README.md 2.4 KB
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.
The "manuals" folder:
This folder contains a PDF on the mathematical principles used in constructing and programming our spherical arena. It was originally intended to provide new lab members a self-contained introduction to these ideas, and is thus written in the style of a manual for undergraduates.
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).