Extended Data Fig. 11: Lack of oscillatory sequences in parasubiculum and visual cortex.

a. Alternative sorting methods, as in Extended Data Fig. 4d, but applied to sessions recorded in the PaS (left) or VIS (right). The PCA sorting method applied to temporally shuffled data did not unveil oscillatory sequences (first row). No oscillatory sequences were recovered when neurons were sorted according to their correlation values (second row), or according to different dimensionality reduction techniques (UMAP, Isomap, LEM, t-SNE). Each row of each raster plot shows the calcium activity of a single neuron, with activity plotted as a function of time, as in Fig 2a. Every dot indicates that one neuron was active at one specific time bin (bin size = 129 ms). Sequence scores and oscillation scores are presented in Fig. 5e,f. b,c. Joint distributions of time lag τ that maximizes the cross-correlation between any given pair of neurons and their distance d in the PCA sorting (as in Extended Data Fig. 5b), applied to the recordings in Fig. 5e (PaS) and Fig. 5f (VIS). Normalized frequency is color-coded. Notice lack of linear relationship between d and τ, in contrast to Extended Data Fig. 5b. d,e. Projection of the neural activity onto the low-dimensional embedding defined by the first two principal components obtained from applying PCA to the matrix of calcium activity of the PaS session (d) and the VIS session (e) shown in Fig. 5e, f. Bin size = 8.5 s. Note lack of obvious ring topology. Time is color-coded. f. Transition probabilities between ensembles across consecutive time bins (bin size ~ 8.5 s, Methods) for the PaS example session in Fig. 5e (left) and the VIS example session in Fig. 5f (right). g. Probability of sequential ensemble activation as a function of the number of ensembles that are sequentially activated in PaS (left) and VIS (right) (mean ± S.D.). Orange, recorded data (25 PaS sessions; 19 VIS sessions); blue, shuffled data. For each session, the probability of sequential ensemble activation was calculated over 500 shuffled realizations, and shuffled realizations were pooled across sessions for each brain area separately. Probability is shown on a log-scale. In PaS the probability of long sequences was significantly larger in experimental data than in shuffled data (n = 25 PaS sessions, 12500 shuffled realizations; For 2 ensembles: p = 0.998, Z = −2.90; For 3–7 ensembles: range of p values: \({5.7\times 10}^{-4}\) to 0.036, range of Z values: 1.80 to 3.25, one-tailed Wilcoxon rank-sum test). This was not the case in VIS (n = 19 VIS sessions, 9500 shuffled realizations; For 2 ensembles: p = 0.106, Z = 1.25; For 3–6 ensembles: range of p values: 0.087 to 0.999, range of Z values: −3.34 to 1.36, one-tailed Wilcoxon rank-sum test). h. Percentage of sessions with significant sequence score (MEC oscillatory sessions: 15 of 15, PaS: 7 of 25; VIS: 1 of 19). The sequence score quantifies the probability of observing sequential activation of 3 or more ensembles. i. Distribution of oscillation scores for the entire calcium imaging data set, as in Extended Data Fig. 5d (19 VIS sessions over 3 animals, 25 PaS sessions over 4 animals, 27 MEC sessions of which 15 were classified as oscillatory, over 5 animals). Dashed line indicates threshold for classifying sessions as oscillatory with reference to the MEC data. Note that the bars for different brain regions sometimes overlap, and that bars are colored with transparency for visualization purposes (e.g. for sessions in PaS with oscillation score 0, the count is 24). j. Normalized distribution of the Pearson correlation values (absolute value) between the activity of cell pairs in VIS (green) and in PaS (yellow). Each dot indicates the mean across sessions (25 PaS sessions, 19 VIS sessions; all sessions in the data set were used, not only those with behavioural tracking synchronized to imaging), error bars indicate S.E.M. Probability is shown on a log-scale. k. Same as (j) but for the distribution of values of coactivity for all sessions recorded in PaS (yellow) and VIS (green). Coactivity was estimated for each session separately as the fraction of the recorded cells that was simultaneously active in 129 ms bins. Probability is shown on a log-scale. l. Cumulative probability of correlation values calculated between the calcium activity of one cell and the speed of the animal in that session for MEC (n = 4595 cells from 10 sessions, 3 animals), PaS (n = 6851 cells from 18 sessions, 3 animals), VIS (n = 6037 cells from 19 sessions, 3 animals). Only sessions for which the imaging data was synchronized to behavioural data were used (VIS-PaS: \(p=3.15\times {10}^{-169}\), Z = 27.7; VIS-MEC: \(p=1.05\times {10}^{-85}\), Z = 19.6, MEC-PaS: \(p=5.16\times {10}^{-12}\), Z = 6.80, one tailed Wilcoxon rank-sum test). Calcium activity was more correlated with the speed of the animal in visual cortex than in MEC and PaS.

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