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larkumlab
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Keisuke_Sehara_EyeTrackingModel
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10.12751/g-node.1kd2qf
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The DeepLabCut project for eye tracking. https://doi.org/10.1523/ENEURO.0089-22.2022

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README.md

Eye-tracking model

The DeepLabCut project for eye tracking for the "AirtrackMotorPlanning" project (examines whether whiskers and pupil positions predict the animal's motor plans).

The dataset stored here is part of the root data repository, and it is:

How to use

Install DeepLabCut before use.

We recommend using the following version:

$ git clone https://github.com/gwappa/DeepLabCut.git && cd DeepLabCut
$ git checkout v2.1.8ks
  1. Clone this repository.
    • probably you will also need to run gin get-content . inside the directory dlc-models/iteration-6 (but only the snapshot 1030000 will be needed).
  2. Modify the path in eyes-Keisuke-2019-12-08/config.yaml to match the actual situation.

Then the deeplabcut library can be used with eyes-Keisuke-2019-12-08.

License

Copyright (c) 2022, Ronny Bergmann, Keisuke Sehara, Sina E. Dominiak, Julien Colomb, Jens Kremkow, Matthew E. Larkum, Robert N. S. Sachdev, CC-BY 4.0

datacite.yml
Title DeepLabCut model repository 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 Model 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 DeepLabCut model to track (i) edges of the pupil, and (ii) the corners of the eye (not used in the later analysis).
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, Colomb J, Kremkow J, Larkum ME, Sachdev RN (2022) Data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack). G-Node. https://doi.org/10.12751/g-node.j9wxqe [https://doi.org/10.12751/g-node.j9wxqe] (IsPartOf)
Bergmann R, Sehara K, Dominiak SE, Colomb J, Kremkow J, Larkum ME, Sachdev RN (2022) Raw data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack). G-Node. https://doi.org/10.12751/g-node.g8f1jc [https://doi.org/10.12751/g-node.g8f1jc] (IsDerivedFrom)
Bergmann R, Sehara K, Dominiak SE, Colomb J, Kremkow J, Larkum ME, Sachdev RN (2022) Eye-tracking data for Bergmann, Sehara et al., 2022 eNeuro (eye-whisker coordination on Airtrack). G-Node. https://doi.org/10.12751/g-node.5jz67s [https://doi.org/10.12751/g-node.5jz67s] (Compiles)
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