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基于 Biobeam 的多路复用波导光学仿真在光切显微镜中的应用。

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

机构信息

Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany.

Center for Systems Biology Dresden, Dresden, Germany.

出版信息

PLoS Comput Biol. 2018 Apr 13;14(4):e1006079. doi: 10.1371/journal.pcbi.1006079. eCollection 2018 Apr.

DOI:10.1371/journal.pcbi.1006079
PMID:29652879
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC5898703/
Abstract

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.

摘要

在光片显微镜中，样品诱导的图像退化仍然是一个复杂的波动光学问题。在这里，我们介绍了 biobeam，这是一个开源软件包，通过结合来自 105-106 个复用和 GPU 加速的点扩散函数计算的数据，它可以模拟运行中的光片显微镜。这些模拟的波动光学性质导致对空间变化的像差、衍射伪影、几何图像失真、自适应光学和新兴的波动光学现象的忠实再现，并使光片显微镜中的图像形成在计算上变得可行。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f39e/5898703/c5a78285b20e/pcbi.1006079.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f39e/5898703/30cb2b761271/pcbi.1006079.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f39e/5898703/c5a78285b20e/pcbi.1006079.g002.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f39e/5898703/30cb2b761271/pcbi.1006079.g001.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/f39e/5898703/c5a78285b20e/pcbi.1006079.g002.jpg

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本文引用的文献

[1]
Correlative three-dimensional fluorescence and refractive index tomography: bridging the gap between molecular specificity and quantitative bioimaging.

Biomed Opt Express. 2017-11-17

[2]
Progress and Opportunities in Soft Photonics and Biologically Inspired Optics.

Adv Mater. 2017-10-23

[3]
Fractal propagation method enables realistic optical microscopy simulations in biological tissues.

Optica. 2016

[4]
Three-dimensional correlative single-cell imaging utilizing fluorescence and refractive index tomography.

J Biophotonics. 2018-3

[5]
A guide to light-sheet fluorescence microscopy for multiscale imaging.

Nat Methods. 2017-3-31

[6]
Reconfigurable and responsive droplet-based compound micro-lenses.

Nat Commun. 2017-3-7

[7]
Imagining the future of bioimage analysis.

Nat Biotechnol. 2016-12-7

[8]
SuReSim: simulating localization microscopy experiments from ground truth models.

Nat Methods. 2016-2-29

[9]
A platform for brain-wide imaging and reconstruction of individual neurons.

Elife. 2016-1-20

[10]
Site-Specific Cryo-focused Ion Beam Sample Preparation Guided by 3D Correlative Microscopy.

Biophys J. 2016-2-23

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