Extended Data Fig. 7: Generation of brain-wide activity maps during optical pacing.

a, Representative whole-brain CLARITY sagittal (top) and axial (bottom) images of control and ChRmine expressing mice exposed to optical pacing. Heart-targeted ChRmine expression resulted in increased tdTomato+ cells throughout the brain (seen as black dots) relative to control. b, Following light-sheet imaging, each image stack was registered to a common Allen Reference Atlas using our previously reported computational pipeline⁴⁰. Depicted are coronal slices across the brain with the overlaid anatomical atlas, where different anatomical regions are depicted with different colours. c, Representative raw image of single plane of TRAP2-tdTomato brain imaged under light-sheet microscope (left), and after detection by a supervised classifier (Ilastik, Arivis plugin), where single-cells are outlined in red (right, bottom). Blue arrows indicate example features that were detected by the classifier. d, Example CLARITY light-sheet images of control and ChRmine-paced mice in the visceral cortex (VISC), Medulla-behavioural state related (MY), and in the lateral amygdalar nucleus (LA), which are outlined in green in the axial reference slice. Scale bar=500 µm. e, Regional cell counts of paced (ChRmine, red) vs control (grey) cohorts sorted from anterior to posterior in all anatomical regions (n = 9 per group, multiple two-sided t-tests corrected for multiple comparisons with the Benjamini and Hochberg method (*FDR=10%). p-values: MO p = 0.025, SS p = 0.038, AUD p = 0.082, VIS p = 0.31, ACA p = 0.050, PL p = 0.027, ILA p = 0.0086, ORB p = 0.012, GU p = 0.013, VISC p = 0.018, AI p = 0.016, RSP p = 0.20, TEA p = 0.11, PERI p = 0.074, ECT p = 0.10, OLF p = 0.017, HIP p = 0.10, RHP p = 0.052, CLA p = 0.092, EP p = 0.035, LA p = 0.028, BLA p = 0.051, BMA p = 0.036, PA p = 0.043, STRd p = 0.029, STRv p = 0.015, LSX p = 0.012, sAMY p = 0.037, PALd p = 0.036, PALv p = 0.033, PALm p = 0.024, PALc p = 0.012, DORsm p = 0.16, DORpm p = 0.095, PVZ p = 0.016, PVR p = 0.020, MEZ p = 0.029, LZ p = 0.033, MB p = 0.28, P p = 0.030, MY p = 0.054, VERM p = 0.50, HEM p = 0.043, CBN p = 0.92). Acronyms for each major brain region is listed.