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larkumlab
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Bergmann_2022_DataRepository
DOI
10.12751/g-node.j9wxqe
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01_data
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02_whisker-tracking @ cf386c40b5 d8aa0ab8aa update sub-repositories 2 anni fa
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README.md

Datasets

schematics of the flow of analysis

  • 01_raw: the raw data being analyzed:
    • top-view videos (top): AVI files taken at 200 Hz using ZR View (a custom video acquisition software) under the near-UV lighting, trial-based.
    • eye videos (left-eye and right-eye): AVI files taken at 100 Hz using PylonPD (a custom video acquisition software) under the IR-lighting, trial-based.
    • behavioral annotation (states): CSV files containing manual annotation of behavioral states based on the top-view videos, trial-based.
  • 02_whisker-tracking: whisker tracking data based on the top-view videos, using the videobatch python module:
    • maximal projections (projection): PNG files containing a maximal projection of top-view video frames from each single trial.
    • ROIs (ROI): PNG files representing the mask for ROIs generated from the maximal projection images. These ROIs were used for the subsequent tracking.
    • color-tracking mask videos (mask): MP4 files containing color masks generated by color-tracking procedure of videobatch.
    • tracked whisker positions (result): CSV files containing the center-of-mass positions of tracked whiskers (in pixels).
  • 03_eye-tracking: CSV files containing information about eye- and pupil-tracking based on the eye videos, using DeepLabCut and fitting2d.
  • 04_formatted: the data being used for analysis. Includes a set of videos where the eye videos and behavioral annotations are aligned and overlaid on top of the top-view videos (video quality is not so high).
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) [] (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) [] (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) [] (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) [] (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) [] (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