Extended Data Figure 2 : Neural ensembles of environments are reliably reactivated at recall of an open field and linear track.

From: A shared neural ensemble links distinct contextual memories encoded close in time

Extended Data Figure 2

a, Experimental design. Mice were imaged while exploring contexts A and B separated by 7 days and imaged while exploring contexts C and C separated by 7 days. b, There was a higher percentage of cells reactivated when animals explored the same context (C–C) than when animals explored different contexts (A–B) (paired t-test, t3 = 6.305, P = 0.0081, n = 4 mice). c, Mice were trained to run on a 2-m linear track with the miniature microscope for water rewards. Mice were trained 3 days a week for 3 weeks with a delay interval of 2–3 days between each session. Place fields were calculated by deconvolving calcium ΔF/F traces with an exponential to extract approximate spike times. Spikes that remained after crosstalk removal were included for analysis. Animal position was extracted using an automated LED tracking algorithm. A speed threshold (3 cm s−1) was applied to both the animal position and extracted spike timing and the resulting data was spatially binned (6.5-cm bins). Spatial firing rates were calculated by dividing the binned spike counts by the binned occupancy and smoothing with a Gaussian filter (sigma = 6.5 cm). Cells which showed consistent spatial firing modulation on at least three trials, with all other trials showing no bursting activity, were considered as place cells. Normalized spatial firing rates of all matched cells independently meeting the place cell criteria for both days. The data are pooled across 3 mice and include both motion directions. Place fields are ordered by centroid location on session 2. d, A shift of the image registration between sessions results in a decrease in matched place cells. A translational shift both horizontally and vertically was applied to the image registration transformation used in A. Cells were then matched across days and those which met our place cell criteria were kept. The heat map shows the count of matched place cells with a centroid shift of the place field that is less than 33 cm. Optimum matching of cells occurred within a 1-pixel translation of the calculated alignment transformation. e, Distribution of centroid shifts of place fields shown in A compared to the null hypothesis that the cell matching between sessions matches random cells.