Hippocampal Representations Drift in Stable Multisensory Environments

This is the code and data repository for the Climer*, Davoudi*, Oh*, and Dombeck paper titled "Hippocampal representations drift in stable multisensory environments". Code was run in MATLAB 2024a Each folder contains the data for five days of recording for measurements of hippocampal representational drift. Data from 30 mice were included in the paper. Mouse 1-5 contains a folder called "Training ABFs", which contains the training and test day behavioral data. In the codebase, use "figure1e_d.m" to import and plot it. In each folder is a folder named "alignment". This contains subfolders with various data. CellReg - This contains the outputs of CellReg (https://github.com/zivlab/CellReg) and the results of the manual curation (curated_data.mat). mat - This contains the mat files for the data in each session. The fields are: corrected_ROIs: The aligned ROIs from CellReg F: The florescence traces (AU) Fc: The baseline corrected florescence (dfof) Fc3: The significant transients (dfof) fr: The sample rate (Hz) lapEpochs: The epochs of each lap lickBinned: The counts of licks in each frame mi: The mean imaging field ROIs: The ROI masks s: The deconvolved signal spks: The thresholded deconvoled signal analysis - Contains the data for the Analysis class in the codebase. Each file is formatted for the particular analysis. For more information, refer to the docs for a particular function in the "Analysis" folder in the code base.本仓库为Climer*、Davoudi*、Oh*与Dombeck团队发表于题为《稳定多感官环境中海马体表征漂移》的论文配套的代码与数据集。本代码基于MATLAB 2024a环境运行。 每个文件夹存储了对应小鼠5天的海马体表征漂移记录数据。本论文共纳入30只小鼠的实验数据。 小鼠1至5的文件夹中包含名为“Training ABFs”的子文件夹，其内存储了训练与测试阶段的行为学数据。在代码库中，可通过运行“figure1e_d.m”导入并可视化该数据。 每个小鼠文件夹中均包含名为“alignment”的子文件夹，其内存储各类细分数据集，具体包含以下三个子文件夹： 1. CellReg：存储CellReg（https://github.com/zivlab/CellReg）的输出结果，以及手动标注校正后的结果（curated_data.mat）。 2. mat：存储各实验会话的MAT格式数据文件，其包含的字段如下： - corrected_ROIs：经CellReg对齐后的校正感兴趣区域（ROI，Region of Interest） - F：荧光强度轨迹（单位：任意单位，AU） - Fc：经基线校正后的荧光信号（dfof，即ΔF/F0，荧光强度变化与基线荧光的比值） - Fc3：经dfof处理后得到的显著钙瞬变信号 - fr：成像采样率（单位：赫兹，Hz） - lapEpochs：每一轮跑动的时段标记 - lickBinned：每帧图像对应的舔舐次数统计 - mi：成像视野的平均信号 - ROIs：感兴趣区域掩膜 - s：反卷积后的钙信号 - spks：经阈值处理后的反卷积尖峰信号 3. analysis：存储代码库中Analysis类对应的分析数据。每个文件均针对特定分析任务进行格式适配。如需了解更多细节，请查阅代码库中“Analysis”文件夹内对应函数的文档。