DOI: 10.5061/dryad.v9s4mw6qx
title: From behavior to circuit modeling of light-seeking navigation in zebrafish larvae

description: Bridging brain-scale circuit dynamics and organism-scale behavior is a
 central challenge in neuroscience. It requires the concurrent development
 of minimal behavioral and neural circuit models that can quantitatively
 capture basic sensorimotor operations. Here we focus on light-seeking
 navigation in zebrafish larvae. Using a virtual reality assay, we first
 characterize how motor and visual stimulation sequences govern the
 selection of discrete swim-bout events that subserve the fish navigation
 in the presence of a distant light source. These mechanisms are combined
 into a comprehensive Markov-chain model of navigation that quantitatively
 predict the stationary distribution of the fish’s body orientation under
 any given illumination profile. We then map this behavioral description
 onto a neuronal model of the ARTR, a small neural circuit involved in the
 orientation-selection of swim bouts. We demonstrate that this
 visually-biased decision-making circuit can similarly capture the
 statistics of both spontaneous and contrast-driven navigation.
description: Data acquisition and pre-processing are described in the
 associated manuscript, which can be found at:
 https://www.biorxiv.org/content/10.1101/810960v1
description: Contains Data and Matlab codes for analysis of orientational
 light-seeking behavior experiments analysis Data
 Pooled Folder 'Data_pooled' contains matlab
 datafiles with the sequences of navigation under different modalities (see
 below). Each line is one trajectory. AngleSource is the fish's body
 angle to the virtual light source, expressed in radian. AngleLab is the
 fish's body angle in the frame of reference of the laboratory. xCoord
 and yCoord are the fish center of mass position expressed in pixel size
 (11,5 px = 1mm). Time of bout (TimeBout) is measured from the onset of the
 recording sequence, in seconds. FishN is the number of individual
 fish. Different modalities : - No
 stimulus (Figure 1) :<br>   
  'spontaneous_swim.mat'<br> -
 Stereo-visual/Contrast-driven orientational phototaxis (Figure 2)
 :<br>     'lateralized_exps.mat'<br> - Temporal
 orientational phototaxis (Figure 3) :<br>   
  'temporal_exps.mat'<br> - Temporal orientational
 phototaxis with enucleated fish (Figure 3 supplement) :<br>   
  'enucleated_exps.mat' Programs
 Folder 'Programs' contains matlab scripts and functions
 in following folders: - Matlab routines used to analyse
 the fish trajectories in no stimulus (Figure 1) modality:<br>   
  'Spontaneous'<br> - Matlab routines used to analyse the
 fish trajectories in stereo-visual/Contrast-driven orientational
 phototaxis (Figure 2) modality :<br>   
  'Lateralized'<br> - Matlab routines used to analyse the
 fish trajectories in temporal orientational phototaxis (Figure 3)
 :<br>     'Temporal'  <br> - Matlab routines used to
 analyse the fish trajectories in temporal orientational phototaxis with
 enucleated fish (Figure 3 supplement) :<br>   
  'Enucleated'<br> - Matlab routines used to analyse the
 fish trajectories for behavioral (biased) random walk simulations (Figure
 4) :<br>     'Simulations/BehavioralModel'<br>
 - Matlab routines used to analyse the fish trajectories for neural model
 simulations (Figure 5) :<br>   
  'Simulations/NeuralModel'