Biobeam—Multiplexed wave-optical simulations of light-sheet microscopy

<div><p>Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present <i>biobeam</i>, an open-source software package that enables simulation of operational light-sheet microscopes by combining data from 10⁵–10⁶ multiplexed and GPU-accelerated point-spread-function calculations. The wave-optical nature of these simulations leads to the faithful reproduction of spatially varying aberrations, diffraction artifacts, geometric image distortions, adaptive optics, and emergent wave-optical phenomena, and renders image-formation in light-sheet microscopy computationally tractable.</p></div

Optical capabilities of the biobeam image-formation pipeline.

<p>(a) A test chart at the mid-section of an optically heterogeneous embryo-model (<i>n</i> = 1.35–1.39 diameter 140<i>μm</i>) is illuminated by cylindrical light sheet (<i>NA</i> = 0.15), and imaged from an orthogonal position (<i>NA</i> = 0.6). (b) Details of these wave-optically calculated images reveal <i>i)</i> spatially varying image blur, contrast loss and absorption induced by the heterogeneity of the sample, <i>ii)</i> diffraction artifacts from the light-sheet-typical coherent illumination, and <i>iii)</i> geometric image distortions such as lensing, split-screen type image distortions, and object displacements lensing. (c) <i>Biobeam</i> is further capable of adaptive optics simulations by which reversal of guide star emitted light fields yields perfect foci in scattering tissues. (d) Adaptive optics simulations faithfully reproduces the shift-shift memory effect, an emergent wave-optical phenomenon, here at 4 mean-free-paths deep inside the tissue.</p

Rigorous wave-optical simulation of image formation process in light-sheet microscopy.

<p>(a) Synthetic tissue phantom of a multicellular organism (100 × 200 × 100<i>μm</i>) comprising a complex refractive index distribution (left, <i>n</i> = 1.33–1.38) and a fluorophore distribution of interest (right). (b) Wave optical simulation of the illuminating light sheet and resulting excitation distribution within the sample at a given z position. (c) Partially coherent simulation of the detection path by multiplexed calculation of all independent point spread functions (left) and the resulting simulated camera image combining illumination and fluorescence path of light through the scattering sample. (d) Alternative light-sheet modalities (see also <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006079#pcbi.1006079.s002" target="_blank">S1</a> and <a href="http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1006079#pcbi.1006079.s006" target="_blank">S5</a> Videos and main text for details).</p