Fig. 6: Hybrid imaging of an entire cleared mouse brain.

a, Schematic of the setup with chamber, lenses and a small camera unit for capturing a preview image of a large sample and selecting the tiles. b, Entire reconstructed mouse brain from lateral and axial views. The image is an example from one of two imaged samples. c, Re-imaged selected ROI in b and the reconstructed axial view (second row). d, Enlarged view of selected small vessel in c (first row) and reconstructed axial view (second row), highlighting individual vessel cells (arrowheads). e, Selected ROI2 from the cortex in b, which was recorded with the highest possible isotropic resolution. The image is an example from one of two imaged samples. f, Selected penetrating arterier and cross-sections at different depths and branches. The vertical line (orange solid line) and horizontal line (blue solid line) profiles indicate the measured line profiles from the cross-sections of the zero-order artery and the last SMA-positive termini. The inner distance between the artery walls was measured and indicated with a white double arrowhead line. g, Enlarged view of one of the penetrating subarteries in f. The color-coded arrowheads indicate the last SMA-positive arterial termini with the same color from both lateral and axial views. h, Left: segmentation of the entire penetrating artery and the counted sub-branches until the last SMA-positive termini. Right, the calculated volume of the main and subarteries. i, Selected ROI3 from the cerebellum in b, which was recorded with the highest possible isotropic resolution. The image is an example from one of two imaged samples. j, Full segmentation of three selected penetrating arteries named a, b and c. The segmentation and artery tracing enabled us to find the length of the main and subarteries in all directions.