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

Weigert, Martin; Subramanian, Kaushikaram; Bundschuh, Sebastian; Myers, Eugene W.; Kreysing, Moritz

doi:10.1371/journal.pcbi.1006079

Cited by 30 publications

(14 citation statements)

References 39 publications

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“…The beam propagation method (BPM) represents an extension to the propagator approach which uses approximations but works in optically inhomogeneous media. The BPM has been used in a software package termed BioBeam that simulates light propagation through optically inhomogeneous media both in the illumination and detection path for different light sheet types at greatly improved speed by relying on a GPU [29]. In principle, our analysis can be readily applied to BioBeam results as well as to assess performance in inhomogeneous media.…”

Section: Discussionmentioning

confidence: 99%

How to define and optimize axial resolution in light-sheet microscopy: a simulation-based approach

Remacha¹,

Friedrich²,

Vermot³

et al. 2019

Biomed. Opt. Express

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How thick is your light sheet?" is a question that has been asked frequently after talks showing impressive renderings of 3D data acquired by a light-sheet microscope. This question is motivated by the fact that most of the time the thickness of the light-sheet is uniquely associated to the axial resolution of the microscope. However, the link between light-sheet thickness and axial resolution has never been systematically assessed and it is still unclear how both are connected. The question is not trivial because commonly employed measures cannot readily be applied or do not lead to easily interpretable results for the many different types of light sheet. Here, we introduce a set of intuitive measures that helps to define the relationship between light sheet thickness and axial resolution by using simulation data. Unexpectedly, our analysis revealed a trade-off between better axial resolution and thinner light-sheet thickness. Our results are surprising because thicker light-sheets that provide lower image contrast have previously not been associated with better axial resolution. We conclude that classical Gaussian illumination beams should be used when image contrast is most important, and more advanced types of illumination represent a way to optimize axial resolution at the expense of image contrast.

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Section: Discussionmentioning

confidence: 99%

How to define and optimize axial resolution in light-sheet microscopy: a simulation-based approach

Remacha¹,

Friedrich²,

Vermot³

et al. 2019

Biomed. Opt. Express

View full text Add to dashboard Cite

show abstract

“…The beam propagation method (BPM) represents an extension to the propagator approach which uses approximations but works in optically inhomogeneous media [12]. The BPM has been used in a software package termed BioBeam that simulates light propagation through optically inhomogeneous media both in the illumination and detection path for different light sheet types at greatly improved speed by relying on a GPU [29]. In principle, our analysis can be readily applied to BioBeam results as well to assess performance in inhomogeneous media.…”

Section: Discussionmentioning

confidence: 99%

How to define and optimize axial resolution in light-sheet microscopy: a simulation-based approach

Remacha

Friedrich²,

Vermot

et al. 2019

Preprint

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How thick is your light sheet?" is a question that has been asked frequently after talks showing impressive renderings of 3D data acquired by a light-sheet microscope. This question is motivated by the fact that most of the time the thickness of the light-sheet is uniquely associated to the axial resolution of the microscope. However, the link between lightsheet thickness and axial resolution has never been systematically assessed and it is still unclear how both are connected. The question is not trivial because commonly employed measures cannot readily be applied or do not lead to easily interpretable results for the many different types of light sheet. Here, by using simulation data we introduce a set of intuitive measures that helps to define the relationship between light sheet thickness and axial resolution. Unexpectedly, our analysis revealed a trade-off between better axial resolution and thinner light-sheet thickness. Our results are surprising because thicker light-sheets that provide lower image contrast have previously not been associated with better axial resolution. We conclude that classical Gaussian illumination beams should be used when image contrast is most important, and more advanced types of illumination represent a way to optimize axial resolution at the expense of image contrast.

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“…The addition of GPUs and GPU clusters along with the proposed quantized rotation-based OVSS system may make the system even faster. It is reported that, GPUs can further accelerate volume imaging 56 . Moreover, the use of multiple CPUs and optionally GPU has accelerated the reconstruction process in less than a 15 min on a NVdia P6000 graphics board 57 .…”

Section: Discussionmentioning

confidence: 99%

“…Moreover, the use of multiple CPUs and optionally GPU has accelerated the reconstruction process in less than a 15 min on a NVdia P6000 graphics board 57 . Specifically, Biobeam computational software based on GPU implementations has substantially reduced volume reconstruction time 56 . Current state-of-the-art light-sheet microscopes requires a lot of precious data-acquisition time that severely slows down the imaging process 58 , 59 .…”

Section: Discussionmentioning

confidence: 99%

Fluorescence based rapid optical volume screening system (OVSS) for interrogating multicellular organisms

Basumatary

Ara

Mukherjee

et al. 2021

Sci Rep

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Continuous monitoring of large specimens for long durations requires fast volume imaging. This is essential for understanding the processes occurring during the developmental stages of multicellular organisms. One of the key obstacles of fluorescence based prolonged monitoring and data collection is photobleaching. To capture the biological processes and simultaneously overcome the effect of bleaching, we developed single- and multi-color lightsheet based OVSS imaging technique that enables rapid screening of multiple tissues in an organism. Our approach based on OVSS imaging employs quantized step rotation of the specimen to record 2D angular data that reduces data acquisition time when compared to the existing light sheet imaging system (SPIM). A co-planar multicolor light sheet PSF is introduced to illuminate the tissues labelled with spectrally-separated fluorescent probes. The detection is carried out using a dual-channel sub-system that can simultaneously record spectrally separate volume stacks of the target organ. Arduino-based control systems were employed to automatize and control the volume data acquisition process. To illustrate the advantages of our approach, we have noninvasively imaged the Drosophila larvae and Zebrafish embryo. Dynamic studies of multiple organs (muscle and yolk-sac) in Zebrafish for a prolonged duration (5 days) were carried out to understand muscle structuring (Dystrophin, microfibers), primitive Macrophages (in yolk-sac) and inter-dependent lipid and protein-based metabolism. The volume-based study, intensity line-plots and inter-dependence ratio analysis allowed us to understand the transition from lipid-based metabolism to protein-based metabolism during early development (Pharyngula period with a critical transition time, $$\tau _c = 50$$ τ c = 50 h post-fertilization) in Zebrafish. The advantage of multicolor lightsheet illumination, fast volume scanning, simultaneous visualization of multiple organs and an order-less photobleaching makes OVSS imaging the system of choice for rapid monitoring and real-time assessment of macroscopic biological organisms with microscopic resolution.

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

Cited by 30 publications

References 39 publications

How to define and optimize axial resolution in light-sheet microscopy: a simulation-based approach

How to define and optimize axial resolution in light-sheet microscopy: a simulation-based approach

How to define and optimize axial resolution in light-sheet microscopy: a simulation-based approach

Fluorescence based rapid optical volume screening system (OVSS) for interrogating multicellular organisms

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