Extended Data Fig. 3: Clustering of velocity data into different behavioral modes.

(a,b) Representative velocity histograms of lights-off (a) and lights-on (b) trials from the same fish with three clusters: slow (orange), fast positive (green) and fast negative (blue). The clustering was based on identifying velocity thresholds vL and vH on the Gaussian mixture model (GMM) fit (grey line) as indicated by blue and green markers, respectively (see Methods for details). (c,d) Top: two-state (F: fast velocity both positive and negative combined and S: slow velocity) Markov process showing mean transition rates for a representative individual in lights-off (a) and lights-on trials (b). Bottom: transition rates corresponding to state transitions: F → S in (e) and S → F in (f), respectively for lights-off (black) and lights-on (red) trials. The transition rate for F → S was higher in lights-on trials (one-sided p-values are 0.0068, 0.0001, 0.0046, 0.0023, and 0.0093, respectively) whereas the rate for S → F was higher in lights-off trials (one-sided p-values are 0.0006, 0.0001, 0.0001, 0.0018, and 0.0001, respectively). (e-h) Velocity histograms (e,f) and traces (g,h) from lights-off (e,g) and lights-on (f,h) trials from the same fish from (a,b) showing three clusters using Hidden Markov model (HMM) based clustering. The colors are same as in (a,b). (i-l) Velocity histograms (i,j) and traces (k,l) from lights-off (i,k) and lights-on (j,l) trials from the same fish from (a,b) showing three clusters using maximum a posteriori (MAP) clustering based on three-component GMM fits. The probability density functions (pdf) of respective components are shown as dashed lines in (i,j). (m) Box and whisker plots showing residence time in slow mode, computed as the percent of the trial duration (40 s), for lights-off (black) and lights-on (red) trials computed using different clustering algorithm. For details see Methods. For all the clustering algorithms, the computed residence time was significantly higher during lights-on trials than lights-off trials (one sided p-values are 0.0002, 0.0034, 0.0001, and 0.0001, respectively). All box and whisker plots include the median line, the box denotes the interquartile range (IQR), whiskers denote the rest of the data distribution and outliers are denoted by points greater than ± 1.5 × IQR. In (c,d) the total number of lights-off trials (n) for fish 1 and 3 was 7, and for the rest, it was 10 trials per condition per fish. All p-values were calculated using the Mann-Whitney-Wilcoxon test.