Fig. 3: Computational aberration compensation on variety of fluorescence microscopy image volumes.

a Live C. elegans embryos expressing a pan-nuclear GFP histone marker were imaged with light sheet microscopy (i, left column) and the raw data processed with Richardson-Lucy deconvolution (ii, 10 iterations, middle column) or with a trained DeAbe model (iii, right column). First two rows show single planes 20.0 and 27.7 μm into the sample, third row shows axial view. Comparative line profiles through blue, yellow, and green lines are shown in insets, comparing ability to discriminate nuclei. Red arrow highlights nuclei for visual comparison. See also Supplementary Movie 3. b NK-92 cells stained with Alexa Fluor 555 wheat germ agglutinin and embedded in collagen matrices were fixed and imaged with instant SIM, a super-resolution imaging technique. Left: raw data, right: after application of DeAbe and deconvolution (DeAbe + , 20 iterations Richardson-Lucy). Lateral maximum intensity projections (MIP, top) or single axial planes (bottom) are shown in (b), and (c, d) show higher magnification views corresponding to green (c) or blue (d) dashed rectangular regions in (b). Colored arrows in (c, d) highlight fine features obscured in the raw data and better revealed in the DeAbe+ reconstructions. See also Supplementary Movie 5, Supplementary Fig. 19. e Live cardiac tissue containing cardiomyocytes expressing Tomm20-GFP was imaged with two photon microscopy. Raw data (left) are compared with DeAbe prediction (right) at indicated depths, with insets showing corresponding Fourier transform magnitudes. Blue circles in Fourier insets in (e) indicate 1/300 nm⁻¹ spatial frequency just beyond resolution limit. See also Supplementary Movie 6. f Higher magnification views of white dashed rectangular region in (e), emphasizing recovery of mitochondrial boundaries by DeAbe model. See also Supplementary Fig. 21, Supplementary Movie 7. Scale bars: 10 μm (a, e); 5 μm (b, f); 2 μm (c, d); (e) diameter of Fourier circle: 300 nm⁻¹. Data shown are representative samples from N = 3 experiments.