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Data & code for Zhang, Huang, Nörenberg & Arrenberg 2020

This repository contains data and code for our 2021 manuscript "A robust receptive field code for optic flow detection and decomposition during self-motion" by Zhang, Huang, Nörenberg & Arrenberg. The corresponding author is Aristides B. Arrenberg.

Prerequisites:

Code was developed and tested in MATLAB version 2021b. The content of this package can be placed anywhere on your MATLAB path.

Please add all files in the data and bin folders to the Matlab search path before running any scripts by:

Go to the Home tab → click Set Path
Click Add with Subfolders and select the data and bin folder
Click save and close.

The "code" folder:

This folder contains the Matlab functions/classes used in the Matlab scripts in the figure scripts folder.

imread_big.m: An open-source matlab function for loading large multipage TIFF file, published by user "Tristan Ursell" on MATLAB Central.

The "data" and "figure script" folders:

The data and figure script folders contains the required processed data and the Matlab live scripts (.mlx) respectively for reproducing figures and supplementary figures in the manuscript. The plotting scripts load the processed data by their hard-coded relative path.

The subfolder raw Ca Data in the data folder contains an example raw calcium imaging TIFF file and the corresponding text file for stimulus-recording timeline synchronization for the demonstration file for calcium preprocessing, ca_prep_demo.mlx .

License:

Data

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

Software

All files in the code and figure scripts folder will be published under Creative MIT license (see the LICENSE file in the code folder).

datacite.yml
Title	The perception of optic flow is essential for any visually guided behavior of a moving animal. To mechanistically predict behavior and understand the emergence of self-motion perception in vertebrate brains, it is essential to systematically characterize the motion receptive fields (RFs) of optic flow processing neurons. Here, we present the fine-scale RFs of thousands of motion-sensitive neurons studied in the diencephalon and the midbrain of zebrafish. We found neurons that serve as linear filters and robustly encode directional and speed information of translation-induced optic flow. These neurons are topographically arranged in pretectum according to translation direction. The unambiguous encoding of translation enables the decomposition of translational and rotational self-motion information from mixed optic flow. In behavioural experiments, we successfully demonstrated the predicted decomposition in the optokinetic and optomotor responses. Together, our study reveals the algorithm and the neural implementation for self-motion estimation in a vertebrate visual system.
Authors	Zhang,Yue;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany Huang,Ruoyu;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany Nörenberg,Wiebke;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany Arrenberg,Aristides B.;University of Tübingen, Werner Reichardt Centre for Integrative Neuroscience and Institute of Neurobiology, 72076 Tübingen, Germany;ORCID:0000-0001-8262-7381
License	MIT license (https://creativecommons.org/licenses/by-nc-sa/4.0/)
References	Zhang, Y., Huang, R., Nörenberg, W., & Arrenberg, A. (2021). A robust receptive field code for optic flow detection and decomposition during self-motion. bioRxiv. [https://doi.org/10.1101/2021.10.06.463330] (IsSupplementTo) Zhang, Y., Huang, R., Nörenberg, W., & Arrenberg, A. A robust receptive field code for optic flow detection and decomposition during self-motion (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 Zebrafish Receptive field Visual motion integration Optic flow decomposition Matched filter algorithm Opotmotor responses Optokinetic responses visually guided behaviour Diencephalon
Resource Type	Dataset

README.md