Mouse CA1 Calcium Imaging and Behavioural Dataset in 3x3 Geometric Morph Paradigm

The following dataset was collected by Dr. J. Quinn Lee, Dr. Alexandra T. Keinath, and Erica Cianfarano in the laboratory of Dr. Mark P. Brandon. All methods and details are described in the original research article reporting these data published in Neuron: Lee, Keinath, Cianfarano, and Brandon (2025) Identifying representational structure in CA1 to benchmark theoretical models of cognitive mapping. Any use of the following dataset must cite the original publication in Neuron. The code base to reproduce all analyses and figures can be found at: https://github.com/jquinnlee/georepca1

The dataset (Python joblib files or MATLAB .mat files in the zipped "data" folder) are given names of animal IDs from the original study that can be downloaded from Zenodo and contain the following fields in each file:

SFPs: spatial footprints (also known as ROI) for every registered cell, centered over each cell. Shape - Dimx, dimy, number of SFPs (ROIs), number of days. If cell is not registered it will be nan along dimx and dimy for a given day.

blocked: location of blocked (occluded) partitions in 3x3 design of environment. Location of partitions are shown in paper, but are organized in the following way – [[0, 1, 2], [3, 4, 5], [6, 7, 8]]. If no partitions are blocked, value is -1.

centroids: centroid of spatial footprint. Shape – number of cells, x-y location, number of days.

envs: environment shape identified with string name

maps: three types of maps generated from the dataset. “sampling” is the occupancy of animal in each spatial bin, shape – xbins, ybins, number of days. “smoothed” is the event rate map smoothed with 2.5 cm gaussian kernel, shape – xbins, ybins, number of cells, number of days. “unsmoothed” is the same event rate map data without smoothing.

position: x-y position data for all days. List shape number of days, with shape on each day indicating x-y position in first dimension, and number of temporal bins / frames in second dimension.

trace: rise-extracted calcium traces, where “1” indicates a significant event. See paper for details on processing pipeline. If cell is not registered on given day, will appear as nan the same shape.

Precomputed results can also be downloaded in the zipped "results" folder to avoid recomputing main results from scratch using the Github code base linked above.