Data and code for the 2020 manuscript "Gaze stabilisation behaviour is anisotropic across visual field locations in zebrafish" by Dehmelt, Meier, Hinz et al.

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README.md

Data & code for Dehmelt, Meier, Hinz et al. 2020

This repository contains data and code for our 2020 manuscript "Gaze stabilisation behaviour is anisotropic across visual field locations in zebrafish" by Dehmelt, Meier, Hinz et al. The corresponding author is Aristides B. Arrenberg.

Prerequisites:

Code was developed and tested in MATLAB version 2018b. Both older and newer version should be compatible. Running the code additionally requires the open-source cbrewer package published by user "Charles" on MATLAB Central, which implements custom colour maps by Cynthia Brewer. The content of this package can be placed anywhere on your MATLAB path. If you do not wish to use the cbrewer package, comment out all lines of code containing "cbrewer", and replace them with your preferred colour maps.

The "data" and "code" folders:

These contain pre-processed data in MAT files with structure arrays, and MATLAB code to reproduce all or parts of Figures 3-6, as well as Figure 3-figure supplement 5. Data file paths are relative to the code file paths, and are hard-coded as such in the M files; so the "data" and "code" folders should always be placed in the same location. If you want to download only some of the subfolders (e.g., only those pertaining to a single figure), make sure to nonetheless place them in two neighbouring folders called "data" and "code".

The "raw data examples" folder:

The repository also contains examples of raw data files (in the "raw data examples" folder), namely tab-separated TXT eye tracking data files. These match the conventions described in our published protocol, "Evoking and tracking zebrafish eye movement in multiple larvae with ZebEyeTrack" by Dehmelt et al., Nature Protocols 2018.

License:

Upon publication of the manuscript in a peer-reviewed journal, all files will be published under Creative Commons license CC BY-NC-SA 4.0 (see the LICENSE file above).

datacite.yml
Title Gaze stabilisation behaviour is anisotropic across visual field locations in zebrafish
Authors Dehmelt,Florian Alexander;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany;ORCID:0000-0001-6135-4652
Meier,Rebecca;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany
Hinz,Julian;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany
Yoshimatsu,Takeshi;Sussex Neuroscience, School of Life Sciences, University of Sussex, UK
Simacek,Clara A.;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany
Wang,Kun;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany
Baden,Tom;Sussex Neuroscience, School of Life Sciences, University of Sussex, UK
Arrenberg,Aristides B.;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany;ORCID:0000-0001-8262-7381
Description Many animals have large visual fields, and sensory circuits may sample those regions of visual space most relevant to behaviours such as gaze stabilisation and hunting. Despite this, relatively small displays are often used in vision neuroscience. To sample stimulus locations across most of the visual field, we built a spherical stimulus arena with 14,848 independently controllable LEDs, measured the optokinetic response gain of immobilised zebrafish larvae, and related behaviour to previously published retinal photoreceptor densities. We measured tuning to steradian stimulus size and spatial frequency, and show it to be independent of visual field position. However, zebrafish react most strongly and consistently to lateral, nearly equatorial stimuli, consistent with previously reported higher spatial densities in the central retina of red, green and blue photoreceptors. Upside-down experiments suggest further extra-retinal processing. Our results demonstrate that motion vision circuits in zebrafish are anisotropic, and preferentially monitor areas with putative behavioural relevance.
License Creative Commons CC BY-NC-SA 4.0 International (Attribution-NonCommercial-ShareAlike) (https://creativecommons.org/licenses/by-nc-sa/4.0/)
References Dehmelt FA, Meier R, Hinz J, Yoshimatsu T, Simacek CA, Wang K, Baden T, Arrenberg AB (2020). Gaze stabilisation behaviour is anisotropic across visual field locations in zebrafish [doi:10.1101/754408 ] (IsSupplementTo)
Dehmelt FA, Meier R, Hinz J, Yoshimatsu T, Simacek CA, Wang K, Baden T, Arrenberg AB. Gaze stabilisation behaviour is anisotropic across visual field locations in zebrafish (in review) [DOI t.b.d.] (IsSupplementTo)
Funding Deutsche Forschungsgemeinschaft (DFG) grant EXC307 (CIN – Werner Reichardt Centre for Integrative Neuroscience)
Human Frontier Science Program (HFSP) Young Investigator Grant RGY0079
Keywords Neuroscience
optokinetic response
OKR gain
zebrafish
zebrafish larvae
visual stimulus
visual field
retinal photoreceptors
retina
stimulus tuning
stimulus size
temporal frequency
spatial frequency
behaviour
stimulus hardware
spherical
asymmetry
area centralis
yoking
Resource Type Dataset