DOI: 10.5061/dryad.4qrfj6qm8
title: Larval salamander retinal population data in response to natural movies from the Chicago Motion Database

description: Everything that the brain sees must first be encoded by the retina, which
 maintains a reliable representation of the visual world in many different,
 complex natural scenes while also adapting to stimulus changes. This study
 quantifies whether and how the brain selectively encodes stimulus features
 about scene identity in complex naturalistic environments. While a wealth
 of previous work has dug into the static and dynamic features of the
 population code in retinal ganglion cells, less is known about how
 populations form both flexible and reliable encoding in natural moving
 scenes. We record the larval salamander retina responding to five
 different natural movies, over many repeats and use these data to
 characterize the population code in terms of single-cell fluctuations in
 rate and pairwise couplings between cells. Decomposing the population code
 into independent and cell-cell interactions reveals how broad scene
 structure is encoded in the retinal output. while the single-cell activity
 adapts to different stimuli, the population structure captured in the
 sparse, strong couplings is consistent across natural movies as well as
 synthetic stimuli. We show that these interactions contribute to encoding
 scene identity. We also demonstrate that this structure likely arises in
 part from shared bipolar cell input as well as from gap junctions between
 retinal ganglion cells and amacrine cells.
description: <strong>Neural data</strong> Voltage traces from the
 output, retinal ganglion cell layer of a larval tiger salamander retina
 were recorded following the methods outlined in O. Marre et al., Mapping a
 complete neural population in the retina. J. Neurosci. 32, 14859–14873
 (2012). In brief, the retina was isolated in darkness and pressed against
 a 252-channel multielectrode array. Voltage recordings were taken during
 stimulus presentation of both natural movies and white noise stimuli and
 spike-sorted using an automated clustering algorithm that was hand-curated
 after initial template clustering and fits. This technique captured a
 highly overlapping neural population of 93 cells that fully tiled the
 recorded region of visual space. Spike times were binned at 16.667ms for
 all analyses presented. <strong>Visual
 stimuli</strong> A white noise checkerboard stimulus (with binary
 white and black squares) was played at 30 frames per second (fps) for 30
 minutes prior to and after the natural scene stimuli. Five different
 natural movies lasting 20 seconds were played in a pseudorandom order, and
 each was displayed a minimum of 80 times. The movies labeled tree, water,
 grasses, fish, and self-motion were repeated 83, 80, 84, 91, and 85 times,
 respectively. All natural scenes except for the tree stimulus were
 displayed at 60fps. The tree stimulus was updated at a rate of 30fps with
 each frame repeated twice to match the 60fps frame rate of the other
 movies.  In all movies, the cells significantly
 increase their firing rates in the first 200 ms following the switch to a
 new stimulus. This is followed by a rapid decay back to a baseline firing
 rate. This is likely due to a strong population response to abrupt changes
 in luminance within their receptive fields. In subsequent analysis, we
 exclude the first 500ms of every trial to isolate the more steady-state
 response of the retina to scene-specific features and dynamics.
description: # Larval salamander retinal population data in response to natural movies
 from the Chicago Motion Database
 [https://doi.org/10.5061/dryad.4qrfj6qm8](https://doi.org/10.5061/dryad.4qrfj6qm8) ## Description of the data and file structure This data is described in the 2024 paper "Stimulus-invariant aspects of the retinal code drive discriminability of natural scenes". If this data is used for a publication, please cite that paper. The file contains the following files: \- MultipleMoviesStim_1_tree.avi \- MultipleMoviesStim_2_water.avi \- MultipleMoviesStim_3_grasses.avi \- MultipleMoviesStim_4_fish.avi \- MultipleMoviesStim_5_opticflow.avi \- movieBinnedSpiking.mat \- binaryCheckerboard.mat All of the .avi files are the movie stimulus that was shown to the salamander retina as described in our publication. The file "binaryCheckerboard.mat" contains three variables: the samplingFreq (the frequency of the response and stimulus timescales measured in hertz), binaryCheckerboard (a 93x120289 matrix corresponding to the binarized neural response of each of the 93 cells to each frame of the checkerboard stimulus), and stimulusFrames (a 40x40x120289 matrix corresponding to the actual checkerboard stimulus). Specifically, the i'th frame of the stimulus is stimulusFrames(:,:,i) and the response of the j'th neuron to the i'th frame is binaryCheckerboard(j,i). The file "movieBinedSpikes.mat" contains the following variables: \- movnames, which contains the names of each of the five movies in order \- ncell, the number of cells we took recordings from (93) \- nmov, the number of movies in the dataset (5) \- nreps, the number of reps for each of the movies \- samplingfreq, the sampling frequency of the data described here (Hz) \- binned, a matrix that contains the binarized responses from each cell to the movie stimuli. The data corresponding to the i'th movie is binned(1:nreps(i), :, :, i). The responses of the j'th neuron to the i'th movie are binned(1:nreps(i),:,j,i). ### Files and variables #### File: movieBinnedSpiking.mat **Description:** MatLab file containing the binned, binary spikes from the population. ##### Variables * see above #### File: binaryCheckerboard.mat **Description:** The stimulus used for receptive field mapping ##### Variables * see above #### File: MultipleMoviesStim\_1\_tree.avi **Description:** natural movie of a tree blowing in the wind #### File: MultipleMoviesStim\_4\_fish.avi **Description:** natural movie of fish swimming in a tank with real plants #### File: MultipleMoviesStim\_5\_opticflow\.avi **Description:** natural movie of a leafy woods scene, with a camera moving through the underbrush #### File: MultipleMoviesStim\_3\_grasses.avi **Description:** natural movie of a stand of tall grasses blowing in the wind #### File: MultipleMoviesStim\_2\_water.avi **Description:** natural movie of water flowing through a small canal