Fig. 1: Deep-brain in vivo structure imaging using 110 μm thick MMF endo-microscope.

a Experimental geometry for TM acquisition and imaging (see "Methods" for details). b To-scale fibre probe and mouse brain. The brain model has been compiled using Allen Reference Atlas—Adult Mouse⁵⁶, available from atlas.brain-map.org. c Detail of the side-view fibre probe and 3-D grid of foci scanning the scene. d Overlay in vivo MMF endo-microscope record detailed in (e–h) with post-mortem bright-field and confocal fluorescence microscopy. Another parallel endoscope insertion trace is visible on the right. e Record of endoscope progression (single focal plane set to the distance of 25 μm away from the probe tip) throughout the whole-brain depth of a Thy1-GFP line M mouse (see also Supplementary Movie 1 for volumetric data). f, g Details of the same record from the location of cortex and amygdala border, shown in full resolution. h Volumetric data corresponding to left part of (f) organised in 9 parallel planes 15 μm to 35 μm away from the probe tip, displaced by 2.5 μm from one another. Fluorescence intensity data in (e–h) are shown in logarithmic scale as indicated by a colour bar in (g). i, j Records of fluorescently labelled (FITC-dextran) blood vessels in cortex area of a wild-type mouse taken 25 μm away from the probe tip (intensity is shown in logarithmic scale as indicated by the colour bar). k Dual-channel volumetric imaging of neuronal processes and blood vessel walls (see "Methods" for details of labelling) in Thy1-GFP line M mouse. Focal planes cover an interval of distances from 20 μm to 27.5 μm away from the fibre tip and are displaced 2.5 μm from one another. l Volumetric records of sub-cellular structures' dynamics within a single neurone (focal planes organised as in (h), see also Supplementary movie 2 and “Methods” for cross-breeding details). The horizontal scale bar in (d) corresponds to the length of 1 mm. Vertical scale bars in (f, h, i, k, l) correspond to the length of 20 μm.