doi.org/10.12751/g-node.5jz67s] (HasPart)
Bergmann R, Sehara K, Dominiak SE, Kremkow J, Larkum ME, Sachdev RNS (2022) Formatted data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack) [https://doi.org/10.12751/g-node.hhxe3v] (HasPart)
Bergmann R, Sehara K, Dominiak SE, Kremkow J, Larkum ME, Sachdev RNS (2022) DeepLabCut model repository for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack) [https://doi.org/10.12751/g-node.1kd2qf] (HasPart)
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