Extended Data Fig. 3: Topological changes between exposure and re-exposure in the CPP task do not relate to differences in spatial exploration or mere fluctuations in co-firing.

a, Spatial occupancy during exposure and re-exposure for example CPP days from four mice (one mouse day per row; using examples shown in Extended Data Fig. 1). Shown for each day, from left to right: (i) animal’s trajectory for each familiar session, (ii) map of pixel-wise dwell time difference across the two sessions (for each pixel, the time spent in that pixel during exposure minus re-exposure), (iii) distribution of pixel-wise dwell time differences for all pixels covering the familiar enclosure, showing no significant difference of the mean from 0 (all Ps>0.05), and (iv) corresponding Gardner-Altman estimation plot to visualize the effect size of the pixel-wise dwell time difference across the two sessions. For each Gardner-Altman plot: left panels show the raw data points for exposure (grey) and re-exposure (green), with each point representing the dwell time in a given pixel; right panel: mean (black-dot), 95% confidence interval (black-ticks) and sampling-error distribution (filled-curve) of the difference between re-exposure and exposure, computed from 5,000 bootstrapped resamples and with the difference-axis (dashed-line) origin aligned to the mean of the exposure distribution. b, Pixel-wise dwell time difference in spatial occupancy across the two sessions for all CPP days, as in (a). Average time difference distribution (left) not significantly different from 0 (1-sample t-test, p=0.53, t=0.62, df=1461; in sec per spatial bin: mean difference=0.05±0.08; 95% confidence interval=[0.106, -0.205]; interquartile range=[1.306, -0.870]), as also shown in the corresponding Gardner-Altman plot (right). c, Cumming estimation plots showing the absolute number of pixels visited in each CPP task session (top; each dot representing one mouse CPP day) and the fraction of visited pixels in each enclosure (bottom). Note that the animal’s coverage was not significantly different between exposure and re-exposure. The higher number of pixels visited during pre-test and CPP test merely reflects the higher dimension of the whole-CPP apparatus. d, Example time course of a mouse instantaneous speed during exposure (top) and re-exposure (bottom) in one CPP day. e, Instantaneous speed across the six sessions for all CPP days (bar charts: mean±SEM; with each superimposed dot representing one mouse CPP day). No significant differences across sessions with respect to exposure (P values: pre-text=0.25; +Suc.=0.38; +Wat.=0.76; CPP test=0.82; Re-exposure=0.98; all 2-sample Kolmogorov-Smirnov tests). f, Average speed across the six CPP task sessions (top) along with the total distance travelled (bottom; calculated for the first 15 min of each session). Note that the significant increased speed and distance travelled during pre-test (when the mouse is exposed for the first time to the novel CPP apparatus) do not translate in topological differences (Fig. 1f). These analyses (a-f) show that the topological hysteresis during re-exposure compared to exposure (Fig. 1f) does not reflect non-specific changes in spatial exploration. g, Topology alterations of hippocampal graphs in re-exposure (Fig. 1f) do not reflect mere fluctuations in co-firing. To control for natural variations in co-firing graphs, we split both exposure and re-exposure in two sections (1 and 2) with equal duration of active exploration (speed>2 cm/sec; exposure: 6.89±0.13 versus 6.97±0.10 min; re-exposure: 6.99±0.30 versus 6.85±0.31 min, all Ps>0.05; Wilcoxon signed-rank test) and quantified topological changes across. As for all topological analyses, sharp-wave/ripples were excluded (though their occurrence did not differ between exposure and re-exposure; t=-1.55, p=0.14, paired t-test). For each measure: the top panel shows the raw data points for each (color-coded) section (with the gapped lines on the right as mean (gap) ± SD (vertical ends)); the bottom-left panel shows the difference between the bootstrapped distribution with respect to first section of exposure; the bottom-right panel shows the difference between the distribution of the second compared to the first section within each familiar session. Note that co-firing topology did not significantly change during each individual familiar exploration. For each section: black-dot, median; black-ticks, 95% confidence interval; filled-curve: bootstrapped sampling-error distribution.