Larval salamander retinal population data in response to natural movies from the Chicago Motion Database

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 activit..., Neural data 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. Visual stimuli 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 m..., , # 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 ...大脑所感知的一切视觉信息，首先都需经由视网膜进行编码。视网膜不仅能在多样且复杂的自然场景中维持视觉世界的可靠表征，同时还能自适应刺激的变化。本研究量化分析了大脑在复杂自然环境中，是否以及如何选择性编码与场景标识相关的刺激特征。尽管既往已有大量研究深入探究了视网膜神经节细胞（retinal ganglion cells）群体编码的静态与动态特征，但对于群体如何在自然动态场景中实现兼具灵活性与可靠性的编码，目前仍所知甚少。我们对虎纹螈幼体视网膜进行多次重复记录，使其响应五种不同的自然影片，并以单细胞放电率波动及细胞间成对耦合为指标，对群体编码特征进行表征。将群体编码拆解为独立分量与细胞间交互作用后，可揭示大范围场景结构如何在视网膜输出信号中得到编码。而单细胞激活…… **神经数据**：本研究遵循O. Marre等人于2012年发表于《Journal of Neuroscience》第32卷14859–14873页的《Mapping a complete neural population in the retina》一文所述方法，对虎纹螈幼体视网膜神经节细胞层的输出电位进行记录。简言之，实验在黑暗环境中分离视网膜，并将其贴附于252通道多电极阵列之上。在自然影片与白噪声刺激呈现期间同步采集电位信号，并通过自动聚类算法完成峰电位（spike）分选，初始模板聚类与拟合完成后还需人工对结果进行校验。该技术成功捕获了覆盖全部记录视觉空间的93个高度重叠的神经元群体。本研究所有分析均将峰电位时间以16.667ms为间隔进行分箱处理。 **视觉刺激**：在自然场景刺激呈现前后，均会播放时长30分钟的白噪声棋盘格刺激（由黑白二进制方块组成），播放帧率为30帧每秒（fps）。五种不同的自然影片…… # 虎纹螈幼体视网膜群体响应芝加哥运动数据库中自然影片的记录数据 数据集链接：https://doi.org/10.5061/dryad.4qrfj6qm8 ## 数据与文件结构说明 本数据相关研究发表于2024年论文"Stimulus-invariant aspects of the retinal code drive discriminability of natural scenes"。若将本数据用于学术发表，请引用该论文。 本数据集包含以下文件： - MultipleMoviesStim_1_tree.avi - MultipleMoviesStim_2_water.avi - MultipleMoviesStim_3_grasses.avi - MultipleMoviesStim_4_fish.avi - MultipleMoviesStim_5_opticflow.avi - movieBinnedSpiking.mat - binaryCheckerboard.mat 所有.avi文件均为本研究中用于呈现给蝾螈视网膜的影片刺激。文件"binaryCheckerboard.mat"包含三个变量：samplingFreq（响应与刺激时程的测量频率，单位为赫兹）、binaryCheckerboard（……）