1
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Huang Z, Sun Y, Liu S, Chen X, Ping J, Fei P, Gong Z, Zheng N. A machine learning based method for tracking of simultaneously imaged neural activity and body posture of freely moving maggot. Biochem Biophys Res Commun 2024; 727:150290. [PMID: 38941792 DOI: 10.1016/j.bbrc.2024.150290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/16/2024] [Accepted: 06/19/2024] [Indexed: 06/30/2024]
Abstract
To understand neural basis of animal behavior, it is necessary to monitor neural activity and behavior in freely moving animal before building relationship between them. Here we use light sheet fluorescence microscope (LSFM) combined with microfluidic chip to simultaneously capture neural activity and body movement in small freely behaving Drosophila larva. We develop a transfer learning based method to simultaneously track the continuously changing body posture and activity of neurons that move together using a sub-region tracking network with a precise landmark estimation network for the inference of target landmark trajectory. Based on the tracking of each labelled neuron, the activity of the neuron indicated by fluorescent intensity is calculated. For each video, annotation of only 20 frames in a video is sufficient to yield human-level accuracy for all other frames. The validity of this method is further confirmed by reproducing the activity pattern of PMSIs (period-positive median segmental interneurons) and larval movement as previously reported. Using this method, we disclosed the correlation between larval movement and left-right asymmetry in activity of a group of unidentified neurons labelled by R52H01-Gal4 and further confirmed the roles of these neurons in bilateral balance of body contraction during larval crawling by genetic inhibition of these neurons. Our method provides a new tool for accurate extraction of neural activities and movement of freely behaving small-size transparent animals.
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Affiliation(s)
- Zenan Huang
- Zhejiang Lab, Hangzhou, 311121, China; Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, 310007, China
| | - Yixuan Sun
- Zhejiang Lab, Hangzhou, 311121, China; Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Affiliated Mental Health Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China
| | | | - Xiaopeng Chen
- Zhejiang Lab, Hangzhou, 311121, China; School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong, University of Science and Technology, Wuhan, 430074, China
| | - Junyu Ping
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong, University of Science and Technology, Wuhan, 430074, China
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong, University of Science and Technology, Wuhan, 430074, China
| | - Zhefeng Gong
- Zhejiang Lab, Hangzhou, 311121, China; Department of Neurobiology and Department of Neurology of Second Affiliated Hospital, Affiliated Mental Health Center, Zhejiang University School of Medicine, Hangzhou, 310058, China; NHC and CAMS Key Laboratory of Medical Neurobiology, MOE Frontier Science Center for Brain Research and Brain-Machine Integration, School of Brain Science and Brain Medicine, Zhejiang University, Hangzhou, 310058, China.
| | - Nenggan Zheng
- Zhejiang Lab, Hangzhou, 311121, China; Qiushi Academy for Advanced Studies, Zhejiang University, Hangzhou, 310007, China
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2
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Bentahar S, Gómez-Gaviro MV, Desco M, Ripoll J, Fernández R. Multispectral imaging for characterizing autofluorescent tissues. Sci Rep 2024; 14:12084. [PMID: 38802477 PMCID: PMC11130125 DOI: 10.1038/s41598-024-61020-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
Selective Plane Illumination Microscopy (SPIM) has become an emerging technology since its first application for 3D in-vivo imaging of the development of a living organism. An extensive number of works have been published, improving both the speed of acquisition and the resolution of the systems. Furthermore, multispectral imaging allows the effective separation of overlapping signals associated with different fluorophores from the spectrum over the whole field-of-view of the analyzed sample. To eliminate the need of using fluorescent dyes, this technique can also be applied to autofluorescence imaging. However, the effective separation of the overlapped spectra in autofluorescence imaging necessitates the use of mathematical tools. In this work, we explore the application of a method based on Principal Component Analysis (PCA) that enables tissue characterization upon spectral autofluorescence data without the use of fluorophores. Thus, enabling the separation of different tissue types in fixed and living samples with no need of staining techniques. Two procedures are described for acquiring spectral data, including a single excitation based method and a multi-excitation scanning approach. In both cases, we demonstrate the effective separation of various tissue types based on their unique autofluorescence spectra.
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Affiliation(s)
- Sara Bentahar
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain
| | | | - Manuel Desco
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
- Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), Madrid, Spain
- Centro Nacional de Investigaciones Cardiovasculares Carlos III (CNIC), Madrid, Spain
| | - Jorge Ripoll
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain.
- Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain.
| | - Roberto Fernández
- Departamento de Bioingeniería, Universidad Carlos III de Madrid, Madrid, Spain.
- Departamento de Física, Ingeniería de Sistemas y Teoría de la Señal, Universidad de Alicante, Alicante, Spain.
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3
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Borne V, Weiss M. Robust spatiotemporal organization of mitotic events in mechanically perturbed C. elegans embryos. Biophys J 2024:S0006-3495(24)00243-1. [PMID: 38576160 DOI: 10.1016/j.bpj.2024.03.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Revised: 02/22/2024] [Accepted: 03/29/2024] [Indexed: 04/06/2024] Open
Abstract
Early embryogenesis of the nematode Caenorhabditis elegans progresses in an autonomous fashion within a protective chitin eggshell. Cell-division timing and the subsequent mechanically guided positioning of cells is virtually invariant between individuals, especially before gastrulation. Here, we have challenged this stereotypical developmental program in early stages by mechanically perturbing the embryo without breaking its eggshell. Compressing embryos to about two-thirds of their unperturbed diameter only resulted in markedly slower cell divisions. In contrast, compressing embryos to half of their native diameter frequently resulted in a loss of cytokinesis, yielding a non-natural syncytium that still allowed for multiple divisions of nuclei. Although the orientation of mitotic axes was strongly altered in the syncytium, key features of division timing and spatial arrangement of nuclei remained surprisingly similar to those of unperturbed embryos in the first few division cycles. This suggests that few, very robust mechanisms provide a basic and resilient program for safeguarding the early embryogenesis of C. elegans.
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Affiliation(s)
- Vincent Borne
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, Bayreuth, Germany
| | - Matthias Weiss
- Experimental Physics I, University of Bayreuth, Universitätsstr. 30, Bayreuth, Germany.
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4
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Strobl F, Ratke J, Krämer F, Utta A, Becker S, Stelzer EHK. Next generation marker-based vector concepts for rapid and unambiguous identification of single and double homozygous transgenic organisms. Biol Open 2023; 12:bio060015. [PMID: 37855381 PMCID: PMC10602009 DOI: 10.1242/bio.060015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 08/15/2023] [Indexed: 10/20/2023] Open
Abstract
For diploid model organisms, the actual transgenesis processes require subsequent periods of transgene management, which are challenging in emerging model organisms due to the lack of suitable methodology. We used the red flour beetle Tribolium castaneum, a stored-grain pest, to perform a comprehensive functional evaluation of our AClashOfStrings (ACOS) and the combined AGameOfClones/AClashOfStrings (AGOC/ACOS) vector concepts, which use four clearly distinguishable markers to provide full visual control over up to two independent transgenes. We achieved comprehensive statistical validation of our approach by systematically creating seventeen novel single and double homozygous sublines intended for fluorescence live imaging, including several sublines in which the microtubule cytoskeleton is labeled. During the mating procedures, we genotyped more than 20,000 individuals in less than 80 working hours, which corresponds to about 10 to 15 s per individual. We also confirm the functionality of our combined concept in two double transgene special cases, i.e. integration of both transgenes in close proximity on the same chromosome and integration of one transgene on the X allosome. Finally, we discuss our vector concepts regarding performance, genotyping accuracy, throughput, resource saving potential, fluorescent protein choice, modularity, adaptation to other diploid model organisms and expansion capability.
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Affiliation(s)
- Frederic Strobl
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Julia Ratke
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Franziska Krämer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ana Utta
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Sigrun Becker
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
| | - Ernst H. K. Stelzer
- Physical Biology / Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt – Macromolecular Complexes (CEF – MC), Goethe-Universität Frankfurt am Main (Campus Riedberg),Max-von-Laue-Straße 15, D-60438 Frankfurt am Main, Germany
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5
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Stockhausen A, Rodriguez-Gatica JE, Schweihoff J, Schwarz MK, Kubitscheck U. Airy beam light sheet microscopy boosted by deep learning deconvolution. OPTICS EXPRESS 2023; 31:10918-10935. [PMID: 37157627 DOI: 10.1364/oe.485699] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Common light sheet microscopy comes with a trade-off between light sheet width defining the optical sectioning and the usable field of view arising from the divergence of the illuminating Gaussian beam. To overcome this, low-diverging Airy beams have been introduced. Airy beams, however, exhibit side lobes degrading image contrast. Here, we constructed an Airy beam light sheet microscope, and developed a deep learning image deconvolution to remove the effects of the side lobes without knowledge of the point spread function. Using a generative adversarial network and high-quality training data, we significantly enhanced image contrast and improved the performance of a bicubic upscaling. We evaluated the performance with fluorescently labeled neurons in mouse brain tissue samples. We found that deep learning-based deconvolution was about 20-fold faster than the standard approach. The combination of Airy beam light sheet microscopy and deep learning deconvolution allows imaging large volumes rapidly and with high quality.
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6
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Han Q, Shi J, Shi F. Sidelobe suppression in structured light sheet fluorescence microscopy by the superposition of two light sheets. BIOMEDICAL OPTICS EXPRESS 2023; 14:1178-1191. [PMID: 36950249 PMCID: PMC10026568 DOI: 10.1364/boe.481508] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/25/2023] [Accepted: 02/08/2023] [Indexed: 06/18/2023]
Abstract
Light sheet microscopy has emerged as a powerful technique for three-dimensional and long-term vivo imaging within neuroscience and developmental biology. A light sheet illumination with structured light fields allows a better tradeoff between the field of view and axial resolution but suffers from strong side lobes. Here, we propose a method of producing structured light sheet illumination with suppressed side lobes by applying the superposition of two light sheets. The side lobe suppression results from the destructive interference between the side lobes and constructive interference between the main lobe of the two light sheets. In the proposed method, the incident light pattern in the rear pupil plane of the illumination objective is a combination of the incident light line beams required for the generation of the two interfering light sheets. We present a fast and simple calculation method to determine the incident light pattern in the rear pupil plane. Simulation results demonstrate the effectiveness of the proposed sidelobe suppression method for double-line light sheet, four-line light sheet, as well as line Bessel sheet. In particular, an 81% decrease in the relative side lobe energy can be achieved in case of double-line light sheet with an almost nonchanging propagation length. We show a way of using combined incident light patterns to generate structured light sheets with interference-resulted side lobe suppression, which is straightforward in design and with advantages of improved imaging performance.
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7
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Darling C, Davis SPX, Kumar S, French PMW, McGinty J. Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples. JOURNAL OF BIOPHOTONICS 2023; 16:e202200232. [PMID: 36087031 DOI: 10.1002/jbio.202200232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic biological samples is presented. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio, but the sequential acquisition of projection images typically requires samples to be immobilized during the acquisition. A proof-of-principle system capable of single-shot tomography of a ~1 mm3 volume is presented, demonstrating camera-limited rates of up to 62.5 volumes/s, which has been applied to 3D imaging of a freely swimming zebrafish embryo. This is achieved by recording eight projection views simultaneously on four low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including high throughput flow cytometry applied to model organisms and fluid dynamics studies.
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Affiliation(s)
- Connor Darling
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Samuel P X Davis
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
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8
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Dyer L, Parker A, Paphiti K, Sanderson J. Lightsheet Microscopy. Curr Protoc 2022; 2:e448. [PMID: 35838628 DOI: 10.1002/cpz1.448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
In this paper, we review lightsheet (selective plane illumination) microscopy for mouse developmental biologists. There are different means of forming the illumination sheet, and we discuss these. We explain how we introduced the lightsheet microscope economically into our core facility and present our results on fixed and living samples. We also describe methods of clearing fixed samples for three-dimensional imaging and discuss the various means of preparing samples with particular reference to mouse cilia, adipose spheroids, and cochleae. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC.
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Affiliation(s)
- Laura Dyer
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Andrew Parker
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Keanu Paphiti
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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9
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Leroy O, van Leen E, Girard P, Villedieu A, Hubert C, Bosveld F, Bellaïche Y, Renaud O. Multi-view confocal microscopy enables multiple organ and whole organism live-imaging. Development 2022; 149:274464. [DOI: 10.1242/dev.199760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 01/13/2022] [Indexed: 11/20/2022]
Abstract
ABSTRACT
Understanding how development is coordinated in multiple tissues and gives rise to fully functional organs or whole organisms necessitates microscopy tools. Over the last decade numerous advances have been made in live-imaging, enabling high resolution imaging of whole organisms at cellular resolution. Yet, these advances mainly rely on mounting the specimen in agarose or aqueous solutions, precluding imaging of organisms whose oxygen uptake depends on ventilation. Here, we implemented a multi-view multi-scale microscopy strategy based on confocal spinning disk microscopy, called Multi-View confocal microScopy (MuViScopy). MuViScopy enables live-imaging of multiple organs with cellular resolution using sample rotation and confocal imaging without the need of sample embedding. We illustrate the capacity of MuViScopy by live-imaging Drosophila melanogaster pupal development throughout metamorphosis, highlighting how internal organs are formed and multiple organ development is coordinated. We foresee that MuViScopy will open the path to better understand developmental processes at the whole organism scale in living systems that require gas exchange by ventilation.
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Affiliation(s)
- Olivier Leroy
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Eric van Leen
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Philippe Girard
- Université de Paris, CNRS UMR7592, Institut Jacques Monod and Faculty of Basic and Biomedical Sciences, 75006, Paris, France
| | - Aurélien Villedieu
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | | | - Floris Bosveld
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Yohanns Bellaïche
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
| | - Olivier Renaud
- Institut Curie, Université PSL, Sorbonne Université, CNRS UMR3215, Inserm U934, Genetics and Developmental Biology, 75005 Paris, France
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10
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Möller K, Brambach M, Villani A, Gallo E, Gilmour D, Peri F. A role for the centrosome in regulating the rate of neuronal efferocytosis by microglia in vivo. eLife 2022; 11:82094. [PMID: 36398880 PMCID: PMC9674339 DOI: 10.7554/elife.82094] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 10/25/2022] [Indexed: 11/19/2022] Open
Abstract
During brain development, many newborn neurons undergo apoptosis and are engulfed by microglia, the tissue-resident phagocytes of the brain, in a process known as efferocytosis. A hallmark of microglia is their highly branched morphology characterized by the presence of numerous dynamic extensions that these cells use for scanning the brain parenchyma and engulfing unwanted material. The mechanisms driving branch formation and apoptotic cell engulfment in microglia are unclear. By taking a live-imaging approach in zebrafish, we show that while microglia generate multiple microtubule-based branches, they only successfully engulf one apoptotic neuron at a time. Further investigation into the mechanism underlying this sequential engulfment revealed that targeted migration of the centrosome into one branch is predictive of phagosome formation and polarized vesicular trafficking. Moreover, experimentally doubling centrosomal numbers in microglia increases the rate of engulfment and even allows microglia to remove two neurons simultaneously, providing direct supporting evidence for a model where centrosomal migration is a rate-limiting step in branch-mediated efferocytosis. Conversely, light-mediated depolymerization of microtubules causes microglia to lose their typical branched morphology and switch to an alternative mode of engulfment, characterized by directed migration towards target neurons, revealing unexpected plasticity in their phagocytic ability. Finally, building on work focusing on the establishment of the immunological synapse, we identified a conserved signalling pathway underlying centrosomal movement in engulfing microglia.
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Affiliation(s)
- Katrin Möller
- Department of Molecular Life Sciences, University of ZürichZürichSwitzerland
| | - Max Brambach
- Department of Molecular Life Sciences, University of ZürichZürichSwitzerland
| | - Ambra Villani
- Department of Molecular Life Sciences, University of ZürichZürichSwitzerland
| | - Elisa Gallo
- Department of Molecular Life Sciences, University of ZürichZürichSwitzerland
| | - Darren Gilmour
- Department of Molecular Life Sciences, University of ZürichZürichSwitzerland
| | - Francesca Peri
- Department of Molecular Life Sciences, University of ZürichZürichSwitzerland
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11
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Fiúza UM, Lemaire P. Methods for the Study of Apical Constriction During Ascidian Gastrulation. Methods Mol Biol 2022; 2438:377-413. [PMID: 35147954 DOI: 10.1007/978-1-0716-2035-9_23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Gastrulation is the first major morphogenetic event during ascidian embryogenesis. Ascidian gastrulation begins with the invagination of the endodermal progenitors, a two-step process driven by individual cell shape changes of endoderm cells. During the first step, endoderm cells constrict apically, thereby flattening the vegetal side of the embryo. During the second step, endoderm cells shorten along their apicobasal axis and tissue invagination ensues. Individual cell shape changes are mediated by localized actomyosin contractile activity. Here, we describe methods used during ascidian endoderm apical constriction to study myosin activity and cellular morphodynamics with confocal and light sheet microscopy and followed by quantitative image analysis.
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Affiliation(s)
- Ulla-Maj Fiúza
- Systems Bioengineering, DCEXS Universidad Pompeu Fabra, Barcelona, Spain.
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12
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Recent advances in the standardization of fluorescence microscopy for quantitative image analysis. Biophys Rev 2021; 14:33-39. [DOI: 10.1007/s12551-021-00871-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 10/22/2021] [Indexed: 12/19/2022] Open
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13
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Stower MJ, Srinivas S. Advances in live imaging early mouse development: exploring the researcher's interdisciplinary toolkit. Development 2021; 148:dev199433. [PMID: 34897401 PMCID: PMC7615354 DOI: 10.1242/dev.199433] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Live imaging is an important part of the developmental biologist's armoury of methods. In the case of the mouse embryo, recent advances in several disciplines including embryo culture, microscopy hardware and computational analysis have all contributed to our ability to probe dynamic events during early development. Together, these advances have provided us with a versatile and powerful 'toolkit', enabling us not only to image events during mouse embryogenesis, but also to intervene with them. In this short Spotlight article, we summarise advances and challenges in using live imaging specifically for understanding early mouse embryogenesis.
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Affiliation(s)
- Matthew J. Stower
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
| | - Shankar Srinivas
- Department of Physiology, Anatomy and Genetics, University of Oxford, South Parks Road, Oxford OX1 3QX, UK
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14
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Wolf S, Wan Y, McDole K. Current approaches to fate mapping and lineage tracing using image data. Development 2021; 148:dev198994. [PMID: 34498046 DOI: 10.1242/dev.198994] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Visualizing, tracking and reconstructing cell lineages in developing embryos has been an ongoing effort for well over a century. Recent advances in light microscopy, labelling strategies and computational methods to analyse complex image datasets have enabled detailed investigations into the fates of cells. Combined with powerful new advances in genomics and single-cell transcriptomics, the field of developmental biology is able to describe the formation of the embryo like never before. In this Review, we discuss some of the different strategies and applications to lineage tracing in live-imaging data and outline software methodologies that can be applied to various cell-tracking challenges.
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Affiliation(s)
- Steffen Wolf
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Yinan Wan
- Biozentrum, University of Basel, Basel, 4056, Switzerland
| | - Katie McDole
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
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15
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Khajavi B, Sun R, Chawla HS, Henry HL, Singh M, Schill AW, Dickinson ME, Mayerich D, Larin KV. Multimodal high-resolution embryonic imaging with light sheet fluorescence microscopy and optical coherence tomography. OPTICS LETTERS 2021; 46:4180-4183. [PMID: 34469969 PMCID: PMC8903154 DOI: 10.1364/ol.430202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Accepted: 07/16/2021] [Indexed: 06/13/2023]
Abstract
A high-resolution imaging system combining optical coherence tomography (OCT) and light sheet fluorescence microscopy (LSFM) was developed. LSFM confined the excitation to only the focal plane, removing the out of plane fluorescence. This enabled imaging a murine embryo with higher speed and specificity than traditional fluorescence microscopy. OCT gives information about the structure of the embryo from the same plane illuminated by LSFM. The co-planar OCT and LSFM instrument was capable of performing co-registered functional and structural imaging of mouse embryos simultaneously.
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Affiliation(s)
- Behzad Khajavi
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204, USA
| | - Ruijiao Sun
- Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, USA
| | | | - H. Le Henry
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77584, USA
| | - Manmohan Singh
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204, USA
| | - Alexander W. Schill
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204, USA
| | - Mary E. Dickinson
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77584, USA
| | - David Mayerich
- Department of Electrical and Computer Engineering, University of Houston, Houston, Texas 77204, USA
| | - Kirill V. Larin
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204, USA
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, Texas 77584, USA
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16
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Weaver CJ, Poulain FE. From whole organism to ultrastructure: progress in axonal imaging for decoding circuit development. Development 2021; 148:271122. [PMID: 34328171 DOI: 10.1242/dev.199717] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Since the pioneering work of Ramón y Cajal, scientists have sought to unravel the complexities of axon development underlying neural circuit formation. Micrometer-scale axonal growth cones navigate to targets that are often centimeters away. To reach their targets, growth cones react to dynamic environmental cues that change in the order of seconds to days. Proper axon growth and guidance are essential to circuit formation, and progress in imaging has been integral to studying these processes. In particular, advances in high- and super-resolution microscopy provide the spatial and temporal resolution required for studying developing axons. In this Review, we describe how improved microscopy has revolutionized our understanding of axonal development. We discuss how novel technologies, specifically light-sheet and super-resolution microscopy, led to new discoveries at the cellular scale by imaging axon outgrowth and circuit wiring with extreme precision. We next examine how advanced microscopy broadened our understanding of the subcellular dynamics driving axon growth and guidance. We finally assess the current challenges that the field of axonal biology still faces for imaging axons, and examine how future technology could meet these needs.
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Affiliation(s)
- Cory J Weaver
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
| | - Fabienne E Poulain
- Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA
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17
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Machacova S, Chmelova H, Vavrova A, Kozmik Z, Kozmikova I. Optical Clearing and Light Sheet Microscopy Imaging of Amphioxus. Front Cell Dev Biol 2021; 9:702986. [PMID: 34381783 PMCID: PMC8350520 DOI: 10.3389/fcell.2021.702986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 06/21/2021] [Indexed: 11/13/2022] Open
Abstract
Cephalochordates (amphioxi or lancelets) are representatives of the most basally divergent group of the chordate phylum. Studies of amphioxus development and anatomy hence provide a key insight into vertebrate evolution. More widespread use of amphioxus in the evo-devo field would be greatly facilitated by expanding the methodological toolbox available in this model system. For example, evo-devo research on amphioxus requires deep understanding of animal anatomy. Although conventional confocal microscopy can visualize transparent amphioxus embryos and early larvae, the imaging of later developmental stages is problematic because of the size and opaqueness of the animal. Here, we show that light sheet microscopy combined with tissue clearing methods enables exploration of large amphioxus specimens while keeping the surface and the internal structures intact. We took advantage of the phenomenon of autofluorescence of amphioxus larva to highlight anatomical details. In order to investigate molecular markers at the single-cell level, we performed antibody-based immunodetection of melanopsin and acetylated-α-tubulin to label rhabdomeric photoreceptors and the neuronal scaffold. Our approach that combines light sheet microscopy with the clearing protocol, autofluorescence properties of amphioxus, and antibody immunodetection allows visualizing anatomical structures and even individual cells in the 3D space of the entire animal body.
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Affiliation(s)
- Simona Machacova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Helena Chmelova
- Light Microscopy Core Facility, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Anna Vavrova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Zbynek Kozmik
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
| | - Iryna Kozmikova
- Laboratory of Transcriptional Regulation, Institute of Molecular Genetics of the Czech Academy of Sciences, Prague, Czechia
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18
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Bakas S, Uttamchandani D, Toshiyoshi H, Bauer R. MEMS enabled miniaturized light-sheet microscopy with all optical control. Sci Rep 2021; 11:14100. [PMID: 34238945 PMCID: PMC8266809 DOI: 10.1038/s41598-021-93454-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 06/16/2021] [Indexed: 11/29/2022] Open
Abstract
We have designed and implemented a compact, cost-efficient miniaturised light-sheet microscopy system based on optical microelectromechanical systems scanners and tunable lenses. The system occupies a footprint of 20 × 28 × 13 cm3 and combines off-the-shelf optics and optomechanics with 3D-printed structural and optical elements, and an economically costed objective lens, excitation laser and camera. All-optical volume scanning enables imaging of 435 × 232 × 60 µm3 volumes with 0.25 vps (volumes per second) and minimum lateral and axial resolution of 1.0 µm and 3.8 µm respectively. An open-top geometry allows imaging of samples on flat bottomed holders, allowing integration with microfluidic devices, multi-well plates and slide mounted samples, with applications envisaged in biomedical research and pre-clinical settings.
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Affiliation(s)
- Spyridon Bakas
- Department of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK.
| | - Deepak Uttamchandani
- Department of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK
| | | | - Ralf Bauer
- Department of Electronic and Electrical Engineering, University of Strathclyde, Glasgow, UK
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19
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Susaki EA, Takasato M. Perspective: Extending the Utility of Three-Dimensional Organoids by Tissue Clearing Technologies. Front Cell Dev Biol 2021; 9:679226. [PMID: 34195197 PMCID: PMC8236633 DOI: 10.3389/fcell.2021.679226] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 05/11/2021] [Indexed: 01/06/2023] Open
Abstract
An organoid, a self-organizing organ-like tissue developed from stem cells, can exhibit a miniaturized three-dimensional (3D) structure and part of the physiological functions of the original organ. Due to the reproducibility of tissue complexity and ease of handling, organoids have replaced real organs and animals for a variety of uses, such as investigations of the mechanisms of organogenesis and disease onset, and screening of drug effects and/or toxicity. The recent advent of tissue clearing and 3D imaging techniques have great potential contributions to organoid studies by allowing the collection and analysis of 3D images of whole organoids with a reasonable throughput and thus can expand the means of examining the 3D architecture, cellular components, and variability among organoids. Genetic and histological cell-labeling methods, together with organoid clearing, also allow visualization of critical structures and cellular components within organoids. The collected 3D data may enable image analysis to quantitatively assess structures within organoids and sensitively/effectively detect abnormalities caused by perturbations. These capabilities of tissue/organoid clearing and 3D imaging techniques not only extend the utility of organoids in basic biology but can also be applied for quality control of clinical organoid production and large-scale drug screening.
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Affiliation(s)
- Etsuo A. Susaki
- Department of Biochemistry and Systems Biomedicine, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Laboratory for Synthetic Biology, RIKEN Center for Biosystems Dynamics Research, Osaka, Japan
| | - Minoru Takasato
- Laboratory for Human Organogenesis, RIKEN Center for Biosystems Dynamics Research, Kobe, Japan
- Laboratory of Molecular Cell Biology and Development, Department of Animal Development and Physiology, Graduate School of Biostudies, Kyoto University, Kyoto, Japan
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20
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Iyer S, Mukherjee S, Kumar M. Watching the embryo: Evolution of the microscope for the study of embryogenesis. Bioessays 2021; 43:e2000238. [PMID: 33837551 DOI: 10.1002/bies.202000238] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Revised: 03/09/2021] [Accepted: 03/10/2021] [Indexed: 11/08/2022]
Abstract
Embryos and microscopes share a long, remarkable history and biologists have always been intrigued to watch how embryos develop under the microscope. Here we discuss the advances in microscopy which have greatly influenced our current understanding of embryogenesis. We highlight the evolution of microscopes and the optical technologies that have been instrumental in studying various developmental processes. These imaging modalities provide mechanistic insights into the dynamic cellular and molecular events which drive lineage commitment and morphogenetic changes in the developing embryo. We begin the journey with a brief history of microscopy to study embryos. First, we review the principles and optics of light, fluorescence, confocal, and electron microscopy which have been key techniques for imaging cellular and molecular events during embryonic development. Next, we discuss recent key imaging modalities such as light-sheet microscopy, which are suitable for whole embryo imaging. Further, we highlight imaging techniques like multiphoton and super resolution microscopy for beyond light diffraction limit, high resolution imaging. Lastly, we review some of the scattering-based imaging methods and techniques used for imaging human embryos.
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Affiliation(s)
- Sharada Iyer
- Academy of Scientific and Innovative Research (AcCSIR), CSIR-CCMB campus, Uppal road, Hyderabad, 500007, India.,CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
| | | | - Megha Kumar
- CSIR - Centre for Cellular and Molecular Biology, Hyderabad, India
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21
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Gutiérrez-Medina B, Vázquez-Villa A. Visualizing three-dimensional fungal growth using light sheet fluorescence microscopy. Fungal Genet Biol 2021; 150:103549. [PMID: 33675987 DOI: 10.1016/j.fgb.2021.103549] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 02/25/2021] [Indexed: 12/26/2022]
Abstract
The evaluation of morphology is fundamental to comprehend how fungi grow, develop, and interact with the environment. Although fungal growth has been extensively studied associated to two-dimensional geometries, lack of appropriate experimental tools has limited exploration of the complex three-dimensional (3D) structures exhibited by mycelia in more general contexts. In this paper, we report the construction of a light-sheet fluorescence microscope (LSFM) capable of performing time-lapse visualization of 3D biological structures (4D microscopy), and the use of this instrument to follow the dynamics of fungal growth. LSFM uses scanning of selective plane illumination and digital reconstruction to provide 3D images of the specimen. We describe the optical, electronic, and computational means to implement two-color LSFM, and provide detailed procedures for aligning and testing the setup. We successfully demonstrate use of both autofluorescence and specific tagging to image Trichoderma atroviride and Neurospora crassa strains growing in liquid media, over extended times (~12 h) and volumes (~400 × 1500 × 800 μm3) at single-hypha resolution. The excellent image contrast provided by LSFM enables us to visualize the dynamics of mycelial architecture, interactions among hyphae, and measure rates of 3D apical extension. Altogether, our work shows a powerful imaging tool to perform 3D morphological analysis of fungi, from hyphae to mycelium.
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Affiliation(s)
- Braulio Gutiérrez-Medina
- Division of Advanced Materials, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, Mexico.
| | - Alexis Vázquez-Villa
- Division of Advanced Materials, Instituto Potosino de Investigación Científica y Tecnológica, Camino a la Presa San José 2055, 78216 San Luis Potosí, Mexico
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22
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Li B, Ponjavic A, Chen WH, Hopkins L, Hughes C, Ye Y, Bryant C, Klenerman D. Single-Molecule Light-Sheet Microscopy with Local Nanopipette Delivery. Anal Chem 2021; 93:4092-4099. [PMID: 33595281 DOI: 10.1021/acs.analchem.0c05296] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The detection of single molecules in biological systems has rapidly increased in resolution over the past decade. However, the delivery of single molecules remains to be a challenge. Currently, there is no effective method that can both introduce a precise amount of molecules onto or into a single cell at a defined position and then image the cellular response. Here, we have combined light-sheet microscopy with local delivery, using a nanopipette, to accurately deliver individual proteins to a defined position. We call this method local-delivery selective-plane illumination microscopy (ldSPIM). ldSPIM uses a nanopipette and ionic feedback current at the nanopipette tip to control the position from which the molecules are delivered. The number of proteins delivered can be controlled by varying the voltage applied. For single-molecule detection, we implemented single-objective SPIM using a reflective atomic force microscopy cantilever to create a 2 μm thin sheet. Using this setup, we demonstrate that ldSPIM can deliver single fluorescently labeled proteins onto the plasma membrane of HK293 cells or into the cytoplasm. Next, we deposited the aggregates of amyloid-β, which causes proteotoxicity relevant to Alzheimer's disease, onto a single macrophage stably expressing a MyDD88-eGFP fusion construct. Whole-cell imaging in the three-dimensional (3D) mode enables the live detection of MyDD88 accumulation and the formation of myddosome signaling complexes, as a result of the aggregate-induced triggering of toll-like receptor 4. Overall, we demonstrate a novel multifunctional imaging system capable of precise delivery of single proteins to a specific location on the cell surface or inside the cytoplasm and high-speed 3D detection at single-molecule resolution within live cells.
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Affiliation(s)
- Bing Li
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK
| | - Aleks Ponjavic
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK
| | - Wei-Hsin Chen
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK
| | - Lee Hopkins
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, UK
| | - Craig Hughes
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK
| | - Yu Ye
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK
| | - Clare Bryant
- Department of Veterinary Medicine, University of Cambridge, Madingley Rd, Cambridge CB3 0ES, UK
| | - David Klenerman
- Department of Chemistry, University of Cambridge, Lensfield Rd, Cambridge CB2 1EW, UK.,UK Dementia Research Institute at Cambridge, Cambridge CB2 0XY, UK
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23
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Hutson KA, Pulver SH, Ariel P, Naso C, Fitzpatrick DC. Light sheet microscopy of the gerbil cochlea. J Comp Neurol 2020; 529:757-785. [PMID: 32632959 DOI: 10.1002/cne.24977] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 05/13/2020] [Accepted: 06/21/2020] [Indexed: 01/19/2023]
Abstract
Light sheet fluorescence microscopy (LSFM) provides a rapid and complete three-dimensional image of the cochlea. The method retains anatomical relationships-on a micrometer scale-between internal structures such as hair cells, basilar membrane (BM), and modiolus with external surface structures such as the round and oval windows. Immunolabeled hair cells were used to visualize the spiraling BM in the intact cochlea without time intensive dissections or additional histological processing; yet material prepared for LSFM could be rehydrated, the BM dissected out and reimaged at higher resolution with the confocal microscope. In immersion-fixed material, details of the cochlear vasculature were seen throughout the cochlea. Hair cell counts (both inner and outer) as well as frequency maps of the BM were comparable to those obtained by other methods, but with the added dimension of depth. The material provided measures of angular, linear, and vector distance between characteristic frequency regions along the BM. Thus, LSFM provides a unique ability to rapidly image the entire cochlea in a manner applicable to model and interpret physiological results. Furthermore, the three-dimensional organization of the cochlea can be studied at the organ and cellular level with LSFM, and this same material can be taken to the confocal microscope for detailed analysis at the subcellular level.
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Affiliation(s)
- Kendall A Hutson
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Stephen H Pulver
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Pablo Ariel
- Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Caroline Naso
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Douglas C Fitzpatrick
- Department of Otolaryngology/Head and Neck Surgery, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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24
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Hosny NA, Seyforth JA, Spickermann G, Mitchell TJ, Almada P, Chesters R, Mitchell SJ, Chennell G, Vernon AC, Cho K, Srivastava DP, Forster R, Vettenburg T. Planar Airy beam light-sheet for two-photon microscopy. BIOMEDICAL OPTICS EXPRESS 2020; 11:3927-3935. [PMID: 33014576 PMCID: PMC7510906 DOI: 10.1364/boe.395547] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Revised: 05/27/2020] [Accepted: 06/08/2020] [Indexed: 05/22/2023]
Abstract
We demonstrate the first planar Airy light-sheet microscope. Fluorescence light-sheet microscopy has become the method of choice to study large biological samples with cellular or sub-cellular resolution. The propagation-invariant Airy beam enables a ten-fold increase in field-of-view with single-photon excitation; however, the characteristic asymmetry of the light-sheet limits its potential for multi-photon excitation. Here we show how a planar light-sheet can be formed from the curved propagation-invariant Airy beam. The resulting symmetric light sheet excites two-photon fluorescence uniformly across an extended field-of-view without the need for deconvolution. We demonstrate the method for rapid two-photon imaging of large volumes of neuronal tissue.
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Affiliation(s)
- Neveen A. Hosny
- M Squared Life, The Surrey Technology Centre, Guildford, Surrey, GU2 7YG, UK
| | - James A. Seyforth
- M Squared Life, The Surrey Technology Centre, Guildford, Surrey, GU2 7YG, UK
| | - Gunnar Spickermann
- M Squared Life, The Surrey Technology Centre, Guildford, Surrey, GU2 7YG, UK
| | - Thomas J. Mitchell
- M Squared Life, The Surrey Technology Centre, Guildford, Surrey, GU2 7YG, UK
| | - Pedro Almada
- M Squared Life, The Surrey Technology Centre, Guildford, Surrey, GU2 7YG, UK
| | - Robert Chesters
- Basic and Clinical Neuroscience Department, King’s College London, London, SE5 9NU, UK
| | - Scott J. Mitchell
- Basic and Clinical Neuroscience Department, King’s College London, London, SE5 9NU, UK
- UK Dementia Research Institute, King’s College London, London, UK
| | - George Chennell
- Basic and Clinical Neuroscience Department, King’s College London, London, SE5 9NU, UK
| | - Anthony C. Vernon
- Basic and Clinical Neuroscience Department, King’s College London, London, SE5 9NU, UK
- MRC centre For Neurodevelopmental Disorders, King’s College London, London, UK
| | - Kwangwook Cho
- Basic and Clinical Neuroscience Department, King’s College London, London, SE5 9NU, UK
- UK Dementia Research Institute, King’s College London, London, UK
| | - Deepak P. Srivastava
- Basic and Clinical Neuroscience Department, King’s College London, London, SE5 9NU, UK
- MRC centre For Neurodevelopmental Disorders, King’s College London, London, UK
| | - Robert Forster
- M Squared Life, The Surrey Technology Centre, Guildford, Surrey, GU2 7YG, UK
| | - Tom Vettenburg
- School of Physics and Astronomy, University of Exeter, EX4 4QL, Exeter, UK
- School of Science and Engineering, University of Dundee, DD1 4HN, Dundee, UK
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25
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Shemesh Z, Chaimovich G, Gino L, Ozana N, Nylk J, Dholakia K, Zalevsky Z. Reducing data acquisition for light-sheet microscopy by extrapolation between imaged planes. JOURNAL OF BIOPHOTONICS 2020; 13:e202000035. [PMID: 32239792 DOI: 10.1002/jbio.202000035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 03/17/2020] [Accepted: 03/23/2020] [Indexed: 06/11/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) is a powerful technique that can provide high-resolution images of biological samples. Therefore, this technique offers significant improvement for three-dimensional (3D) imaging of living cells. However, producing high-resolution 3D images of a single cell or biological tissues, normally requires high acquisition rate of focal planes, which means a large amount of sample sections. Consequently, it consumes a vast amount of processing time and memory, especially when studying real-time processes inside living cells. We describe an approach to minimize data acquisition by interpolation between planes using a phase retrieval algorithm. We demonstrate this approach on LSFM data sets and show reconstruction of intermediate sections of the sparse samples. Since this method diminishes the required amount of acquisition focal planes, it also reduces acquisition time of samples as well. Our suggested method has proven to reconstruct unacquired intermediate planes from diluted data sets up to 10× fold. The reconstructed planes were found correlated to the original preacquired samples (control group) with correlation coefficient of up to 90%. Given the findings, this procedure appears to be a powerful method for inquiring and analyzing biological samples.
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Affiliation(s)
- Ziv Shemesh
- Faculty of Engineering and the Nanotechnology Center, Bar Ilan University, Ramat-Gan, Israel
| | - Gal Chaimovich
- Faculty of Engineering and the Nanotechnology Center, Bar Ilan University, Ramat-Gan, Israel
| | - Liron Gino
- Faculty of Engineering and the Nanotechnology Center, Bar Ilan University, Ramat-Gan, Israel
| | - Nisan Ozana
- Faculty of Engineering and the Nanotechnology Center, Bar Ilan University, Ramat-Gan, Israel
| | - Jonathan Nylk
- SUPA, School of Physics & Astronomy, Physical Science Building, St Andrews University, St Andrews, UK
| | - Kishan Dholakia
- SUPA, School of Physics & Astronomy, Physical Science Building, St Andrews University, St Andrews, UK
- Department of Physics, College of Science, Yonsei University, Seoul, South Korea
| | - Zeev Zalevsky
- Faculty of Engineering and the Nanotechnology Center, Bar Ilan University, Ramat-Gan, Israel
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26
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Xu Z, Forsberg E, Guo Y, Cai F, He S. Light-Sheet Microscopy for Surface Topography Measurements and Quantitative Analysis. SENSORS 2020; 20:s20102842. [PMID: 32429437 PMCID: PMC7288151 DOI: 10.3390/s20102842] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/06/2020] [Accepted: 05/13/2020] [Indexed: 12/13/2022]
Abstract
A novel light-sheet microscopy (LSM) system that uses the laser triangulation method to quantitatively calculate and analyze the surface topography of opaque samples is discussed. A spatial resolution of at least 10 μm in z-direction, 10 μm in x-direction and 25 μm in y-direction with a large field-of-view (FOV) is achieved. A set of sample measurements that verify the system′s functionality in various applications are presented. The system has a simple mechanical structure, such that the spatial resolution is easily improved by replacement of the objective, and a linear calibration formula, which enables convenient system calibration. As implemented, the system has strong potential for, e.g., industrial sample line inspections, however, since the method utilizes reflected/scattered light, it also has the potential for three-dimensional analysis of translucent and layered structures.
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Affiliation(s)
- Zhanpeng Xu
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
| | - Erik Forsberg
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
| | - Yang Guo
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
| | - Fuhong Cai
- School of Biomedical Engineering, Hainan University, Haikou 570228, China;
| | - Sailing He
- Centre for Optical and Electromagnetic Research, National Engineering Research Center for Optical Instruments, Zhejiang Provincial Key Laboratory for Sensing Technologies, College of Optical Science and Engineering, Zhejiang University, Hangzhou 310058, China; (Z.X.); (E.F.); (Y.G.)
- Correspondence: ; Tel.: +86-571-8820-6525
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27
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von Molitor E, Nürnberg E, Ertongur-Fauth T, Scholz P, Riedel K, Hafner M, Rudolf R, Cesetti T. Analysis of calcium signaling in live human Tongue cell 3D-Cultures upon tastant perfusion. Cell Calcium 2020; 87:102164. [PMID: 32014795 DOI: 10.1016/j.ceca.2020.102164] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 11/29/2019] [Accepted: 01/16/2020] [Indexed: 02/06/2023]
Abstract
Bridging the gap between two-dimensional cell cultures and complex in vivo tissues, three-dimensional cell culture models are of increasing interest in the fields of cell biology and pharmacology. However, present challenges hamper live cell imaging of three-dimensional cell cultures. These include (i) the stabilization of these structures under perfusion conditions, (ii) the recording of many z-planes at high spatio-temporal resolution, (iii) and the data analysis that ranges in complexity from whole specimens to single cells. Here, we addressed these issues for the time-lapse analysis of Ca2+ signaling in spheroids composed of human tongue-derived HTC-8 cells upon perfusion of gustatory substances. Live cell imaging setups for confocal and light sheet microscopy were developed that allow simple and robust spheroid stabilization and high-resolution microscopy with perfusion. Visualization of spheroids made of HTC-8 cells expressing the G-GECO fluorescent Ca2+ sensor revealed Ca2+ transients that showed similar kinetics but different amplitudes upon perfusion of bitter compounds Salicine and Saccharin. Dose-dependent responses to Saccharin required extracellular Ca2+. From the border towards the center of spheroids, compound-induced Ca2+ signals were progressively delayed and decreased in amplitude. Stimulation with ATP led to strong Ca2+ transients that were faster than those evoked by the bitter compounds and blockade of purinergic receptors with Suramin abutted the response to Saccharin, suggesting that ATP mediates a positive autocrine and paracrine feedback. Imaging of ATP-induced Ca2+ transients with light sheet microscopy allowed acquisition over a z-depth of 100 μm without losing spatial and temporal resolution. In summary, the presented approaches permit the study of fast cellular signaling in three-dimensional cultures upon compound perfusion.
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Affiliation(s)
- Elena von Molitor
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany
| | - Elina Nürnberg
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany
| | | | | | | | - Mathias Hafner
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany.
| | - Rüdiger Rudolf
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany; Interdisciplinary Center for Neurosciences, Heidelberg University, 69120 Heidelberg, Germany.
| | - Tiziana Cesetti
- Institute of Molecular and Cell Biology, Hochschule Mannheim, 68163 Mannheim, Germany
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28
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An S, Ziegler KF, Zhang P, Wang Y, Kwok T, Xu F, Bi C, Matosevic S, Yin P, Li T, Huang F. Axial plane single-molecule super-resolution microscopy of whole cells. BIOMEDICAL OPTICS EXPRESS 2020; 11:461-479. [PMID: 32010528 PMCID: PMC6968758 DOI: 10.1364/boe.377890] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 12/12/2019] [Accepted: 12/13/2019] [Indexed: 06/10/2023]
Abstract
Fluorescence nanoscopy has become an indispensable tool for studying organelle structures, protein dynamics, and interactions in biological sciences. Single-molecule localization microscopy can now routinely achieve 10-50 nm resolution through fluorescently labeled specimens in lateral optical sections. However, visualizing structures organized along the axial direction demands scanning and imaging each of the lateral imaging planes with fine intervals throughout the whole cell. This iterative process suffers from photobleaching of tagged probes, is susceptible to alignment artifacts and also limits the imaging speed. Here, we focused on the axial plane super-resolution imaging which integrated the single-objective light-sheet illumination and axial plane optical imaging with single-molecule localization technique to resolve nanoscale cellular architectures along the axial (or depth) dimension without scanning. We demonstrated that this method is compatible with DNA points accumulation for imaging in nanoscale topography (DNA-PAINT) and exchange-PAINT by virtue of its light-sheet illumination, allowing multiplexed super-resolution imaging throughout the depth of whole cells. We further demonstrated this proposed system by resolving the axial distributions of intracellular organelles such as microtubules, mitochondria, and nuclear pore complexes in both COS-7 cells and glioblastoma patient-derived tumor cells.
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Affiliation(s)
- Sha An
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
- State Key Laboratory of Transient Optics and Photonics, Xi'an Institute of Optics and Precision Mechanics, Chinese Academy of Sciences, Xi'an 710119, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- S.A. and K.F.Z. contributed equally to this work
| | - Karl Ferdinand Ziegler
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- S.A. and K.F.Z. contributed equally to this work
| | - Peiyi Zhang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Yu Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tim Kwok
- Birck Nanotechnology Center, Purdue University, West Lafayette, IN 47907, USA
| | - Fan Xu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Cheng Bi
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Sandro Matosevic
- Department of Industrial and Physical Pharmacy, Purdue University, West Lafayette, IN 47907, USA
| | - Peng Yin
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA
| | - Tongcang Li
- Department of Physics and Astronomy, Purdue University, West Lafayette, IN 47907, USA
- School of Electrical and Computer Engineering, Purdue University, West Lafayette, IN 47907, USA
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, IN 47907, USA
- Purdue Institute of Inflammation, Immunology and Infectious Disease, Purdue University, West Lafayette, IN 47907, USA
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29
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Vallejo Ramirez PP, Zammit J, Vanderpoorten O, Riche F, Blé FX, Zhou XH, Spiridon B, Valentine C, Spasov SE, Oluwasanya PW, Goodfellow G, Fantham MJ, Siddiqui O, Alimagham F, Robbins M, Stretton A, Simatos D, Hadeler O, Rees EJ, Ströhl F, Laine RF, Kaminski CF. OptiJ: Open-source optical projection tomography of large organ samples. Sci Rep 2019; 9:15693. [PMID: 31666606 PMCID: PMC6821862 DOI: 10.1038/s41598-019-52065-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.
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Affiliation(s)
- Pedro P Vallejo Ramirez
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Joseph Zammit
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Oliver Vanderpoorten
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Fergus Riche
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Francois-Xavier Blé
- Clinical Discovery Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Xiao-Hong Zhou
- Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Bogdan Spiridon
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | | | - Simeon E Spasov
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | | | - Gemma Goodfellow
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Marcus J Fantham
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Omid Siddiqui
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Farah Alimagham
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Miranda Robbins
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Andrew Stretton
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Dimitrios Simatos
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Oliver Hadeler
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Eric J Rees
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Florian Ströhl
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory for Molecular Cell Biology (LMCB), University College London, Gower Street, London, WC1E 6BT, UK
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.
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Abstract
Among optical imaging techniques light sheet fluorescence microscopy is one of the most attractive for capturing high-speed biological dynamics unfolding in three dimensions. The technique is potentially millions of times faster than point-scanning techniques such as two-photon microscopy. However light sheet microscopes are limited by volume scanning rate and/or camera speed. We present speed-optimized Objective Coupled Planar Illumination (OCPI) microscopy, a fast light sheet technique that avoids compromising image quality or photon efficiency. Our fast scan system supports 40 Hz imaging of 700 μm-thick volumes if camera speed is sufficient. We also address the camera speed limitation by introducing Distributed Planar Imaging (DPI), a scaleable technique that parallelizes image acquisition across cameras. Finally, we demonstrate fast calcium imaging of the larval zebrafish brain and find a heartbeat-induced artifact, removable when the imaging rate exceeds 15 Hz. These advances extend the reach of fluorescence microscopy for monitoring fast processes in large volumes. Light sheet microscopy holds potential for imaging dynamics in 3D biological specimens, but is limited by scan speed and camera acquisition rate. Here the authors address both issues by developing speed-optimized Objective Coupled Planar Illumination and parallelizing image acquisition across cameras to achieve 40 Hz imaging over thick samples.
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31
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Next-generation imaging of the skeletal system and its blood supply. Nat Rev Rheumatol 2019; 15:533-549. [PMID: 31395974 DOI: 10.1038/s41584-019-0274-y] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 12/16/2022]
Abstract
Bone is organized in a hierarchical 3D architecture. Traditionally, analysis of the skeletal system was based on bone mass assessment by radiographic methods or on the examination of bone structure by 2D histological sections. Advanced imaging technologies and big data analysis now enable the unprecedented examination of bone and provide new insights into its 3D macrostructure and microstructure. These technologies comprise ex vivo and in vivo methods including high-resolution computed tomography (CT), synchrotron-based imaging, X-ray microscopy, ultra-high-field magnetic resonance imaging (MRI), light-sheet fluorescence microscopy, confocal and intravital two-photon imaging. In concert, these techniques have been used to detect and quantify a novel vascular system of trans-cortical vessels in bone. Furthermore, structures such as the lacunar network, which harbours and connects osteocytes, become accessible for 3D imaging and quantification using these methods. Next-generation imaging of the skeletal system and its blood supply are anticipated to contribute to an entirely new understanding of bone tissue composition and function, from macroscale to nanoscale, in health and disease. These insights could provide the basis for early detection and precision-type intervention of bone disorders in the future.
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32
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Sonnen KF, Merten CA. Microfluidics as an Emerging Precision Tool in Developmental Biology. Dev Cell 2019; 48:293-311. [PMID: 30753835 DOI: 10.1016/j.devcel.2019.01.015] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2018] [Revised: 12/13/2018] [Accepted: 01/10/2019] [Indexed: 12/18/2022]
Abstract
Microfluidics has become a precision tool in modern biology. It enables omics data to be obtained from individual cells, as compared to averaged signals from cell populations, and it allows manipulation of biological specimens in entirely new ways. Cells and organisms can be perturbed at extraordinary spatiotemporal resolution, revealing mechanistic insights that would otherwise remain hidden. In this perspective article, we discuss the current and future impact of microfluidic technology in the field of developmental biology. In addition, we provide detailed information on how to start using this technology even without prior experience.
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Affiliation(s)
| | - Christoph A Merten
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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33
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Abstract
Embryonic development is highly complex and dynamic, requiring the coordination of numerous molecular and cellular events at precise times and places. Advances in imaging technology have made it possible to follow developmental processes at cellular, tissue, and organ levels over time as they take place in the intact embryo. Parallel innovations of in vivo probes permit imaging to report on molecular, physiological, and anatomical events of embryogenesis, but the resulting multidimensional data sets pose significant challenges for extracting knowledge. In this review, we discuss recent and emerging advances in imaging technologies, in vivo labeling, and data processing that offer the greatest potential for jointly deciphering the intricate cellular dynamics and the underlying molecular mechanisms. Our discussion of the emerging area of “image-omics” highlights both the challenges of data analysis and the promise of more fully embracing computation and data science for rapidly advancing our understanding of biology.
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Affiliation(s)
- Francesco Cutrale
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
| | - Scott E. Fraser
- Department of Biomedical Engineering, University of Southern California, Los Angeles, California 90089, USA
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Le A. Trinh
- Translational Imaging Center, University of Southern California, Los Angeles, California 90089, USA
- Division of Molecular and Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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34
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Longitudinal monitoring of cancer cell subpopulations in monolayers, 3D spheroids, and xenografts using the photoconvertible dye DiR. Sci Rep 2019; 9:5713. [PMID: 30952965 PMCID: PMC6450962 DOI: 10.1038/s41598-019-42165-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 03/26/2019] [Indexed: 12/21/2022] Open
Abstract
A central challenge in cancer biology is the identification, longitudinal tracking, and -omics analysis of specific cells in vivo. To this aim, photoconvertible fluorescent dyes are reporters that are characterized by a set of excitation and emission spectra that can be predictably altered, resulting in a distinct optical signature following irradiation with a specific light source. One such dye, DiR, is an infrared fluorescent membrane probe that can irreversibly undergo such a switch. Here, we demonstrate a method using DiR for the spatiotemporal labeling of specific cells in the context of cancer cell monolayer cultures, 3D tumor spheroids, and in vivo melanoma xenograft models to monitor the proliferation of cellular subpopulations of interest over time. Importantly, the photoconversion process is performed in situ, supporting the pursuit of novel avenues of research in molecular pathology.
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35
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Haouas M, Chebbi B, Golub I. Extension of the span and optimization of the optical "magic carpet": generation of a wide quasi-nondiffracting light sheet. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2019; 36:124-131. [PMID: 30645347 DOI: 10.1364/josaa.36.000124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 11/27/2018] [Indexed: 06/09/2023]
Abstract
Light sheet illumination is the basis in developing light sheet microscopy (LSM), a technique with significant advantages compared with other classical techniques. Most proposed optical systems to generate light sheets for LSM use many optical elements, which require extensive adjustments and are costly; moreover, they generate a nonuniform or semiuniform light sheet or have a short depth of field (DOF). A simple scheme using a pair of double slits and a cylindrical lens for generating a quasi-nondiffracting 2D light sheet was reported in Opt. Lett.40, 5121 (2015)OPLEDP0146-959210.1364/OL.40.005121. In the present investigation, we elaborate on the optimization of the mask used. As the separation between the two slits increases, the light sheet becomes thinner and the DOF smaller and vice versa. The slits' width does not affect the light sheet thickness, but it does affect the intensity of the side lobes. For convergence angles of the inner slits from 0.75° to 8°, an optimum ratio of the slits' separation/width of 2.182 is recommended. The obtained light sheet is quasi-diffraction-free, namely, while its DOF is comparable with that of a Gaussian beam, its diffraction broadening is substantially smaller. We also add to the previously developed configuration a Powell lens in order to expand the beam in the spanwise direction while keeping nearly constant intensity in this dimension. We perform scalar diffraction theory calculations and conduct measurements showing the nearly constant intensity in the significantly broadened span of the light sheet. Potential applications for the augmented width include imaging of certain large embryos, laser micromachining, and microparticle image velocimetry.
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36
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Baek KI, Ding Y, Chang CC, Chang M, Sevag Packard RR, Hsu JJ, Fei P, Hsiai TK. Advanced microscopy to elucidate cardiovascular injury and regeneration: 4D light-sheet imaging. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2018; 138:105-115. [PMID: 29752956 PMCID: PMC6226366 DOI: 10.1016/j.pbiomolbio.2018.05.003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Revised: 04/30/2018] [Accepted: 05/04/2018] [Indexed: 12/20/2022]
Abstract
The advent of 4-dimensional (4D) light-sheet fluorescence microscopy (LSFM) has provided an entry point for rapid image acquisition to uncover real-time cardiovascular structure and function with high axial resolution and minimal photo-bleaching/-toxicity. We hereby review the fundamental principles of our LSFM system to investigate cardiovascular morphogenesis and regeneration after injury. LSFM enables us to reveal the micro-circulation of blood cells in the zebrafish embryo and assess cardiac ventricular remodeling in response to chemotherapy-induced injury using an automated segmentation approach. Next, we review two distinct mechanisms underlying zebrafish vascular regeneration following tail amputation. We elucidate the role of endothelial Notch signaling to restore vascular regeneration after exposure to the redox active ultrafine particles (UFP) in air pollutants. By manipulating the blood viscosity and subsequently, endothelial wall shear stress, we demonstrate the mechanism whereby hemodynamic shear forces impart both mechanical and metabolic effects to modulate vascular regeneration. Overall, the implementation of 4D LSFM allows for the elucidation of mechanisms governing cardiovascular injury and regeneration with high spatiotemporal resolution.
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Affiliation(s)
- Kyung In Baek
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Yichen Ding
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Chih-Chiang Chang
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Megan Chang
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - René R Sevag Packard
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Jeffrey J Hsu
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA.
| | - Peng Fei
- School of Optical and Electronic Information, Huazhong University of Science and Technology, Wuhan 430074, China.
| | - Tzung K Hsiai
- Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, Los Angeles, CA 90095, USA; Medical Engineering, California Institute of Technology, Pasadena, CA 91106, USA.
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37
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Ovečka M, von Wangenheim D, Tomančák P, Šamajová O, Komis G, Šamaj J. Multiscale imaging of plant development by light-sheet fluorescence microscopy. NATURE PLANTS 2018; 4:639-650. [PMID: 30185982 DOI: 10.1038/s41477-018-0238-2] [Citation(s) in RCA: 63] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Accepted: 07/31/2018] [Indexed: 05/21/2023]
Abstract
Light-sheet fluorescence microscopy (LSFM) methods collectively represent the major breakthrough in developmental bio-imaging of living multicellular organisms. They are becoming a mainstream approach through the development of both commercial and custom-made LSFM platforms that are adjusted to diverse biological applications. Based on high-speed acquisition rates under conditions of low light exposure and minimal photo-damage of the biological sample, these methods provide ideal means for long-term and in-depth data acquisition during organ imaging at single-cell resolution. The introduction of LSFM methods into biology extended our understanding of pattern formation and developmental progress of multicellular organisms from embryogenesis to adult body. Moreover, LSFM imaging allowed the dynamic visualization of biological processes under almost natural conditions. Here, we review the most important, recent biological applications of LSFM methods in developmental studies of established and emerging plant model species, together with up-to-date methods of data editing and evaluation for modelling of complex biological processes. Recent applications in animal models push LSFM into the forefront of current bio-imaging approaches. Since LSFM is now the single most effective method for fast imaging of multicellular organisms, allowing quantitative analyses of their long-term development, its broader use in plant developmental biology will likely bring new insights.
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Affiliation(s)
- Miroslav Ovečka
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Daniel von Wangenheim
- Plant Sciences Division, School of Biosciences, University of Nottingham, Sutton Bonington Campus, Loughborough, UK
| | - Pavel Tomančák
- Max Planck Institute of Molecular Cell Biology and Genetics, Dresden, Germany
| | - Olga Šamajová
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - George Komis
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic
| | - Jozef Šamaj
- Centre of the Region Haná for Biotechnological and Agricultural Research, Palacký University Olomouc, Olomouc, Czech Republic.
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38
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Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC. Recent Progress in Light Sheet Microscopy for Biological Applications. APPLIED SPECTROSCOPY 2018; 72:1137-1169. [PMID: 29926744 DOI: 10.1177/0003702818778851] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.
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Affiliation(s)
- Krishnendu Chatterjee
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 3 Department of Engineering and System Science, National Tsing-Hua University, Hsinchu, Taiwan
| | - Feby Wijaya Pratiwi
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 4 Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Peilin Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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39
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Mzinza DT, Fleige H, Laarmann K, Willenzon S, Ristenpart J, Spanier J, Sutter G, Kalinke U, Valentin-Weigand P, Förster R. Application of light sheet microscopy for qualitative and quantitative analysis of bronchus-associated lymphoid tissue in mice. Cell Mol Immunol 2018; 15:875-887. [PMID: 29429996 PMCID: PMC6207560 DOI: 10.1038/cmi.2017.150] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2017] [Revised: 10/27/2017] [Accepted: 10/28/2017] [Indexed: 01/09/2023] Open
Abstract
Bronchus-associated lymphoid tissue (BALT) develops at unpredictable locations around lung bronchi following pulmonary inflammation. The formation and composition of BALT have primarily been investigated by immunohistology that, due to the size of the invested organ, is usually restricted to a limited number of histological sections. To assess the entire BALT of the lung, other approaches are urgently needed. Here, we introduce a novel light sheet microscopy-based approach for assessing lymphoid tissue in the lung. Using antibody staining of whole lung lobes and optical clearing by organic solvents, we present a method that allows in-depth visualization of the entire bronchial tree, the lymphatic vasculature and the immune cell composition of the induced BALT. Furthermore, three-dimensional analysis of the entire lung allows the qualitative and quantitative enumeration of the induced BALT. Using this approach, we show that a single intranasal application of the replication-deficient poxvirus MVA induces BALT that constitutes up to 8% of the entire lung volume in mice deficient in CCR7, in contrast to wild type mice (WT). Furthermore, BALT induced by heat-inactivated E. coli is dominated by a pronounced T cell infiltration in Cxcr5-deficient mice, in contrast to WT mice.
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Affiliation(s)
| | - Henrike Fleige
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Kristin Laarmann
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | | | | | - Julia Spanier
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz-Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Gerd Sutter
- Institute for Infectious Diseases and Zoonoses, University of Munich LMU, Munich, Germany
| | - Ulrich Kalinke
- Institute for Experimental Infection Research, TWINCORE, Centre for Experimental and Clinical Infection Research, a joint venture between the Helmholtz-Centre for Infection Research and the Hannover Medical School, Hannover, Germany
| | - Peter Valentin-Weigand
- Institute for Microbiology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Reinhold Förster
- Institute of Immunology, Hannover Medical School, Hannover, Germany.
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40
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Wu C, Le H, Ran S, Singh M, Larina IV, Mayerich D, Dickinson ME, Larin KV. Comparison and combination of rotational imaging optical coherence tomography and selective plane illumination microscopy for embryonic study. BIOMEDICAL OPTICS EXPRESS 2017; 8:4629-4639. [PMID: 29082090 PMCID: PMC5654805 DOI: 10.1364/boe.8.004629] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2017] [Revised: 09/16/2017] [Accepted: 09/16/2017] [Indexed: 05/04/2023]
Abstract
Several optical imaging techniques have been applied for high-resolution embryonic imaging using different contrast mechanisms, each with their own benefits and limitations. In this study, we imaged the same E9.5 mouse embryo with rotational imaging optical coherence tomography (RI-OCT) and selective plane illumination microscopy (SPIM). RI-OCT overcomes optical penetration limits of traditional OCT imaging that prohibit full-body imaging of mouse embryos at later stages by imaging the samples from multiple angles. SPIM enables high-resolution, 3D imaging with less phototoxicity and photobleaching than laser scanning confocal microscopy (LSCM) by illuminating the sample with a focused sheet of light. Side by side comparisons are supplemented with co-registered images. The results demonstrate that SPIM and RI-OCT are highly complementary and could provide more comprehensive tissue characterization for mouse embryonic research.
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Affiliation(s)
- Chen Wu
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
| | - Henry Le
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77584, USA
| | - Shihao Ran
- Department of Electrical and Computer Engineering, University of Houston, Houston, TX 77204, USA
| | - Manmohan Singh
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
| | - Irina V. Larina
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77584, USA
| | - David Mayerich
- Department of Electrical and Computer Engineering, University of Houston, Houston, TX 77204, USA
| | - Mary E. Dickinson
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77584, USA
- Equal contribution
| | - Kirill V. Larin
- Department of Biomedical Engineering, University of Houston, Houston, TX 77204, USA
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77584, USA
- Interdisciplinary Laboratory of Biophotonics, Tomsk State University, Tomsk 634050, Russia
- Equal contribution
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41
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Gibbs HC, Chang-Gonzalez A, Hwang W, Yeh AT, Lekven AC. Midbrain-Hindbrain Boundary Morphogenesis: At the Intersection of Wnt and Fgf Signaling. Front Neuroanat 2017; 11:64. [PMID: 28824384 PMCID: PMC5541008 DOI: 10.3389/fnana.2017.00064] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 07/17/2017] [Indexed: 01/09/2023] Open
Abstract
A constriction in the neural tube at the junction of the midbrain and hindbrain is a conserved feature of vertebrate embryos. The constriction is a defining feature of the midbrain-hindbrain boundary (MHB), a signaling center that patterns the adjacent midbrain and rostral hindbrain and forms at the junction of two gene expression domains in the early neural plate: an anterior otx2/wnt1 positive domain and a posterior gbx/fgf8 positive domain. otx2 and gbx genes encode mutually repressive transcription factors that create a lineage restriction boundary at their expression interface. Wnt and Fgf genes form a mutually dependent feedback system that maintains their expression domains on the otx2 or gbx side of the boundary, respectively. Constriction morphogenesis occurs after these conserved gene expression domains are established and while their mutual interactions maintain their expression pattern; consequently, mutant studies in zebrafish have led to the suggestion that constriction morphogenesis should be considered a unique phase of MHB development. We analyzed MHB morphogenesis in fgf8 loss of function zebrafish embryos using a reporter driven by the conserved wnt1 enhancer to visualize anterior boundary cells. We found that fgf8 loss of function results in a re-activation of wnt1 reporter expression posterior to the boundary simultaneous with an inactivation of the wnt1 reporter in the anterior boundary cells, and that these events correlate with relaxation of the boundary constriction. In consideration of other results that correlate the boundary constriction with Wnt and Fgf expression, we propose that the maintenance of an active Wnt-Fgf feedback loop is a key factor in driving the morphogenesis of the MHB constriction.
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Affiliation(s)
- Holly C Gibbs
- Department of Biomedical Engineering, Texas A&M UniversityCollege Station, TX, United States
| | - Ana Chang-Gonzalez
- Department of Biomedical Engineering, Texas A&M UniversityCollege Station, TX, United States
| | - Wonmuk Hwang
- Department of Biomedical Engineering, Texas A&M UniversityCollege Station, TX, United States.,Department of Materials Science and Engineering, Texas A&M UniversityCollege Station, TX, United States.,School of Computational Sciences, Korea Institute for Advanced StudySeoul, South Korea
| | - Alvin T Yeh
- Department of Biomedical Engineering, Texas A&M UniversityCollege Station, TX, United States
| | - Arne C Lekven
- Department of Biology, Texas A&M UniversityCollege Station, TX, United States
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42
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Singh JN, Nowlin TM, Seedorf GJ, Abman SH, Shepherd DP. Quantifying three-dimensional rodent retina vascular development using optical tissue clearing and light-sheet microscopy. JOURNAL OF BIOMEDICAL OPTICS 2017; 22:76011. [PMID: 28717817 PMCID: PMC5514054 DOI: 10.1117/1.jbo.22.7.076011] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 06/23/2017] [Indexed: 05/03/2023]
Abstract
Retinal vasculature develops in a highly orchestrated three-dimensional (3-D) sequence. The stages of retinal vascularization are highly susceptible to oxygen perturbations. We demonstrate that optical tissue clearing of intact rat retinas and light-sheet microscopy provides rapid 3-D characterization of vascular complexity during retinal development. Compared with flat mount preparations that dissect the retina and primarily image the outermost vascular layers, intact cleared retinas imaged using light-sheet fluorescence microscopy display changes in the 3-D retinal vasculature rapidly without the need for point scanning techniques. Using a severe model of retinal vascular disruption, we demonstrate that a simple metric based on Sholl analysis captures the vascular changes observed during retinal development in 3-D. Taken together, these results provide a methodology for rapidly quantifying the 3-D development of the entire rodent retinal vasculature.
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Affiliation(s)
- Jasmine N. Singh
- University of Colorado Denver, Department of Physics, Denver, Colorado, United States
- University of Colorado Anschutz Medical Campus, Pediatric Heart Lung Center, Department of Pediatrics, Aurora, Colorado, United States
| | - Taylor M. Nowlin
- University of Colorado Anschutz Medical Campus, Pediatric Heart Lung Center, Department of Pediatrics, Aurora, Colorado, United States
| | - Gregory J. Seedorf
- University of Colorado Anschutz Medical Campus, Pediatric Heart Lung Center, Department of Pediatrics, Aurora, Colorado, United States
| | - Steven H. Abman
- University of Colorado Anschutz Medical Campus, Pediatric Heart Lung Center, Department of Pediatrics, Aurora, Colorado, United States
| | - Douglas P. Shepherd
- University of Colorado Denver, Department of Physics, Denver, Colorado, United States
- University of Colorado Anschutz Medical Campus, Pediatric Heart Lung Center, Department of Pediatrics, Aurora, Colorado, United States
- Address all correspondence to: Douglas P. Shepherd, E-mail:
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43
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Abstract
Live imaging provides the ability to continuously track dynamic cellular and developmental processes in real time. Drosophila larval imaginal discs have been used to study many biological processes, such as cell proliferation, differentiation, growth, migration, apoptosis, competition, cell-cell signaling, and compartmental boundary formation. However, methods for the long-term ex vivo culture and live imaging of the imaginal discs have not been satisfactory, despite many efforts. Recently, we developed a method for the long-term ex vivo culture and live imaging of imaginal discs for up to 18 h. In addition to using a high insulin concentration in the culture medium, a low-melting agarose was also used to embed the disc to prevent it from drifting during the imaging period. This report uses the eye-antennal discs as an example. Photoreceptor R3/4-specific mδ0.5-Ga4 expression was followed to demonstrate that photoreceptor differentiation and ommatidial rotation can be observed during a 10 h live imaging period. This is a detailed protocol describing this simple method.
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Affiliation(s)
- Chia-Kang Tsao
- Institute of Genomic Sciences, National Yang-Ming University; Institute of Molecular Biology, Academia Sinica
| | - Hui-Yu Ku
- Institute of Genomic Sciences, National Yang-Ming University; Institute of Molecular Biology, Academia Sinica
| | - Y Henry Sun
- Institute of Genomic Sciences, National Yang-Ming University; Institute of Molecular Biology, Academia Sinica;
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44
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Andilla J, Jorand R, Olarte OE, Dufour AC, Cazales M, Montagner YLE, Ceolato R, Riviere N, Olivo-Marin JC, Loza-Alvarez P, Lorenzo C. Imaging tissue-mimic with light sheet microscopy: A comparative guideline. Sci Rep 2017; 7:44939. [PMID: 28322312 PMCID: PMC5381005 DOI: 10.1038/srep44939] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/16/2017] [Indexed: 01/04/2023] Open
Abstract
Tissue mimics (TMs) on the scale of several hundred microns provide a beneficial cell culture configuration for in vitro engineered tissue and are currently under the spotlight in tissue engineering and regenerative medicine. Due to the cell density and size, TMs are fairly inaccessible to optical observation and imaging within these samples remains challenging. Light Sheet Fluorescence Microscopy (LSFM)- an emerging and attractive technique for 3D optical sectioning of large samples- appears to be a particularly well-suited approach to deal with them. In this work, we compared the effectiveness of different light sheet illumination modalities reported in the literature to improve resolution and/or light exposure for complex 3D samples. In order to provide an acute and fair comparative assessment, we also developed a systematic, computerized benchmarking method. The outcomes of our experiment provide meaningful information for valid comparisons and arises the main differences between the modalities when imaging different types of TMs.
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Affiliation(s)
- Jordi Andilla
- ICFO-Institut de Ciences Fotonique, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
| | | | - Omar E Olarte
- ICFO-Institut de Ciences Fotonique, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
| | - Alexandre C Dufour
- Institut Pasteur BioImage Analysis Unit, F-75015, Paris, France.,CNRS, UMR-3691, F-75015 Paris, France
| | | | - Yoann L E Montagner
- Institut Pasteur BioImage Analysis Unit, F-75015, Paris, France.,CNRS, UMR-3691, F-75015 Paris, France
| | - Romain Ceolato
- Onera, The French Aerospace Lab, F-31100 Toulouse, France
| | | | | | - Pablo Loza-Alvarez
- ICFO-Institut de Ciences Fotonique, Av. Carl Friedrich Gauss, 3, 08860 Castelldefels, Barcelona, Spain
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45
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Schmitz A, Fischer SC, Mattheyer C, Pampaloni F, Stelzer EHK. Multiscale image analysis reveals structural heterogeneity of the cell microenvironment in homotypic spheroids. Sci Rep 2017; 7:43693. [PMID: 28255161 PMCID: PMC5334646 DOI: 10.1038/srep43693] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2016] [Accepted: 01/30/2017] [Indexed: 12/31/2022] Open
Abstract
Three-dimensional multicellular aggregates such as spheroids provide reliable in vitro substitutes for tissues. Quantitative characterization of spheroids at the cellular level is fundamental. We present the first pipeline that provides three-dimensional, high-quality images of intact spheroids at cellular resolution and a comprehensive image analysis that completes traditional image segmentation by algorithms from other fields. The pipeline combines light sheet-based fluorescence microscopy of optically cleared spheroids with automated nuclei segmentation (F score: 0.88) and concepts from graph analysis and computational topology. Incorporating cell graphs and alpha shapes provided more than 30 features of individual nuclei, the cellular neighborhood and the spheroid morphology. The application of our pipeline to a set of breast carcinoma spheroids revealed two concentric layers of different cell density for more than 30,000 cells. The thickness of the outer cell layer depends on a spheroid’s size and varies between 50% and 75% of its radius. In differently-sized spheroids, we detected patches of different cell densities ranging from 5 × 105 to 1 × 106 cells/mm3. Since cell density affects cell behavior in tissues, structural heterogeneities need to be incorporated into existing models. Our image analysis pipeline provides a multiscale approach to obtain the relevant data for a system-level understanding of tissue architecture.
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Affiliation(s)
- Alexander Schmitz
- Physical Biology/Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt - Macromolecular Complexes (CEF - MC), Goethe Universität - Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15 - D-60348 Frankfurt am Main, Germany
| | - Sabine C Fischer
- Physical Biology/Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt - Macromolecular Complexes (CEF - MC), Goethe Universität - Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15 - D-60348 Frankfurt am Main, Germany
| | - Christian Mattheyer
- Physical Biology/Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt - Macromolecular Complexes (CEF - MC), Goethe Universität - Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15 - D-60348 Frankfurt am Main, Germany
| | - Francesco Pampaloni
- Physical Biology/Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt - Macromolecular Complexes (CEF - MC), Goethe Universität - Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15 - D-60348 Frankfurt am Main, Germany
| | - Ernst H K Stelzer
- Physical Biology/Physikalische Biologie (IZN, FB 15), Buchmann Institute for Molecular Life Sciences (BMLS), Cluster of Excellence Frankfurt - Macromolecular Complexes (CEF - MC), Goethe Universität - Frankfurt am Main (Campus Riedberg), Max-von-Laue-Straße 15 - D-60348 Frankfurt am Main, Germany
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46
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47
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Pampaloni F, Knuppertz L, Hamann A, Osiewacz HD, Stelzer EHK. Three-Dimensional Live Imaging of Filamentous Fungi with Light Sheet-Based Fluorescence Microscopy (LSFM). Methods Mol Biol 2017; 1563:19-31. [PMID: 28324599 DOI: 10.1007/978-1-4939-6810-7_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We describe a method for the three-dimensional live imaging of filamentous fungi with light sheet-based fluorescence microscopy (LSFM). LSFM provides completely new opportunities to investigate the biology of fungal cells and other microorganisms with high spatial and temporal resolution. As an example, we study the established aging model Podospora anserina. The protocol explains the mounting of the live fungi for the light sheet imaging, the imaging procedure and illustrates basic image processing of data.
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Affiliation(s)
- Francesco Pampaloni
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 15, D-60438, Frankfurt am Main, Germany.
| | - Laura Knuppertz
- Institute of Molecular Biosciences and Cluster of Excellence Frankfurt Macromolecular Complexes, Department of Biosciences, Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Andrea Hamann
- Institute of Molecular Biosciences and Cluster of Excellence Frankfurt Macromolecular Complexes, Department of Biosciences, Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Heinz D Osiewacz
- Institute of Molecular Biosciences and Cluster of Excellence Frankfurt Macromolecular Complexes, Department of Biosciences, Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 9, 60438, Frankfurt am Main, Germany
| | - Ernst H K Stelzer
- Physical Biology Group, Buchmann Institute for Molecular Life Sciences (BMLS), Goethe Universität Frankfurt am Main, Max-von-Laue-Str. 15, D-60438, Frankfurt am Main, Germany
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48
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Fahrbach SE. Editorial overview: Neuroscience: Back to the future in the developing insect nervous system. CURRENT OPINION IN INSECT SCIENCE 2016; 18:iv-vi. [PMID: 27939719 DOI: 10.1016/j.cois.2016.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Affiliation(s)
- Susan E Fahrbach
- Department of Biology, Wake Forest University, Winston-Salem, NC 27109, USA.
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49
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Hernández-Vega A, Marsal M, Pouille PA, Tosi S, Colombelli J, Luque T, Navajas D, Pagonabarraga I, Martín-Blanco E. Polarized cortical tension drives zebrafish epiboly movements. EMBO J 2016; 36:25-41. [PMID: 27834222 DOI: 10.15252/embj.201694264] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2016] [Revised: 09/18/2016] [Accepted: 09/26/2016] [Indexed: 11/09/2022] Open
Abstract
The principles underlying the biomechanics of morphogenesis are largely unknown. Epiboly is an essential embryonic event in which three tissues coordinate to direct the expansion of the blastoderm. How and where forces are generated during epiboly, and how these are globally coupled remains elusive. Here we developed a method, hydrodynamic regression (HR), to infer 3D pressure fields, mechanical power, and cortical surface tension profiles. HR is based on velocity measurements retrieved from 2D+T microscopy and their hydrodynamic modeling. We applied HR to identify biomechanically active structures and changes in cortex local tension during epiboly in zebrafish. Based on our results, we propose a novel physical description for epiboly, where tissue movements are directed by a polarized gradient of cortical tension. We found that this gradient relies on local contractile forces at the cortex, differences in elastic properties between cortex components and the passive transmission of forces within the yolk cell. All in all, our work identifies a novel way to physically regulate concerted cellular movements that might be instrumental for the mechanical control of many morphogenetic processes.
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Affiliation(s)
- Amayra Hernández-Vega
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - María Marsal
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Philippe-Alexandre Pouille
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
| | - Sébastien Tosi
- Advanced Digital Microscopy Core Facility (ADMCF), Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Julien Colombelli
- Advanced Digital Microscopy Core Facility (ADMCF), Institute for Research in Biomedicine (IRB Barcelona) The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Tomás Luque
- Institute for Bioengineering of Catalonia, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Facultad de Medicina i Ciencies de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Daniel Navajas
- Institute for Bioengineering of Catalonia, Barcelona, Spain.,CIBER de Enfermedades Respiratorias (CIBERES), Madrid, Spain.,Facultad de Medicina i Ciencies de la Salut, Universitat de Barcelona, Barcelona, Spain
| | - Ignacio Pagonabarraga
- Departament de Física de la Matèria Condensada, Facultat de Física, Universitat de Barcelona, Barcelona, Spain
| | - Enrique Martín-Blanco
- Instituto de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona, Spain
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50
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Schonbrun E, Di Caprio G. A virtually imaged defocused array (VIDA) for high-speed 3D microscopy. JOURNAL OF BIOPHOTONICS 2016; 9:1044-1049. [PMID: 26694084 DOI: 10.1002/jbio.201500265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Revised: 11/29/2015] [Accepted: 11/30/2015] [Indexed: 06/05/2023]
Abstract
We report a method to capture a multifocus image stack based on recording multiple reflections generated by imaging through a custom etalon. The focus stack is collected in a single camera exposure and consequently the information needed for 3D reconstruction is recorded in the camera integration time, which is only 100 µs. We have used the VIDA microscope to temporally resolve the multi-lobed 3D morphology of neutrophil nuclei as they rotate and deform through a microfluidic constriction. In addition, we have constructed a 3D imaging flow cytometer and quantified the nuclear morphology of nearly a thousand white blood cells flowing at a velocity of 3 mm per second. The VIDA microscope is compact and simple to construct, intrinsically achromatic, and the field-of-view and stack number can be easily reconfigured without redesigning diffraction gratings and prisms.
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Affiliation(s)
- Ethan Schonbrun
- Rowland Institute at Harvard, 100 Edwin H. Land Blvd., Cambridge, MA 02142, USA.
| | - Giuseppe Di Caprio
- Rowland Institute at Harvard, 100 Edwin H. Land Blvd., Cambridge, MA 02142, USA
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