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

Sample-induced image-degradation remains an intricate wave-optical problem in light-sheet microscopy. Here we present biobeam, 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.

[1]  J. Goodman.  Introduction to Fourier optics , 1969 .

[2]  Changhuei Yang,et al.  Translation correlations in anisotropically scattering media , 2014, 1411.7157.

[3]  Stefan Schinkinger,et al.  Müller cells are living optical fibers in the vertebrate retina , 2007, Proceedings of the National Academy of Sciences.

[4]  Jonathan T. C. Liu,et al.  Fractal propagation method enables realistic optical microscopy simulations in biological tissues. , 2016, Optica.

[5]  T. Zimmermann,et al.  Live cell spinning disk microscopy. , 2005, Advances in biochemical engineering/biotechnology.

[6]  Hwee Kuan Lee,et al.  Restoration of Uneven Illumination in Light Sheet Microscopy Images , 2011, Microscopy and Microanalysis.

[7]  R. Chmelík,et al.  Coherence-controlled holographic microscopy in diffuse media. , 2014, Optics express.

[8]  C. Fang-Yen,et al.  Tomographic phase microscopy , 2008, Nature Methods.

[9]  Karel Svoboda,et al.  A platform for brain-wide imaging and reconstruction of individual neurons , 2016, eLife.

[10]  K. Kawano,et al.  Introduction to Optical Waveguide Analysis , 2001 .

[11]  Gerwin Osnabrugge,et al.  A convergent Born series for solving the inhomogeneous Helmholtz equation in arbitrarily large media , 2016, J. Comput. Phys..

[12]  Philipp J. Keller,et al.  Quantitative high-speed imaging of entire developing embryos with simultaneous multiview light-sheet microscopy , 2012, Nature Methods.

[13]  Seungwoo Lee,et al.  Progress and Opportunities in Soft Photonics and Biologically Inspired Optics , 2018, Advanced materials.

[14]  M. Ringler.  Plasmonische Nahfeldresonatoren aus zwei biokonjugierten Goldnanopartikeln , 2008 .

[15]  F. Del Bene,et al.  Optical Sectioning Deep Inside Live Embryos by Selective Plane Illumination Microscopy , 2004, Science.

[16]  Nicolas Pinto,et al.  PyCUDA and PyOpenCL: A scripting-based approach to GPU run-time code generation , 2009, Parallel Comput..

[17]  Jochen Guck,et al.  Three‐dimensional correlative single‐cell imaging utilizing fluorescence and refractive index tomography , 2017, Journal of biophotonics.

[18]  J. Guck,et al.  Physical insight into light scattering by photoreceptor cell nuclei. , 2010, Optics letters.

[19]  Im,et al.  Correlative three-dimensional fluorescence and refractive index tomography : bridging the gap between molecular specificity and quantitative bioimaging , 2017 .

[20]  Lauren D. Zarzar,et al.  Reconfigurable and responsive droplet-based compound micro-lenses , 2017, Nature Communications.

[21]  Paul Lagasse,et al.  Beam-propagation method: analysis and assessment , 1981 .

[22]  Thomas Cremer,et al.  Nuclear Architecture of Rod Photoreceptor Cells Adapts to Vision in Mammalian Evolution , 2009, Cell.

[23]  Steven G. Johnson,et al.  Meep: A flexible free-software package for electromagnetic simulations by the FDTD method , 2010, Comput. Phys. Commun..

[24]  J. Huisken,et al.  A guide to light-sheet fluorescence microscopy for multiscale imaging , 2017, Nature Methods.

[25]  E. Wolf,et al.  Principles of Optics (7th Ed) , 1999 .

[26]  Quan Liu,et al.  Review of Monte Carlo modeling of light transport in tissues , 2013, Journal of biomedical optics.

[27]  Nils Norlin,et al.  Inverted light-sheet microscope for imaging mouse pre-implantation development , 2015, Nature Methods.

[28]  A. I.,et al.  Neural Field Continuum Limits and the Structure–Function Partitioning of Cognitive–Emotional Brain Networks , 2023, Biology.

[29]  J. Guck,et al.  Direct observation of light focusing by single photoreceptor cell nuclei. , 2014, Optics express.

[30]  S. Jacques.  Optical properties of biological tissues: a review , 2013, Physics in medicine and biology.

[31]  John I. Clark,et al.  The transparent lens and cornea in the mouse and zebra fish eye. , 2008, Seminars in cell & developmental biology.

[32]  Stephan Preibisch,et al.  Efficient Bayesian-based multiview deconvolution , 2013, Nature Methods.

[33]  A. Mosk,et al.  Focusing coherent light through opaque strongly scattering media. , 2007, Optics letters.

[34]  E. Boyden,et al.  Simultaneous whole-animal 3D-imaging of neuronal activity using light-field microscopy , 2014, Nature Methods.

[35]  Erik Meijering,et al.  Imagining the future of bioimage analysis , 2016, Nature Biotechnology.

[36]  Ernst H K Stelzer,et al.  Light-sheet fluorescence microscopy for quantitative biology , 2014, Nature Methods.

[37]  Mike Heilemann,et al.  SuReSim: simulating localization microscopy experiments from ground truth models , 2016, Nature Methods.

[38]  D. Milkie,et al.  Rapid Adaptive Optical Recovery of Optimal Resolution over LargeVolumes , 2014, Nature Methods.

[39]  A. Hyman,et al.  Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy. , 2016, Biophysical journal.

[40]  A. Rohrbach,et al.  Microscopy with self-reconstructing beams , 2010 .

[41]  D. Malacara-Hernández,et al.  PRINCIPLES OF OPTICS , 2011 .

[42]  Jan Huisken,et al.  Selective plane illumination microscopy techniques in developmental biology , 2009, Development.

[43]  Alan Boyde,et al.  The tandem scanning reflected light microscope , 1968 .