4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies

Swoger, Jim; Muzzopappa, Mariana; López‐Schier, Hernán; Sharpe, James

doi:10.1002/jbio.201000087

Cited by 54 publications

(48 citation statements)

References 33 publications

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“…By contrast, in light sheet microscopy, such as selective plane illumination microscopy (SPIM) (Huisken et al, 2004) or digital scanned laser light sheet fluorescence microscopy (DSLM) (Keller et al, 2008), the sample is illuminated with a thin laser light sheet in the focal plane of the detection objective and imaged at high speed with a sensitive camera. The energy input into the sample is minimized, making light sheet microscopy ideally suited for time-lapse imaging of biological processes over long periods of time (Huisken and Stainier, 2009;Weber and Huisken, 2011), such as heart function and morphogenesis in zebrafish (Scherz et al, 2008;Arrenberg et al, 2010), neuronal cell migration in C. elegans (Wu et al, 2011), or cell lineage tracing during lateral line formation in zebrafish (Swoger et al, 2011).…”

Section: Introductionmentioning

confidence: 99%

Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope

et al. 2012

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SUMMARYLight sheet microscopy techniques, such as selective plane illumination microscopy (SPIM), are ideally suited for time-lapse imaging of developmental processes lasting several hours to a few days. The success of this promising technology has mainly been limited by the lack of suitable techniques for mounting fragile samples. Embedding zebrafish embryos in agarose, which is common in conventional confocal microscopy, has resulted in severe growth defects and unreliable results. In this study, we systematically quantified the viability and mobility of zebrafish embryos mounted under more suitable conditions. We found that tubes made of fluorinated ethylene propylene (FEP) filled with low concentrations of agarose or methylcellulose provided an optimal balance between sufficient confinement of the living embryo in a physiological environment over 3 days and optical clarity suitable for fluorescence imaging. We also compared the effect of different concentrations of Tricaine on the development of zebrafish and provide guidelines for its optimal use depending on the application. Our results will make light sheet microscopy techniques applicable to more fields of developmental biology, in particular the multiview long-term imaging of zebrafish embryos and other small organisms. Furthermore, the refinement of sample preparation for in toto and in vivo imaging will promote other emerging optical imaging techniques, such as optical projection tomography (OPT).

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Section: Introductionmentioning

confidence: 99%

Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope

et al. 2012

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“…Nevertheless, these disadvantages are compensated by the higher SNR in LSFM. In practice, this results in similar quality images compared to for example spinning disc confocal acquisition 15 . Consequently, this enables reliable extraction of features like cell membranes or nuclei, e.g., for cell lineage tracing 15,19 .…”

Section: Introductionmentioning

confidence: 93%

“…Orienting the sample correctly helps to achieve the best possible image quality 15 . Generally, excitation and emission light should travel through as little tissue and mounting media as possible.…”

Section: Reduced Amount Of Embedding Medium In the Light Pathmentioning

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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“…As mentioned previously, our hOPT setup is fitted with a SPIM illumination arm using a laser, a cylindrical lens and a microscope objective [4,23]. This permits both light-sheet and hOPT measurements to be acquired on the same system and without interacting with the sample.…”

Section: Acquisition Proceduresmentioning

confidence: 99%

“…Since then, OPT has been applied to image in 3D a wide range of samples with different applications. Gene expression studies have been performed in the mouse embryo [2] and Caenorhabditis elegans [16]; observation of internal structures have been possible in adult Drosophila melanogaster [17,18], Parhyale hawaiensis [19] and Danio rerio, which has also been used to obtain flow maps to reconstruct sections of the circulatory system [20][21][22][23]. OPT has also been applied to image fixed and cleared adult mouse organs [24][25][26] and different stages of plant development [27].…”

Section: Introductionmentioning

confidence: 99%

Helical optical projection tomography

Arranz¹,

Dong²,

Zhu³

et al. 2013

Opt. Express

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Abstract:A new technique termed Helical Optical Projection Tomography (hOPT) has been developed with the aim to overcome some of the limitations of current 3D optical imaging techniques. hOPT is based on Optical Projection Tomography (OPT) with the major difference that there is a translation of the sample in the vertical direction during the image acquisition process, requiring a new approach to image reconstruction. Contrary to OPT, hOPT makes possible to obtain 3D-optical images of intact long samples without imposing limits on the sample length. This has been tested using hOPT to image long murine tissue samples such as spinal cords and large intestines. Moreover, 3D-reconstructed images of the colon of DSS-treated mice, a model for Inflammatory Bowel Disease, allowed the identification of the structural alterations. Finally, the geometry of the hOPT device facilitates the addition of a Selective Plane Illumination Microscopy (SPIM) arm, providing the possibility of delivering high resolution images of selected areas together with complete volumetric information. ©2013 Optical Society of AmericaOCIS codes: (180.2520) Fluorescence microscopy; (180.6900) Three-dimensional microscopy; (170.3010) Image reconstruction techniques; (170.3660) Light propagation in tissues. References and links1. V. Ntziachristos, "Going deeper than microscopy: the optical imaging frontier in biology," Nat. Methods 7(8), 603-614 (2010). 2. J. Sharpe, U. Ahlgren, P. Perry, B. Hill, A. Ross, J. Hecksher-Sørensen, R. Baldock, and D. Davidson, "Optical projection tomography as a tool for 3D microscopy and gene expression studies," Science 296(5567), 541-545 (2002). Zieglgänsberger, and K. Becker, "Ultramicroscopy: three-dimensional visualization of neuronal networks in the whole mouse brain," Nat. Methods 4(4), 331-336 (2007

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4D retrospective lineage tracing using SPIM for zebrafish organogenesis studies

Cited by 54 publications

References 33 publications

Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope

Multilayer mounting enables long-term imaging of zebrafish development in a light sheet microscope

Using Light Sheet Fluorescence Microscopy to Image Zebrafish Eye Development

Helical optical projection tomography

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