Anatomical organization of temporally correlated neural calcium activity in the hippocampal CA1 region

Data repository for the publication "Anatomical organization of temporally correlated neural calcium activity in the hippocampal CA1 region"

*Fig_3_barrier is Ai163 mouse line with endogenous calcium fluorescence expression, all other datasets use AAV1-CaMKII-GCaMP6f-WPRE-SV40 to induce calcium fluorescence

Data format:
- for each mice, it contains a neuronIndividuals_new.mat, ConcatenatedNeuronRecording.avi, and behav.mat

neuronIndividuals_new.mat: 1x6 cell.
- Each cell represent the CNMF-E extracted neuron data for the corresponding trial:
- C: denoised calcium data. Each row represent the calcium trace of a single neuron
- C_raw: un-denoised calcium data.
- S: deconvoluted calcium spike train. Each row represent the spike train of a single neuron
- A: neuron footprint. Each column represent the footprint of a single neuron, use reshape(A(:,i), 240,376) to resotre the footprint
- Coor: outer boundary of each individual neurons
- Cn: Original recording ROI enhanced by autocorrelation
- time: timestamp of calcium signal

behav.mat: 1x6 cell
- behavior data of each trial, corresponds to the neuronIndividuals_new.mat
- position: trajectory of mouse in trial
- time: timestamp of position

background:
Hippocampal CA1 neuronal ensembles generate sequential patterns of firing activity that contribute to episodic memory formation and spatial cognition. Here we use in vivo calcium imaging to record neural ensemble activities in mouse hippocampal CA1 and identify CA1 excitatory neuron sub-populations whose members are active across the same second-long period of time. We identified groups of hippocampal neurons sharing temporally correlated neural calcium activity during behavioral exploration, and found that they also organized as clusters in anatomical space. Such clusters vary in membership and activity dynamics with respect to movement in different environments, but also appear during immobility in the dark suggesting an internal dynamic. The strong covariance between dynamics and anatomical location within the CA1 sub-region reveals a previously unrecognized form of topographic representation in hippocampus that may guide generation of hippocampal sequences across time and therefore organize the content of episodic memory.

本数据集为发表论文《海马CA1区时间相关性神经钙活动的解剖组织特性》的配套数据仓库。
其中Fig_3_barrier对应携带内源性钙荧光表达的Ai163小鼠品系，其余所有数据集均采用AAV1-CaMKII-GCaMP6f-WPRE-SV40载体诱导钙荧光表达。

数据格式：
每只小鼠对应三组数据文件：neuronIndividuals_new.mat、ConcatenatedNeuronRecording.avi与behav.mat。

1. neuronIndividuals_new.mat：为1×6元胞数组，每个元胞对应一次实验经CNMF-E提取的神经元数据：
- C：去噪后的钙信号数据，每一行代表单个神经元的钙活动轨迹
- C_raw：未经过去噪处理的原始钙信号数据
- S：反卷积得到的钙信号锋电位（spike）序列，每一行代表单个神经元的锋电位序列
- A：神经元足迹，每一列代表单个神经元的足迹，可通过reshape(A(:,i), 240, 376)还原该足迹
- Coor：单个神经元的外边界坐标
- Cn：经自相关增强后的原始记录感兴趣区（Region of Interest, ROI）
- time：钙信号的时间戳

2. behav.mat：为1×6元胞数组，存储各次实验的行为数据，与neuronIndividuals_new.mat中的实验一一对应：
- position：小鼠在对应实验中的运动轨迹
- time：位置数据的时间戳

数据集背景：
海马CA1区神经元集群可产生连续的放电活动模式，该过程参与情景记忆形成与空间认知。本研究通过在体钙成像技术记录小鼠海马CA1区的神经元集群活动，鉴定出CA1区兴奋性神经元亚群，其成员在相同的秒级时间段内同步激活。研究团队鉴定出在行为探索过程中存在时间相关性神经钙活动的海马神经元集群，并发现这些集群在解剖空间中同样呈簇状分布。此类集群的成员组成与活动动态会随小鼠所处环境的不同发生变化，同时在黑暗环境下的静止状态中也可观测到，提示其存在内在动态特性。CA1亚区内神经元活动动态与解剖位置间存在强相关性，这揭示了海马中此前未被发现的拓扑表征形式，该表征可指导跨时间的海马序列生成，进而组织情景记忆的内容。