SPIM-fluid: open source light-sheet based platform for high-throughput imaging

Gualda, Emilio J.; Pereira, Hugo Cataud Pacheco; Vale, Tiago Gurgel do; Estrada, Marta; Brito, Catarina; Moreno, Nuno

doi:10.1364/boe.6.004447

Cited by 72 publications

(52 citation statements)

References 24 publications

(20 reference statements)

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“…This is a timely technique as biomedical sciences are currently experiencing a strong need to visualize samples in 3D as biological processes occur in volumes. Therefore, despite the fact that 2D cells placed in petri dishes have been widely used to study biological process, LSFM allows the use of agarose or fluorinated ethylene propylene (FEP) tubes [17,42,43] for mounting 3D living samples. Thus, 2D models have been constantly replaced by 3D cell cultures [44][45][46][47], spheroids [48][49][50][51][52], organs and organoids [26,[53][54][55], and model organisms such as Drosophila melanogaster, zebrafish and C. elegans [2,30,33,56].…”

Section: B Lsfm Is An Ad Hoc Technique For 3d Imagingmentioning

confidence: 99%

“…In addition, such translations may be too slow to track some of the fast dynamic processes over the whole sample volume. This has also triggered an interest in developing new sample-scanning techniques [42].…”

Section: A Mechanical Scanning Of the Samplementioning

confidence: 99%

“…Other variations of the system have also been proposed to visualize intracellular organelles [126]. Recently, a system capable of operating LSFM for 3D high-throughput imaging on 3D cell cultures and vertebrate model organisms was reported [42]. To provide automated sample loading, the microscope incorporates a FEP tube that crosses the immersion chamber along its diagonal for transporting the samples inside a maintaining buffer solution stream.…”

Section: D Fluidics Approachmentioning

confidence: 99%

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Light-sheet microscopy: a tutorial

et al. 2018

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This paper is intended to give a comprehensive review of light-sheet (LS) microscopy from an optics perspective. As such, emphasis is placed on the advantages that LS microscope configurations present, given the degree of freedom gained by uncoupling the excitation and detection arms. The new imaging properties are first highlighted in terms of optical parameters and how these have enabled several biomedical applications. Then, the basics are presented for understanding how a LS microscope works. This is followed by a presentation of a tutorial for LS microscope designs, each working at different resolutions and for different applications. Then, based on a numerical Fourier analysis and given the multiple possibilities for generating the LS in the microscope (using Gaussian, Bessel, and Airy beams in the linear and nonlinear regimes), a systematic comparison of their optical performance is presented. Finally, based on advances in optics and photonics, the novel optical implementations possible in a LS microscope are highlighted.

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Section: B Lsfm Is An Ad Hoc Technique For 3d Imagingmentioning

confidence: 99%

Section: A Mechanical Scanning Of the Samplementioning

confidence: 99%

Section: D Fluidics Approachmentioning

confidence: 99%

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Light-sheet microscopy: a tutorial

et al. 2018

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“…Still, in our experience, a lot of useful information can be extracted from that single sample. High throughput imaging of multiple embryos has been recently achieved in home built LSFM setups [46][47][48] , although typically at the expense of freedom of sample positioning and rotation.…”

Section: Bounding Boxmentioning

confidence: 99%

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

Icha

Schmied

Sidhaye

et al. 2016

JoVE

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Light sheet fluorescence microscopy (LSFM) is gaining more and more popularity as a method to image embryonic development. The main advantages of LSFM compared to confocal systems are its low phototoxicity, gentle mounting strategies, fast acquisition with high signal to noise ratio and the possibility of imaging samples from various angles (views) for long periods of time. Imaging from multiple views unleashes the full potential of LSFM, but at the same time it can create terabyte-sized datasets. Processing such datasets is the biggest challenge of using LSFM. In this protocol we outline some solutions to this problem. Until recently, LSFM was mostly performed in laboratories that had the expertise to build and operate their own light sheet microscopes. However, in the last three years several commercial implementations of LSFM became available, which are multipurpose and easy to use for any developmental biologist. This article is primarily directed to those researchers, who are not LSFM technology developers, but want to employ LSFM as a tool to answer specific developmental biology questions.Here, we use imaging of zebrafish eye development as an example to introduce the reader to LSFM technology and we demonstrate applications of LSFM across multiple spatial and temporal scales. This article describes a complete experimental protocol starting with the mounting of zebrafish embryos for LSFM. We then outline the options for imaging using the commercially available light sheet microscope. Importantly, we also explain a pipeline for subsequent registration and fusion of multiview datasets using an open source solution implemented as a Fiji plugin. While this protocol focuses on imaging the developing zebrafish eye and processing data from a particular imaging setup, most of the insights and troubleshooting suggestions presented here are of general use and the protocol can be adapted to a variety of light sheet microscopy experiments.

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“…In addition, imaging through the glass coverslip base of the multi-well plate at 45° to the optical axis introduces astigmatism and higher order aberrations that require subsequent correction and which increase in severity as the NA employed increases. High throughput light sheet fluorescence microscopy has also been demonstrated using fluidic approaches where the sample either flows through the light sheet using an FEP tube at 45° to the light sheet25, or using a millimetre-scale lab-on-a-chip device fabricated using femtosecond micromachining where the sample flows up through the light sheet towards the detection objective26.…”

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confidence: 99%

Time-lapse 3-D measurements of a glucose biosensor in multicellular spheroids by light sheet fluorescence microscopy in commercial 96-well plates

Maioli

Chennell

Sparks

et al. 2016

Sci Rep

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Light sheet fluorescence microscopy has previously been demonstrated on a commercially available inverted fluorescence microscope frame using the method of oblique plane microscopy (OPM). In this paper, OPM is adapted to allow time-lapse 3-D imaging of 3-D biological cultures in commercially available glass-bottomed 96-well plates using a stage-scanning OPM approach (ssOPM). Time-lapse 3-D imaging of multicellular spheroids expressing a glucose Förster resonance energy transfer (FRET) biosensor is demonstrated in 16 fields of view with image acquisition at 10 minute intervals. As a proof-of-principle, the ssOPM system is also used to acquire a dose response curve with the concentration of glucose in the culture medium being varied across 42 wells of a 96-well plate with the whole acquisition taking 9 min. The 3-D image data enable the FRET ratio to be measured as a function of distance from the surface of the spheroid. Overall, the results demonstrate the capability of the OPM system to measure spatio-temporal changes in FRET ratio in 3-D in multicellular spheroids over time in a multi-well plate format.

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SPIM-fluid: open source light-sheet based platform for high-throughput imaging

Cited by 72 publications

References 24 publications

Light-sheet microscopy: a tutorial

Light-sheet microscopy: a tutorial

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

Time-lapse 3-D measurements of a glucose biosensor in multicellular spheroids by light sheet fluorescence microscopy in commercial 96-well plates

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