Fig. 4: Computational aberration compensation on mm-scale cleared mouse embryo volumes.

a Fixed and iDISCO-cleared E11.5-day mouse embryos were immunostained for neurons (TuJ1, cyan) and blood vessels (CD31, magenta), imaged with confocal microscopy and processed with a trained DeAbe model. See also Supplementary Movie 8. b Axial view corresponding to dotted rectangular region in (a), comparing raw data and depth-compensated, de-aberrated, and deconvolved data (DeAbe + ). See also Supplementary Figs. 23, 24. c Higher magnification lateral view at axial depth of 1689 μm indicated by the orange double headed arrowheads in (b). d Higher magnification views of white dotted region in (c), comparing raw (left) and DeAbe+ processing (right) for neuronal (top) and blood vessel (bottom) stains. e Orientation (θ, transverse angle) analysis on blood vessel channel of DeAbe+ data, here shown on single lateral plane at indicated axial depth. See also Supplementary Fig. 25, Supplementary Movie 9. f Higher magnification lateral view of white dotted region in (e) (note that axial plane is different), comparing intensity (left) and orientation (right) views between raw (top row) and DeAbe+ prediction (middle row). Righthand insets show higher magnification views of vessel and surrounding region highlighted by dotted lines. Bottom row indicates histogram of all orientations in the vessel highlighted with dotted ellipse, full-width-at-half maximum (FWHM) in peak region of histogram is also shown. g Directional variance of blood vessel stain within the indicated plane, with higher magnification region of interest (ROI) views at right. Histogram of directional variance in both regions also shown. See also Supplementary Fig. 26. Scale bars: 500 μm (a, b, c, e); 100 μm (d), 50 μm inset; 300 μm (f), 50 μm inset; 300 μm (g), 50 μm inset. Data shown are representative samples from N = 3 experiments for (a–d) and N = 1 for(e–g).