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Musotto R, Wanderlingh U, D’Ascola A, Spatuzza M, Catania MV, De Pittà M, Pioggia G. Dynamics of astrocytes Ca 2+ signaling: a low-cost fluorescence customized system for 2D cultures. Front Cell Dev Biol 2024; 12:1320672. [PMID: 38322166 PMCID: PMC10844566 DOI: 10.3389/fcell.2024.1320672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
In an effort to help reduce the costs of fluorescence microscopy and expand the use of this valuable technique, we developed a low-cost platform capable of visualising and analysing the spatio-temporal dynamics of intracellular Ca2+ signalling in astrocytes. The created platform, consisting of a specially adapted fluorescence microscope and a data analysis procedure performed with Imagej Fiji software and custom scripts, allowed us to detect relative changes of intracellular Ca2+ ions in astrocytes. To demonstrate the usefulness of the workflow, we applied the methodology to several in vitro astrocyte preparations, specifically immortalised human astrocyte cells and wild-type mouse cells. To demonstrate the reliability of the procedure, analyses were conducted by stimulating astrocyte activity with the agonist dihydroxyphenylglycine (DHPG), alone or in the presence of the antagonist 2-methyl-6-phenylethyl-pyridine (MPEP).
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Affiliation(s)
- Rosa Musotto
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Messina, Italy
| | - Ulderico Wanderlingh
- Department of Mathematical and Computer Sciences, Physical Sciences and Earth Sciences, University of Messina, Messina, Italy
| | - Angela D’Ascola
- Department of Clinical and Experimental Medicine, University of Messina, Policlinico Universitario, Messina, Italy
| | - Michela Spatuzza
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Catania, Italy
| | - Maria Vincenza Catania
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Catania, Italy
| | - Maurizio De Pittà
- Division of Clinical and Computational Neurosciences, Krembil Research Institute, University Health Network, Toronto, ON, Canada
- Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
- Basque Center for Applied Mathematics, Bilbao, Spain
- Department of Neurosciences, Faculty of Medicine, The University of the Basque Country (UPV/EHU), Leioa, Spain
| | - Giovanni Pioggia
- Institute for Biomedical Research and Innovation, National Research Council (IRIB-CNR), Messina, Italy
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Awate DM, Pola CC, Shumaker E, Gomes CL, Juárez JJ. 3D printed imaging platform for portable cell counting. Analyst 2021; 146:4033-4041. [PMID: 34036979 DOI: 10.1039/d1an00778e] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Despite having widespread application in the biomedical sciences, flow cytometers have several limitations that prevent their application to point-of-care (POC) diagnostics in resource-limited environments. 3D printing provides a cost-effective approach to improve the accessibility of POC devices in resource-limited environments. Towards this goal, we introduce a 3D-printed imaging platform (3DPIP) capable of accurately counting particles and perform fluorescence microscopy. In our 3DPIP, captured microscopic images of particle flow are processed on a custom developed particle counter code to provide a particle count. This prototype uses a machine vision-based algorithm to identify particles from captured flow images and is flexible enough to allow for labeled and label-free particle counting. Additionally, the particle counter code returns particle coordinates with respect to time which can further be used to perform particle image velocimetry. These results can help estimate forces acting on particles, and identify and sort different types of cells/particles. We evaluated the performance of this prototype by counting 10 μm polystyrene particles diluted in deionized water at different concentrations and comparing the results with a commercial Beckman-Coulter Z2 particle counter. The 3DPIP can count particle concentrations down to ∼100 particles per mL with a standard deviation of ±20 particles, which is comparable to the results obtained on a commercial particle counter. Our platform produces accurate results at flow rates up to 9 mL h-1 for concentrations below 1000 particle per mL, while 5 mL h-1 produces accurate results above this concentration limit. Aside from performing flow-through experiments, our instrument is capable of performing static experiments that are comparable to a plate reader. In this configuration, our instrument is able to count between 10 and 250 cells per image, depending on the prepared concentration of bacteria samples (Citrobacter freundii; ATCC 8090). Overall, this platform represents a first step towards the development of an affordable fully 3D printable imaging flow cytometry instrument for use in resource-limited clinical environments.
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Affiliation(s)
- Diwakar M Awate
- Department of Mechanical Engineering, Iowa State University, 2529 Union Drive, Ames, IA 50011, USA.
| | - Cicero C Pola
- Department of Mechanical Engineering, Iowa State University, 2529 Union Drive, Ames, IA 50011, USA.
| | - Erica Shumaker
- Department of Mechanical Engineering, Iowa State University, 2529 Union Drive, Ames, IA 50011, USA.
| | - Carmen L Gomes
- Department of Mechanical Engineering, Iowa State University, 2529 Union Drive, Ames, IA 50011, USA.
| | - Jaime J Juárez
- Department of Mechanical Engineering, Iowa State University, 2529 Union Drive, Ames, IA 50011, USA. and Center for Multiphase Flow Research and Education, Iowa State University, 2519 Union Drive, Ames, IA 50011, USA
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Jaques C, Liebling M. Aliasing mitigation in optical microscopy of dynamic biological samples by use of temporally modulated color illumination and a standard RGB camera. JOURNAL OF BIOMEDICAL OPTICS 2020; 25:JBO-200079RR. [PMID: 33107247 PMCID: PMC7720908 DOI: 10.1117/1.jbo.25.10.106505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
SIGNIFICANCE Despite recent developments in microscopy, temporal aliasing can arise when imaging dynamic samples. Modern sampling frameworks, such as generalized sampling, mitigate aliasing but require measurement of temporally overlapping and potentially negative-valued inner products. Conventional cameras cannot collect these directly as they operate sequentially and are only sensitive to light intensity. AIM We aim to mitigate aliasing in microscopy of dynamic monochrome samples by implementing generalized sampling via the use of a color camera and modulated color illumination. APPROACH We solve the overlap problem by spectrally multiplexing the acquisitions and using (positive) B-spline segments as projection kernels. Reconstruction involves spectral unmixing and inverse filtering. We implemented this method using a color LED illuminator. We evaluated its performance by imaging a rotating grid and its applicability by imaging the beating zebrafish embryo heart in transmission and light-sheet microscopes. RESULTS Compared to stroboscopic imaging, our method mitigates aliasing with performance improving as the projection order increases. The approach can be implemented in conventional microscopes but is limited by the number of available LED colors and camera channels. CONCLUSIONS Generalized sampling can be implemented via color modulation in microscopy to mitigate temporal aliasing. The simple hardware requirements could make it applicable to other optical imaging modalities.
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Affiliation(s)
- Christian Jaques
- Idiap Research Institute, Martigny, Switzerland
- École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Michael Liebling
- Idiap Research Institute, Martigny, Switzerland
- University of California Santa Barbara, Department of Electrical and Computer Engineering, Santa Barbara, California, United States
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4
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Abstract
The light (or optical) microscope is the icon of science. The aphorism "seeing is believing" is often quoted in scientific papers involving microscopy. Unlike many scientific instruments, the light microscope will deliver an image however badly it is set up. Fluorescence microscopy is a widely used research tool across all disciplines of biological and biomedical science. Most universities and research institutions have microscopes, including confocal microscopes. This introductory paper in a series detailing advanced light microscopy techniques explains the foundations of both electron and light microscopy for biologists and life scientists working with the mouse. An explanation is given of how an image is formed. A description is given of how to set up a light microscope, whether it be a brightfield light microscope on the laboratory bench, a widefield fluorescence microscope, or a confocal microscope. These explanations are accompanied by operational protocols. A full explanation on how to set up and adjust a microscope according to the principles of Köhler illumination is given. The importance of Nyquist sampling is discussed. Guidelines are given on how to choose the best microscope to image the particular sample or slide preparation that you are working with. These are the basic principles of microscopy that a researcher must have an understanding of when operating core bioimaging facility instruments, in order to collect high-quality images. © 2020 The Authors. Basic Protocol 1: Setting up Köhler illumination for a brightfield microscope Basic Protocol 2: Aligning the fluorescence bulb and setting up Köhler illumination for a widefield fluorescence microscope Basic Protocol 3: Generic protocol for operating a confocal microscope.
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Affiliation(s)
- Jeremy Sanderson
- Bioimaging Facility Manager, MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, UK
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5
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Keomanee-Dizon K, Fraser SE, Truong TV. A versatile, multi-laser twin-microscope system for light-sheet imaging. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2020; 91:053703. [PMID: 32486724 PMCID: PMC7255815 DOI: 10.1063/1.5144487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/28/2020] [Indexed: 05/25/2023]
Abstract
Light-sheet microscopy offers faster imaging and reduced phototoxicity in comparison to conventional point-scanning microscopy, making it a preferred technique for imaging biological dynamics for durations of hours or days. Such extended imaging sessions pose a challenge, as it reduces the number of specimens that can be imaged in a given day. Here, we present a versatile light-sheet imaging instrument that combines two independently controlled microscope-twins, built so that they can share an ultrafast near-infrared laser and a bank of continuous-wave visible lasers, increasing the throughput and decreasing the cost. To permit a wide variety of specimens to be imaged, each microscope-twin provides flexible imaging parameters, including (i) operation in one-photon and/or two-photon excitation modes, (ii) delivery of one to three light-sheets via a trio of orthogonal excitation arms, (iii) sub-micron to micron imaging resolution, (iv) multicolor compatibility, and (v) upright (with provision for inverted) detection geometry. We offer a detailed description of the twin-microscope design to aid instrument builders who wish to construct and use similar systems. We demonstrate the instrument's versatility for biological investigation by performing fast imaging of the beating heart in an intact zebrafish embryo, deep imaging of thick patient-derived tumor organoids, and gentle whole-brain imaging of neural activity in behaving larval zebrafish.
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Affiliation(s)
- Kevin Keomanee-Dizon
- Translational Imaging Center, Dornsife College of Letters, Arts and Sciences, and Viterbi School of Engineering, University of Southern California, Los Angeles, California 90089, USA
| | - Scott E. Fraser
- Translational Imaging Center, Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
| | - Thai V. Truong
- Translational Imaging Center, Molecular and Computational Biology Section, Department of Biological Sciences, University of Southern California, Los Angeles, California 90089, USA
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6
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Jaques C, Pignat E, Calinon S, Liebling M. Temporal super-resolution microscopy using a hue-encoded shutter. BIOMEDICAL OPTICS EXPRESS 2019; 10:4727-4741. [PMID: 31565521 PMCID: PMC6757482 DOI: 10.1364/boe.10.004727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 07/22/2019] [Accepted: 08/06/2019] [Indexed: 06/10/2023]
Abstract
Limited time-resolution in microscopy is an obstacle to many biological studies. Despite recent advances in hardware, digital cameras have limited operation modes that constrain frame-rate, integration time, and color sensing patterns. In this paper, we propose an approach to extend the temporal resolution of a conventional digital color camera by leveraging a multi-color illumination source. Our method allows for the imaging of single-hue objects at an increased frame-rate by trading spectral for temporal information (while retaining the ability to measure base hue). It also allows rapid switching to standard RGB acquisition. We evaluated the feasibility and performance of our method via experiments with mobile resolution targets. We observed a time-resolution increase by a factor 2.8 with a three-fold increase in temporal sampling rate. We further illustrate the use of our method to image the beating heart of a zebrafish larva, allowing the display of color or fast grayscale images. Our method is particularly well-suited to extend the capabilities of imaging systems where the flexibility of rapidly switching between high frame rate and color imaging are necessary.
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Affiliation(s)
- Christian Jaques
- Idiap Research Institute, Rue Marconi 19, 1920 Martigny, Switzerland
- École Polytechnique Fédérale de Lausanne, Switzerland
| | - Emmanuel Pignat
- Idiap Research Institute, Rue Marconi 19, 1920 Martigny, Switzerland
- École Polytechnique Fédérale de Lausanne, Switzerland
| | - Sylvain Calinon
- Idiap Research Institute, Rue Marconi 19, 1920 Martigny, Switzerland
- École Polytechnique Fédérale de Lausanne, Switzerland
| | - Michael Liebling
- Idiap Research Institute, Rue Marconi 19, 1920 Martigny, Switzerland
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, CA 93106, USA
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7
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Pawlowski ME, Dwight JG, Nguyen TU, Tkaczyk TS. High performance image mapping spectrometer (IMS) for snapshot hyperspectral imaging applications. OPTICS EXPRESS 2019; 27:1597-1612. [PMID: 30696224 PMCID: PMC6410916 DOI: 10.1364/oe.27.001597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Revised: 11/14/2018] [Accepted: 12/02/2018] [Indexed: 05/21/2023]
Abstract
A high performance, snapshot Image Mapping Spectrometer was developed that provides fast image acquisition (100 Hz) of 16 bit hyperspectral data cubes (210x210x46) over a spectral range of 515-842 nm. Essential details of the opto-mechanical design are presented. Spectral accuracy, precision, and image reconstruction metrics such as resolution are discussed. Fluorescently stained cell samples were used to directly compare the data obtained using newly developed and the reference image mapping spectrometer. Additional experimental results are provided to demonstrate the abilities of the new spectrometer to acquire highly-resolved, motion-artifact-free hyperspectral images at high temporal sampling rates.
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Affiliation(s)
- Michal E. Pawlowski
- Department of Bioengineering, Rice University, 6500 Main St., Houston, Texas 77030, USA
| | - Jason G. Dwight
- Department of Bioengineering, Rice University, 6500 Main St., Houston, Texas 77030, USA
| | - Thuc-Uyen Nguyen
- Department of Bioengineering, Rice University, 6500 Main St., Houston, Texas 77030, USA
| | - Tomasz S. Tkaczyk
- Department of Bioengineering, Rice University, 6500 Main St., Houston, Texas 77030, USA
- Department of Electrical and Computer Engineering, Rice University, 6100 Main St., Houston, Texas 77005, USA
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8
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Mechanosensitive channels and their functions in stem cell differentiation. Exp Cell Res 2018; 374:259-265. [PMID: 30500393 DOI: 10.1016/j.yexcr.2018.11.016] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Revised: 11/17/2018] [Accepted: 11/21/2018] [Indexed: 12/24/2022]
Abstract
Stem cells continuously perceive and respond to various environmental signals during development, tissue homeostasis, and pathological conditions. Mechanical force, one of the fundamental signals in the physical world, plays a vital role in the regulation of multiple functions of stem cells. The importance of cell adhesion to the extracellular matrix (ECM), cell-cell junctions, and a mechanoresponsive cell cytoskeleton has been under intensive study in the fields of stem cell biology and mechanobiology. However, the involvement of mechanosensitive (MS) ion channels in the mechanical regulation of stem cell activity has just begun to be realized. Here, we review the diversity and importance of mechanosensitive channels (MSCs), and discuss recently discovered functions of MSCs in stem cell regulation, especially in the determination of cell fate.
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9
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Veerapathiran S, Wohland T. Fluorescence techniques in developmental biology. J Biosci 2018; 43:541-553. [PMID: 30002271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Advanced fluorescence techniques, commonly known as the F-techniques, measure the kinetics and the interactions of biomolecules with high sensitivity and spatiotemporal resolution. Applications of the F-techniques, which were initially limited to cells, were further extended to study in vivo protein organization and dynamics in whole organisms. The integration of F-techniques with multi-photon microscopy and light-sheet microscopy widened their applications in the field of developmental biology. It became possible to penetrate the thick tissues of living organisms and obtain good signal-to-noise ratio with reduced photo-induced toxicity. In this review, we discuss the principle and the applications of the three most commonly used F-techniques in developmental biology: Fluorescence Recovery After Photo-bleaching (FRAP), Fo¨ rster Resonance Energy Transfer (FRET), and Fluorescence Correlation and Cross-Correlation Spectroscopy (FCS and FCCS).
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Affiliation(s)
- Sapthaswaran Veerapathiran
- Department of Biological Sciences and NUS Centre for Bio-Imaging Sciences, National University of Singapore, 14 Science Drive 4, Singapore 117557, Singapore
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10
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11
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Investigating dye performance and crosstalk in fluorescence enabled bioimaging using a model system. PLoS One 2017; 12:e0188359. [PMID: 29176775 PMCID: PMC5703511 DOI: 10.1371/journal.pone.0188359] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2017] [Accepted: 11/06/2017] [Indexed: 02/02/2023] Open
Abstract
Detailed imaging of biological structures, often smaller than the diffraction limit, is possible in fluorescence microscopy due to the molecular size and photophysical properties of fluorescent probes. Advances in hardware and multiple providers of high-end bioimaging makes comparing images between studies and between research groups very difficult. Therefore, we suggest a model system to benchmark instrumentation, methods and staining procedures. The system we introduce is based on doped zeolites in stained polyvinyl alcohol (PVA) films: a highly accessible model system which has the properties needed to act as a benchmark in bioimaging experiments. Rather than comparing molecular probes and imaging methods in complicated biological systems, we demonstrate that the model system can emulate this complexity and can be used to probe the effect of concentration, brightness, and cross-talk of fluorophores on the detected fluorescence signal. The described model system comprises of lanthanide (III) ion doped Linde Type A zeolites dispersed in a PVA film stained with fluorophores. We tested: F18, MitoTracker Red and ATTO647N. This model system allowed comparing performance of the fluorophores in experimental conditions. Importantly, we here report considerable cross-talk of the dyes when exchanging excitation and emission settings. Additionally, bleaching was quantified. The proposed model makes it possible to test and benchmark staining procedures before these dyes are applied to more complex biological systems.
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12
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Li YX, Gautam V, Brüstle A, Cockburn IA, Daria VR, Gillespie C, Gaus K, Alt C, Lee WM. Flexible polygon-mirror based laser scanning microscope platform for multiphoton in-vivo imaging. JOURNAL OF BIOPHOTONICS 2017; 10:1526-1537. [PMID: 28164461 DOI: 10.1002/jbio.201600289] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/11/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 05/18/2023]
Abstract
Commercial microscopy systems make use of tandem scanning i.e. either slow or fast scanning. We constructed, for the first time, an advanced control system capable of delivering a dynamic line scanning speed ranging from 2.7 kHz to 27 kHz and achieve variable frame rates from 5 Hz to 50 Hz (512 × 512). The dynamic scanning ability is digitally controlled by a new customized open-source software named PScan1.0. This permits manipulation of scanning rates either to gain higher fluorescence signal at slow frame rate without increasing laser power or increase frame rates to capture high speed events. By adjusting imaging speed from 40 Hz to 160 Hz, we capture a range of calcium waves and transient peaks from soma and dendrite of single fluorescence neuron (CAL-520AM). Motion artifacts arising from respiratory and cardiac motion in small animal imaging reduce quality of real-time images of single cells in-vivo. An image registration algorithm, integrated with PScan1.0, was shown to perform both real time and post-processed motion correction. The improvement is verified by quantification of blood flow rates. This work describes all the steps necessary to develop a high performance and flexible polygon-mirror based multiphoton microscope system for in-vivo biological imaging.
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Affiliation(s)
- Y X Li
- Research School of Engineering, College of Engineering and Computer Science, Australia National University, North Road, Canberra ACT, 2601, Australia
| | - V Gautam
- John Curtin School of Medical Research, Australian National University, Garran Road, Canberra ACT, 2601, Australia
| | - A Brüstle
- John Curtin School of Medical Research, Australian National University, Garran Road, Canberra ACT, 2601, Australia
| | - I A Cockburn
- John Curtin School of Medical Research, Australian National University, Garran Road, Canberra ACT, 2601, Australia
| | - V R Daria
- John Curtin School of Medical Research, Australian National University, Garran Road, Canberra ACT, 2601, Australia
| | - C Gillespie
- John Curtin School of Medical Research, Australian National University, Garran Road, Canberra ACT, 2601, Australia
| | - K Gaus
- Australia- EMBL Node in Single Molecule Science, School of Medical Sciences, University of New South Wales, Sydney NSW, 2052, Australia
- Australia Research Council Centre of Excellence in Advanced Molecular Imaging, University of New South Wales, Australia
| | - C Alt
- Wellman Center for Photomedicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - W M Lee
- Research School of Engineering, College of Engineering and Computer Science, Australia National University, North Road, Canberra ACT, 2601, Australia
- Australia Research Council Centre of Excellence in Advanced Molecular Imaging, Australian National University, Australia
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13
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Shabaniverki S, Juárez JJ. Characterizing gelatin hydrogel viscoelasticity with diffusing colloidal probe microscopy. J Colloid Interface Sci 2017; 497:73-82. [PMID: 28273513 DOI: 10.1016/j.jcis.2017.02.057] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2016] [Revised: 02/22/2017] [Accepted: 02/23/2017] [Indexed: 01/15/2023]
Abstract
In this study, we investigate viscoelasticity in gelatin hydrogels using diffusing colloidal probe microscopy (DCPM) to directly measure the elastic potential energy interaction between colloidal probes and the underlying viscoelastic media. Gelatin samples are prepared in four different concentrations between 0.3wt% and 0.6wt% to examine changes in viscoelasticity with concentration. A force balance describing the interaction between the colloidal probes and the hydrogel as a spring-damper system lead to a simple model for mean square displacement. A histogram of locations sampled by the colloidal probes is directly related to the elastic potential energy and the effective spring constant of the gelatin hydrogels. The effective spring constant is a fixed parameter used in the mean square displacement model to find effective viscosity. These parameters are comparable to viscoelastic parameters obtain by a microrheology analysis of two-dimensional mean square displacements. These results can serve as a guide for assessing hydrogel systems where viscoelastic properties are an important factor in biomaterial design.
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Affiliation(s)
- Soheila Shabaniverki
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, United States
| | - Jaime J Juárez
- Department of Mechanical Engineering, Iowa State University, Ames, IA 50011, United States.
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14
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Hyperspectral phasor analysis enables multiplexed 5D in vivo imaging. Nat Methods 2017; 14:149-152. [PMID: 28068315 DOI: 10.1038/nmeth.4134] [Citation(s) in RCA: 86] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Accepted: 11/08/2016] [Indexed: 11/09/2022]
Abstract
Time-lapse imaging of multiple labels is challenging for biological imaging as noise, photobleaching and phototoxicity compromise signal quality, while throughput can be limited by processing time. Here, we report software called Hyper-Spectral Phasors (HySP) for denoising and unmixing multiple spectrally overlapping fluorophores in a low signal-to-noise regime with fast analysis. We show that HySP enables unmixing of seven signals in time-lapse imaging of living zebrafish embryos.
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15
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Pinkard H, Corbin K, Krummel MF. Spatiotemporal Rank Filtering Improves Image Quality Compared to Frame Averaging in 2-Photon Laser Scanning Microscopy. PLoS One 2016; 11:e0150430. [PMID: 26938064 PMCID: PMC4777388 DOI: 10.1371/journal.pone.0150430] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/13/2016] [Indexed: 11/19/2022] Open
Abstract
Live imaging of biological specimens using optical microscopy is limited by tradeoffs between spatial and temporal resolution, depth into intact samples, and phototoxicity. Two-photon laser scanning microscopy (2P-LSM), the gold standard for imaging turbid samples in vivo, has conventionally constructed images with sufficient signal-to-noise ratio (SNR) generated by sequential raster scans of the focal plane and temporal integration of the collected signals. Here, we describe spatiotemporal rank filtering, a nonlinear alternative to temporal integration, which makes more efficient use of collected photons by selectively reducing noise in 2P-LSM images during acquisition. This results in much higher SNR while preserving image edges and fine details. Practically, this allows for at least a four fold decrease in collection times, a substantial improvement for time-course imaging in biological systems.
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Affiliation(s)
- Henry Pinkard
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
- Biological Imaging Development Center, University of California San Francisco, San Francisco, California, United States of America
- Computational Biology Graduate Group, University of California Berkeley, Berkeley, California, United States of America
| | - Kaitlin Corbin
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
- Biological Imaging Development Center, University of California San Francisco, San Francisco, California, United States of America
| | - Matthew F. Krummel
- Department of Pathology, University of California San Francisco, San Francisco, California, United States of America
- Biological Imaging Development Center, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
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16
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Hemodynamics driven cardiac valve morphogenesis. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2015; 1863:1760-6. [PMID: 26608609 DOI: 10.1016/j.bbamcr.2015.11.014] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 11/13/2015] [Accepted: 11/17/2015] [Indexed: 11/22/2022]
Abstract
Mechanical forces are instrumental to cardiovascular development and physiology. The heart beats approximately 2.6 billion times in a human lifetime and heart valves ensure that these contractions result in an efficient, unidirectional flow of the blood. Composed of endocardial cells (EdCs) and extracellular matrix (ECM), cardiac valves are among the most mechanically challenged structures of the body both during and after their development. Understanding how hemodynamic forces modulate cardiovascular function and morphogenesis is key to unraveling the relationship between normal and pathological cardiovascular development and physiology. Most valve diseases have their origins in embryogenesis, either as signs of abnormal developmental processes or the aberrant re-expression of fetal gene programs normally quiescent in adulthood. Here we review recent discoveries in the mechanobiology of cardiac valve development and introduce the latest technologies being developed in the zebrafish, including live cell imaging and optical technologies, as well as modeling approaches that are currently transforming this field. This article is part of a Special Issue entitled: Cardiomyocyte Biology: Integration of Developmental and Environmental Cues in the Heart edited by Marcus Schaub and Hughes Abriel.
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17
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Goetz JG, Monduc F, Schwab Y, Vermot J. Using correlative light and electron microscopy to study zebrafish vascular morphogenesis. Methods Mol Biol 2015; 1189:31-46. [PMID: 25245685 DOI: 10.1007/978-1-4939-1164-6_3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Live imaging is extremely useful to characterize the dynamics of cellular events in vivo, yet it is limited in terms of spatial resolution. Correlative light and electron microscopy (CLEM) allows combining live confocal microscopy with electron microscopy (EM) for the characterization of biological samples at high temporal and spatial resolution. Here we describe a protocol allowing extracting endothelial cell ultrastructure after having imaged the same cell in its in vivo context through live confocal imaging during zebrafish embryonic development.
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Affiliation(s)
- Jacky G Goetz
- The Microenvironmental Niche in Tumorigenesis and Targeted Therapy, Inserm U1109, LabEx Medalis, Fédération de Médecine Translationnelle de Strasbourg (FMTS), 67000, Strasbourg, France
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18
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Abstract
The constant motion of the beating heart presents an obstacle to clear optical imaging, especially 3D imaging, in small animals where direct optical imaging would otherwise be possible. Gating techniques exploit the periodic motion of the heart to computationally "freeze" this movement and overcome motion artifacts. Optically gated imaging represents a recent development of this, where image analysis is used to synchronize acquisition with the heartbeat in a completely non-invasive manner. This article will explain the concept of optical gating, discuss a range of different implementation strategies and their strengths and weaknesses. Finally we will illustrate the usefulness of the technique by discussing applications where optical gating has facilitated novel biological findings by allowing 3D in vivo imaging of cardiac myocytes in their natural environment of the beating heart.
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19
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Peng H, Myers EW. Constructing 5D developing gene expression patterns without live animal imaging. Biomed Eng Lett 2014. [DOI: 10.1007/s13534-014-0167-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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20
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Stasevich TJ, Sato Y, Nozaki N, Kimura H. Quantifying histone and RNA polymerase II post-translational modification dynamics in mother and daughter cells. Methods 2014; 70:77-88. [PMID: 25131722 DOI: 10.1016/j.ymeth.2014.08.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2014] [Revised: 07/18/2014] [Accepted: 08/04/2014] [Indexed: 01/21/2023] Open
Abstract
Post-translational histone modifications are highly correlated with transcriptional activity, but the relative timing of these marks and their dynamic interplay during gene regulation remains controversial. To shed light on this problem and clarify the connections between histone modifications and transcription, we demonstrate how FabLEM (Fab-based Live Endogenous Modification labeling) can be used to simultaneously track histone H3 Lysine 9 acetylation (H3K9ac) together with RNA polymerase II Serine 2 and Serine 5 phosphorylation (RNAP2 Ser2ph/Ser5ph) in single living cells and their progeny. We provide a detailed description of the FabLEM methodology, including helpful tips for preparing and loading fluorescently conjugated antigen binding fragments (Fab) into cells for optimal results. We also introduce simple procedures for analyzing and visualizing FabLEM data, including color-coded scatterplots to track correlations between modifications through the cell cycle and temporal cross-correlation analysis to dissect modification dynamics. Using these methods, we find significant correlations that span cell generations, with a relatively strong correlation between H3K9ac and Ser5ph that appears to peak a few hours before mitosis and may reflect the bookmarking of genes for efficient re-initiation following mitosis. The techniques we have developed are broadly applicable and should help clarify how histone modifications dynamically contribute to gene regulation.
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Affiliation(s)
- Timothy J Stasevich
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Dept. of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, CO 80523-1870, USA; Janelia Farm Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
| | - Yuko Sato
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan
| | | | - Hiroshi Kimura
- Graduate School of Frontier Biosciences, Osaka University, Suita, Osaka 565-0871, Japan; Department of Biological Sciences, Graduate School of Bioscience and Biotechnology, Tokyo Institute of Technology, Yokohama, Japan.
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21
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Cooper JT, Harris JM. Imaging Fluorescence-Correlation Spectroscopy for Measuring Fast Surface Diffusion at Liquid/Solid Interfaces. Anal Chem 2014; 86:7618-26. [DOI: 10.1021/ac5014354] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Justin T. Cooper
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0805, United States
| | - Joel M. Harris
- Department
of Chemistry, University of Utah, 315 South 1400 East, Salt Lake City, Utah 84112-0805, United States
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22
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Lee S, Vinegoni C, Sebas M, Weissleder R. Automated motion artifact removal for intravital microscopy, without a priori information. Sci Rep 2014; 4:4507. [PMID: 24676021 PMCID: PMC3968488 DOI: 10.1038/srep04507] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2013] [Accepted: 03/11/2014] [Indexed: 11/30/2022] Open
Abstract
Intravital fluorescence microscopy, through extended penetration depth and imaging resolution, provides the ability to image at cellular and subcellular resolution in live animals, presenting an opportunity for new insights into in vivo biology. Unfortunately, physiological induced motion components due to respiration and cardiac activity are major sources of image artifacts and impose severe limitations on the effective imaging resolution that can be ultimately achieved in vivo. Here we present a novel imaging methodology capable of automatically removing motion artifacts during intravital microscopy imaging of organs and orthotopic tumors. The method is universally applicable to different laser scanning modalities including confocal and multiphoton microscopy, and offers artifact free reconstructions independent of the physiological motion source and imaged organ. The methodology, which is based on raw data acquisition followed by image processing, is here demonstrated for both cardiac and respiratory motion compensation in mice heart, kidney, liver, pancreas and dorsal window chamber.
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Affiliation(s)
- Sungon Lee
- 1] Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA [2] Interaction and Robotics Research Center, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seongbuk-gu, Seoul, Korea [3]
| | - Claudio Vinegoni
- 1] Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA [2]
| | - Matthew Sebas
- Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA
| | - Ralph Weissleder
- 1] Center for Systems Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA [2] Department of Systems Biology, Harvard Medical School, 200 Longwood Ave., Boston, MA 02115, USA
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23
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Vinegoni C, Lee S, Feruglio PF, Weissleder R. Advanced Motion Compensation Methods for Intravital Optical Microscopy. IEEE JOURNAL OF SELECTED TOPICS IN QUANTUM ELECTRONICS : A PUBLICATION OF THE IEEE LASERS AND ELECTRO-OPTICS SOCIETY 2014; 20:10.1109/JSTQE.2013.2279314. [PMID: 24273405 PMCID: PMC3832946 DOI: 10.1109/jstqe.2013.2279314] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Intravital microscopy has emerged in the recent decade as an indispensible imaging modality for the study of the micro-dynamics of biological processes in live animals. Technical advancements in imaging techniques and hardware components, combined with the development of novel targeted probes and new mice models, have enabled us to address long-standing questions in several biology areas such as oncology, cell biology, immunology and neuroscience. As the instrument resolution has increased, physiological motion activities have become a major obstacle that prevents imaging live animals at resolutions analogue to the ones obtained in vitro. Motion compensation techniques aim at reducing this gap and can effectively increase the in vivo resolution. This paper provides a technical review of some of the latest developments in motion compensation methods, providing organ specific solutions.
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Affiliation(s)
- Claudio Vinegoni
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA
| | - Sungon Lee
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA. He is now with Interaction and Robotics Research Center, Korea Institute of Science and Technology, Hwarangno 14-gil 5, Seoul 136-791 Korea
| | - Paolo Fumene Feruglio
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA and with the Department of Neurological and Movement Sciences, University of Verona, Strada Le Grazie 8, 37134 Verona, Italy
| | - Ralph Weissleder
- Center for System Biology, Massachusetts General Hospital and Harvard Medical School, Richard B. Simches Research Center, 185 Cambridge Street, Boston 02114, USA
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24
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Zheng Z, Christley S, Chiu WT, Blitz IL, Xie X, Cho KWY, Nie Q. Inference of the Xenopus tropicalis embryonic regulatory network and spatial gene expression patterns. BMC SYSTEMS BIOLOGY 2014; 8:3. [PMID: 24397936 PMCID: PMC3896677 DOI: 10.1186/1752-0509-8-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Accepted: 12/19/2013] [Indexed: 11/10/2022]
Abstract
BACKGROUND During embryogenesis, signaling molecules produced by one cell population direct gene regulatory changes in neighboring cells and influence their developmental fates and spatial organization. One of the earliest events in the development of the vertebrate embryo is the establishment of three germ layers, consisting of the ectoderm, mesoderm and endoderm. Attempts to measure gene expression in vivo in different germ layers and cell types are typically complicated by the heterogeneity of cell types within biological samples (i.e., embryos), as the responses of individual cell types are intermingled into an aggregate observation of heterogeneous cell types. Here, we propose a novel method to elucidate gene regulatory circuits from these aggregate measurements in embryos of the frog Xenopus tropicalis using gene network inference algorithms and then test the ability of the inferred networks to predict spatial gene expression patterns. RESULTS We use two inference models with different underlying assumptions that incorporate existing network information, an ODE model for steady-state data and a Markov model for time series data, and contrast the performance of the two models. We apply our method to both control and knockdown embryos at multiple time points to reconstruct the core mesoderm and endoderm regulatory circuits. Those inferred networks are then used in combination with known dorsal-ventral spatial expression patterns of a subset of genes to predict spatial expression patterns for other genes. Both models are able to predict spatial expression patterns for some of the core mesoderm and endoderm genes, but interestingly of different gene subsets, suggesting that neither model is sufficient to recapitulate all of the spatial patterns, yet they are complementary for the patterns that they do capture. CONCLUSION The presented methodology of gene network inference combined with spatial pattern prediction provides an additional layer of validation to elucidate the regulatory circuits controlling the spatial-temporal dynamics in embryonic development.
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Affiliation(s)
| | | | | | | | | | | | - Qing Nie
- Department of Mathematics, University of California, Irvine, CA 92697, USA.
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25
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Carlson GE, Martin EW, Burdick MM. Simultaneously capturing real-time images in two emission channels using a dual camera emission splitting system: applications to cell adhesion. J Vis Exp 2013. [PMID: 24056855 DOI: 10.3791/50604] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Multi-color immunofluorescence microscopy to detect specific molecules in the cell membrane can be coupled with parallel plate flow chamber assays to investigate mechanisms governing cell adhesion under dynamic flow conditions. For instance, cancer cells labeled with multiple fluorophores can be perfused over a potentially reactive substrate to model mechanisms of cancer metastasis. However, multi-channel single camera systems and color cameras exhibit shortcomings in image acquisition for real-time live cell analysis. To overcome these limitations, we used a dual camera emission splitting system to simultaneously capture real-time image sequences of fluorescently labeled cells in the flow chamber. Dual camera emission splitting systems filter defined wavelength ranges into two monochrome CCD cameras, thereby simultaneously capturing two spatially identical but fluorophore-specific images. Subsequently, psuedocolored one-channel images are combined into a single real-time merged sequence that can reveal multiple target molecules on cells moving rapidly across a region of interest.
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Affiliation(s)
- Grady E Carlson
- Department of Chemical and Biomolecular Engineering, Russ College of Engineering and Technology, Ohio University
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26
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Keller PJ. In vivo imaging of zebrafish embryogenesis. Methods 2013; 62:268-78. [PMID: 23523701 PMCID: PMC3907156 DOI: 10.1016/j.ymeth.2013.03.015] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2012] [Revised: 03/07/2013] [Accepted: 03/13/2013] [Indexed: 11/20/2022] Open
Abstract
The zebrafish Danio rerio has emerged as a powerful vertebrate model system that lends itself particularly well to quantitative investigations with live imaging approaches, owing to its exceptionally high optical clarity in embryonic and larval stages. Recent advances in light microscopy technology enable comprehensive analyses of cellular dynamics during zebrafish embryonic development, systematic mapping of gene expression dynamics, quantitative reconstruction of mutant phenotypes and the system-level biophysical study of morphogenesis. Despite these technical breakthroughs, it remains challenging to design and implement experiments for in vivo long-term imaging at high spatio-temporal resolution. This article discusses the fundamental challenges in zebrafish long-term live imaging, provides experimental protocols and highlights key properties and capabilities of advanced fluorescence microscopes. The article focuses in particular on experimental assays based on light sheet-based fluorescence microscopy, an emerging imaging technology that achieves exceptionally high imaging speeds and excellent signal-to-noise ratios, while minimizing light-induced damage to the specimen. This unique combination of capabilities makes light sheet microscopy an indispensable tool for the in vivo long-term imaging of large developing organisms.
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Affiliation(s)
- Philipp J Keller
- Howard Hughes Medical Institute, Janelia Farm Research Campus, 19700 Helix Drive, Ashburn, VA 20147, USA.
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27
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Gorthi SS, Schaak D, Schonbrun E. Fluorescence imaging of flowing cells using a temporally coded excitation. OPTICS EXPRESS 2013; 21:5164-5170. [PMID: 23482050 DOI: 10.1364/oe.21.005164] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Imaging fluorescence in moving cells is fundamentally challenging because the exposure time is constrained by motion-blur, which limits the available signal. We report a method to image fluorescently labeled leukemia cells in fluid flow that has an effective exposure time of up to 50 times the motion-blur limit. Flowing cells are illuminated with a pseudo-random excitation pulse sequence, resulting in a motion-blur that can be computationally removed to produce near diffraction-limited images. This method enables observation of cellular organelles and their behavior in a fluid environment that resembles the vasculature.
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Affiliation(s)
- Sai Siva Gorthi
- Rowland Institute at Harvard, Harvard University, Cambridge, MA 02142, USA
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28
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Taylor JM, Girkin JM, Love GD. High-resolution 3D optical microscopy inside the beating zebrafish heart using prospective optical gating. BIOMEDICAL OPTICS EXPRESS 2012; 3:3043-53. [PMID: 23243558 PMCID: PMC3521314 DOI: 10.1364/boe.3.003043] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2012] [Revised: 09/25/2012] [Accepted: 10/20/2012] [Indexed: 05/03/2023]
Abstract
3D fluorescence imaging is a fundamental tool in the study of functional and developmental biology, but effective imaging is particularly difficult in moving structures such as the beating heart. We have developed a non-invasive real-time optical gating system that is able to exploit the periodic nature of the motion to acquire high resolution 3D images of the normally-beating zebrafish heart without any unnecessary exposure of the sample to harmful excitation light. In order for the image stack to be artefact-free, it is essential to use a synchronization source that is invariant as the sample is scanned in 3D. We therefore describe a scheme whereby fluorescence image slices are scanned through the sample while a brightfield camera sharing the same objective lens is maintained at a fixed focus, with correction of sample drift also included. This enables us to maintain, throughout an extended 3D volume, the same standard of synchronization we have previously demonstrated in and near a single 2D plane. Thus we are able image the complete beating zebrafish heart exactly as if the heart had been artificially stopped, but sidestepping this undesirable interference with the heart and instead allowing the heart to beat as normal.
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Affiliation(s)
- Jonathan M. Taylor
- Centre for Advanced Instrumentation, Department of Physics, Durham University,
UK
- Biophysical Sciences Institute, Durham University, UK
| | - John M. Girkin
- Centre for Advanced Instrumentation, Department of Physics, Durham University,
UK
- Biophysical Sciences Institute, Durham University, UK
| | - Gordon D. Love
- Centre for Advanced Instrumentation, Department of Physics, Durham University,
UK
- Biophysical Sciences Institute, Durham University, UK
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29
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Ohn J, Tsai HJ, Liebling M. Joint dynamic imaging of morphogenesis and function in the developing heart. Organogenesis 2012; 5:248-55. [PMID: 20539745 DOI: 10.4161/org.5.4.10568] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2009] [Revised: 11/07/2009] [Accepted: 11/09/2009] [Indexed: 01/28/2023] Open
Abstract
In the developing heart, time-lapse imaging is particularly challenging. Changes in heart morphology due to tissue growth or long-term reorganization are difficult to follow because they are much subtler than the rapid shape changes induced by the heartbeat. Therefore, imaging heart development usually requires slowing or stopping the heart. This, however, leads to information loss about the unperturbed heart shape and the dynamics of heart function. To overcome this limitation, we have developed a non-invasive heart imaging technique to jointly document heart function (at fixed stages of development) as well as its morphogenesis (at any fixed phase in the heartbeat) that does not require stopping or slowing the heart. We review the challenges for imaging heart development and our methodology, which is based on computationally combining and analyzing multiple high-speed image sequences acquired throughout the course of development. We present results obtained in the developing zebrafish heart. Image analysis of the acquired data yielded blood flow velocity maps and made it possible to follow the relative movement of individual cells over several hours.
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Affiliation(s)
- Jungho Ohn
- Electrical & Computer Engineering; University of California; Santa Barbara, CA USA
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30
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Colas JF, Sharpe J. Live optical projection tomography. Organogenesis 2012; 5:211-6. [PMID: 20539740 DOI: 10.4161/org.5.4.10426] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Revised: 09/06/2009] [Accepted: 10/26/2009] [Indexed: 01/27/2023] Open
Abstract
Optical projection tomography (OPT) is a technology ideally suited for imaging embryonic organs. We emphasize here recent successes in translating this potential into the field of live imaging. Live OPT (also known as 4D OPT, or time-lapse OPT) is already in position to accumulate good quantitative data on the developmental dynamics of organogenesis, a prerequisite for building realistic computer models and tackling new biological problems. Yet, live OPT is being further developed by merging state-of-the-art mouse embryo culture with the OPT system. We discuss the technological challenges that this entails and the prospects for expansion of this molecular imaging technique into a wider range of applications.
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Affiliation(s)
- Jean-François Colas
- EMBL-CRG Systems Biology Program; Centre for Genomic Regulation; UPF; Barcelona, Spain; Istituciô Catalana de Recerca i Estudis Avançats; Barcelona, Spain
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31
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Seamster PE, Loewenberg M, Pascal J, Chauviere A, Gonzales A, Cristini V, Bearer EL. Quantitative measurements and modeling of cargo-motor interactions during fast transport in the living axon. Phys Biol 2012; 9:055005. [PMID: 23011729 DOI: 10.1088/1478-3975/9/5/055005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The kinesins have long been known to drive microtubule-based transport of sub-cellular components, yet the mechanisms of their attachment to cargo remain a mystery. Several different cargo-receptors have been proposed based on their in vitro binding affinities to kinesin-1. Only two of these-phosphatidyl inositol, a negatively charged lipid, and the carboxyl terminus of the amyloid precursor protein (APP-C), a trans-membrane protein-have been reported to mediate motility in living systems. A major question is how these many different cargo, receptors and motors interact to produce the complex choreography of vesicular transport within living cells. Here we describe an experimental assay that identifies cargo-motor receptors by their ability to recruit active motors and drive transport of exogenous cargo towards the synapse in living axons. Cargo is engineered by derivatizing the surface of polystyrene fluorescent nanospheres (100 nm diameter) with charged residues or with synthetic peptides derived from candidate motor receptor proteins, all designed to display a terminal COOH group. After injection into the squid giant axon, particle movements are imaged by laser-scanning confocal time-lapse microscopy. In this report we compare the motility of negatively charged beads with APP-C beads in the presence of glycine-conjugated non-motile beads using new strategies to measure bead movements. The ensuing quantitative analysis of time-lapse digital sequences reveals detailed information about bead movements: instantaneous and maximum velocities, run lengths, pause frequencies and pause durations. These measurements provide parameters for a mathematical model that predicts the spatiotemporal evolution of distribution of the two different types of bead cargo in the axon. The results reveal that negatively charged beads differ from APP-C beads in velocity and dispersion, and predict that at long time points APP-C will achieve greater progress towards the presynaptic terminal. The significance of this data and accompanying model pertains to the role transport plays in neuronal function, connectivity, and survival, and has implications in the pathogenesis of neurological disorders, such as Alzheimer's, Huntington and Parkinson's diseases.
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Affiliation(s)
- Pamela E Seamster
- Department of Pathology, University of New Mexico Health Sciences Center, Albuquerque, NM 87131, USA
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32
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Bhat S, Ohn J, Liebling M. Motion-based structure separation for label-free, high-speed, 3D cardiac microscopy. IEEE TRANSACTIONS ON IMAGE PROCESSING : A PUBLICATION OF THE IEEE SIGNAL PROCESSING SOCIETY 2012; 21:3638-3647. [PMID: 22531765 DOI: 10.1109/tip.2012.2195070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Capturing the dynamics of individual structures in the embryonic heart is an essential step for studying its function and development. Label-free brightfield (BF) microscopy allows for higher acquisition frame-rates than techniques requiring molecular labeling, without interfering with embryo viability or needing complex equipment. However, since different structures contribute similarly to image contrast, label-free microscopy lacks specificity. Here we mitigate this problem by separating a single-channel image series into multiple channels specific to different cardio-vascular structures, based only on their motion patterns. The technique combines images from multiple cardiac cycles and z-sections after non-uniform temporal registration to produce 3D+time image volumes of one full cardiac cycle with separate channels for static, transient and periodically moving structures. The resulting data is well-suited for velocity analysis and 3D-visualization. We characterize the separating capabilities of our technique on a synthetic cardiac dataset and demonstrate its practical applicability, by reconstructing three-channel views of the beating embryonic zebrafish heart with an effective frame rate of 1000 volumes (256×256×20 voxels each) per second. This technique enables quantitative characterization of dynamic heart function during cardiogenesis.
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33
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Cheng LC, Chang CY, Lin CY, Cho KC, Yen WC, Chang NS, Xu C, Dong CY, Chen SJ. Spatiotemporal focusing-based widefield multiphoton microscopy for fast optical sectioning. OPTICS EXPRESS 2012; 20:8939-48. [PMID: 22513605 DOI: 10.1364/oe.20.008939] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
In this study, a microscope based on spatiotemporal focusing offering widefield multiphoton excitation has been developed to provide fast optical sectioning images. Key features of this microscope are the integrations of a 10 kHz repetition rate ultrafast amplifier featuring high instantaneous peak power (maximum 400 μJ/pulse at a 90 fs pulse width) and a TE-cooled, ultra-sensitive photon detecting, electron multiplying charge-coupled camera into a spatiotemporal focusing microscope. This configuration can produce multiphoton images with an excitation area larger than 200 × 100 μm² at a frame rate greater than 100 Hz (current maximum of 200 Hz). Brownian motions of fluorescent microbeads as small as 0.5 μm were observed in real-time with a lateral spatial resolution of less than 0.5 μm and an axial resolution of approximately 3.5 μm. Furthermore, second harmonic images of chicken tendons demonstrate that the developed widefield multiphoton microscope can provide high resolution z-sectioning for bioimaging.
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Affiliation(s)
- Li-Chung Cheng
- Department of Photonics, National Cheng Kung University, Tainan 701, Taiwan
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34
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Segal M, Soifer I, Petzold H, Howard J, Elbaum M, Reiner O. Ndel1-derived peptides modulate bidirectional transport of injected beads in the squid giant axon. Biol Open 2012; 1:220-31. [PMID: 23213412 PMCID: PMC3507287 DOI: 10.1242/bio.2012307] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Bidirectional transport is a key issue in cellular biology. It requires coordination between microtubule-associated molecular motors that work in opposing directions. The major retrograde and anterograde motors involved in bidirectional transport are cytoplasmic dynein and conventional kinesin, respectively. It is clear that failures in molecular motor activity bear severe consequences, especially in the nervous system. Neuronal migration may be impaired during brain development, and impaired molecular motor activity in the adult is one of the hallmarks of neurodegenerative diseases leading to neuronal cell death. The mechanisms that regulate or coordinate kinesin and dynein activity to generate bidirectional transport of the same cargo are of utmost importance. We examined how Ndel1, a cytoplasmic dynein binding protein, may regulate non-vesicular bidirectional transport. Soluble Ndel1 protein, Ndel1-derived peptides or control proteins were mixed with fluorescent beads, injected into the squid giant axon, and the bead movements were recorded using time-lapse microscopy. Automated tracking allowed for extraction and unbiased analysis of a large data set. Beads moved in both directions with a clear bias to the anterograde direction. Velocities were distributed over a broad range and were typically slower than those associated with fast vesicle transport. Ironically, the main effect of Ndel1 and its derived peptides was an enhancement of anterograde motion. We propose that they may function primarily by inhibition of dynein-dependent resistance, which suggests that both dynein and kinesin motors may remain engaged with microtubules during bidirectional transport.
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Affiliation(s)
- Michal Segal
- Department of Molecular Genetics, The Weizmann Institute of Science , Rehovot 76100 , Israel
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35
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Tinevez JY, Dragavon J, Baba-Aissa L, Roux P, Perret E, Canivet A, Galy V, Shorte S. A quantitative method for measuring phototoxicity of a live cell imaging microscope. Methods Enzymol 2012; 506:291-309. [PMID: 22341230 DOI: 10.1016/b978-0-12-391856-7.00039-1] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Fluorescence-based imaging regimes require exposure of living samples under study to high intensities of focused incident illumination. An often underestimated, overlooked, or simply ignored fact in the design of any experimental imaging protocol is that exposure of the specimen to these excitation light sources must itself always be considered a potential source of phototoxicity. This can be problematic, not just in terms of cell viability, but much more worrisome in its more subtle manifestation where phototoxicity causes anomalous behaviors that risk to be interpreted as significant, whereas they are mere artifacts. This is especially true in the case of microbial pathogenesis, where host-pathogen interactions can prove especially fragile to light exposure in a manner that can obscure the very processes we are trying to observe. For these reasons, it is important to be able to bring the parameter of phototoxicity into the equation that brings us to choose one fluorescent imaging modality, or setup, over another. Further, we need to be able to assess the risk that phototoxicity may occur during any specific imaging experiment. To achieve this, we describe here a methodological approach that allows meaningful measurement, and therefore relative comparison of phototoxicity, in most any variety of different imaging microscopes. In short, we propose a quantitative approach that uses microorganisms themselves to reveal the range over which any given fluorescent imaging microscope will yield valid results, providing a metrology of phototoxic damage, distinct from photobleaching, where a clear threshold for phototoxicity is identified. Our method is widely applicable and we show that it can be adapted to other paradigms, including mammalian cell models.
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Affiliation(s)
- Jean-Yves Tinevez
- Institut Pasteur, Imagopole, Plateforme d'imagerie dynamique, Paris, France
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36
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Yoo J, Larina IV, Larin KV, Dickinson ME, Liebling M. Increasing the field-of-view of dynamic cardiac OCT via post-acquisition mosaicing without affecting frame-rate or spatial resolution. BIOMEDICAL OPTICS EXPRESS 2011; 2:2614-22. [PMID: 22091446 PMCID: PMC3184870 DOI: 10.1364/boe.2.002614] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/05/2011] [Revised: 08/03/2011] [Accepted: 08/05/2011] [Indexed: 05/19/2023]
Abstract
Optical coherence tomography (OCT) allows imaging dynamic structures and fluid flow within scattering tissue, such as the beating heart and blood flow in murine embryos. For any given system, the frame rate, spatial resolution, field-of-view (FOV), and signal-to-noise ratio (SNR) are interconnected: favoring one aspect limits at least one of the others due to optical, instrumentation, and software constraints. Here we describe a spatio-temporal mosaicing technique to reconstruct high-speed, high spatial-resolution, and large-field-of-view OCT sequences. The technique is applicable to imaging any cyclically moving structure and operates on multiple, spatially overlapping tiled image sequences (each sequence acquired sequentially at a given spatial location) and effectively decouples the (rigid) spatial alignment and (non-rigid) temporal registration problems. Using this approach we reconstructed full-frame OCT sequences of the beating embryonic rat heart (11.5 days post coitus) and compared it to direct imaging on the same system, demonstrating a six-fold improvement of the frame rate without compromising spatial resolution, FOV, or SNR.
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Affiliation(s)
- JeaBuem Yoo
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, California 93106,
USA
| | - Irina V. Larina
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030,
USA
| | - Kirill V. Larin
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030,
USA
- Department of Biomedical Engineering, University of Houston, Houston, Texas 77204,
USA
| | - Mary E. Dickinson
- Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, Texas 77030,
USA
| | - Michael Liebling
- Department of Electrical and Computer Engineering, University of California, Santa Barbara, California 93106,
USA
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37
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Deep and fast live imaging with two-photon scanned light-sheet microscopy. Nat Methods 2011; 8:757-60. [DOI: 10.1038/nmeth.1652] [Citation(s) in RCA: 367] [Impact Index Per Article: 28.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2010] [Accepted: 06/09/2011] [Indexed: 12/19/2022]
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Liebling M. Imaging the dynamics of biological processes via fast confocal microscopy and image processing. Cold Spring Harb Protoc 2011; 2011:783-9. [PMID: 21724825 DOI: 10.1101/pdb.top117] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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39
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Ohn J, Yang J, Fraser SE, Lansford R, Liebling M. High-speed multicolor microscopy of repeating dynamic processes. Genesis 2011; 49:514-21. [PMID: 21638751 PMCID: PMC3344748 DOI: 10.1002/dvg.20774] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2010] [Revised: 04/18/2011] [Accepted: 05/30/2011] [Indexed: 12/31/2022]
Abstract
Images of multiply labeled fluorescent samples provide unique insights into the localization of molecules, cells, and tissues. The ability to image multiple channels simultaneously at high speed without cross talk is limited to a few colors and requires dedicated multichannel or multispectral detection procedures. Simpler microscopes, in which each color is imaged sequentially, produce a much lower frame rate. Here, we describe a technique to image, at high frame rate, multiply labeled samples that have a repeating motion. We capture images in a single channel at a time over one full occurrence of the motion then repeat acquisition for other channels over subsequent occurrences. We finally build a high-speed multichannel image sequence by combining the images after applying a normalized mutual information-based time registration procedure. We show that this technique is amenable to image the beating heart of a double-labeled embryonic quail in three channels (brightfield, yellow, and mCherry fluorescent proteins) using a fluorescence wide-field microscope equipped with a single monochrome camera and without fast channel switching optics. We experimentally evaluate the accuracy of our method on image series from a two-channel confocal microscope.
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Affiliation(s)
- Jungho Ohn
- Electrical & Computer Engineering, University of California, Santa Barbara, CA 93106
| | - Jennifer Yang
- Biological Imaging Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Scott E. Fraser
- Biological Imaging Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Rusty Lansford
- Biological Imaging Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125
| | - Michael Liebling
- Electrical & Computer Engineering, University of California, Santa Barbara, CA 93106
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40
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Bower DV, Sato Y, Lansford R. Dynamic lineage analysis of embryonic morphogenesis using transgenic quail and 4D multispectral imaging. Genesis 2011; 49:619-43. [PMID: 21509927 DOI: 10.1002/dvg.20754] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2010] [Revised: 03/27/2011] [Accepted: 03/28/2011] [Indexed: 12/17/2022]
Abstract
We describe the development of transgenic quail that express various fluorescent proteins in targeted manners and their use as a model system that integrates advanced imaging approaches with conventional and emerging molecular genetics technologies. We also review the progression and complications of past fate mapping techniques that led us to generate transgenic quail, which permit dynamic imaging of amniote embryogenesis with unprecedented subcellular resolution.
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Affiliation(s)
- Danielle V Bower
- Department of Biology and the Biological Imaging Center, California Institute of Technology, Pasadena, California 91125, USA
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41
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Ritter JG, Spille JH, Kaminski T, Kubitscheck U. A cylindrical zoom lens unit for adjustable optical sectioning in light sheet microscopy. BIOMEDICAL OPTICS EXPRESS 2010; 2:185-93. [PMID: 21326648 PMCID: PMC3028493 DOI: 10.1364/boe.2.000185] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/26/2010] [Accepted: 12/15/2010] [Indexed: 05/26/2023]
Abstract
Light sheet microscopy became a powerful tool in life sciences. Often, however, the sheet geometry is fixed, whereas it would be advantageous to adjust the sheet geometry to specimens of different dimensions. Therefore we developed an afocal cylindrical zoom lens system comprising only 5 lenses and a total system length of less than 160 mm. Two movable optical elements were directly coupled, so that the zoom factor could be adjusted from 1x to 6.3x by a single motor. Using two different illumination objectives we achieved a light sheet thickness ranging from 2.4 µm to 36 µm corresponding to lateral fields of 54 µm to 12.3 mm, respectively. Polytene chromosomes of salivary gland cell nuclei of C.tentans larvae were imaged in vivo to demonstrate the advantages in image contrast by imaging with different light sheet dimensions.
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43
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Biehlmaier O, Hehl J, Csucs G. Acquisition speed comparison of microscope software programs. Microsc Res Tech 2010; 74:539-45. [PMID: 21604324 DOI: 10.1002/jemt.20944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2010] [Accepted: 08/27/2010] [Indexed: 11/06/2022]
Abstract
Reliable software is a prerequisite for successful operation of a modern wide field fluorescence microscope. When used for live cell imaging, acquisition speed is of particular interest. This is both because biological processes can be highly-dynamic, and to avoid unnecessary photobleaching and phototoxicity of living samples. This article shows that besides the hardware (microscope) components themselves, the acquisition control software is an important influencing factor of speed performance. We tested and compared the speed performance of five different generic applications (Image-Pro Plus, MetaMorph, Micro-Manager, SlideBook, and Volocity) using typical experimental setups involving a single specific state-of-the-art fluorescence microscope configuration. The test measurements included multichannel experiments, z-stacking, burst acquisition, as well as combinations of these measurements with time-lapse acquisitions. The measured data provided values for guiding the testing and analysis of other microscope systems with similar configurations. Despite the identical hardware settings, significant and surprisingly large speed differences were evident among the various software applications. Additionally, no application was identifiable as the fastest in all tests. Our work pinpoints the importance of the control software in determining a system's "real" maximal imaging speed. The study could serve as basis for further tests, eventually influencing the system selection criteria for speed-sensitive applications.
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Affiliation(s)
- Oliver Biehlmaier
- Light Microscopy Centre, Swiss Federal Institute of Technology, Zürich, Switzerland
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44
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Canaria CA, Lansford R. Advanced optical imaging in living embryos. Cell Mol Life Sci 2010; 67:3489-97. [PMID: 20614161 PMCID: PMC2943067 DOI: 10.1007/s00018-010-0440-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2010] [Revised: 06/12/2010] [Accepted: 06/15/2010] [Indexed: 11/28/2022]
Abstract
Developmental biology investigations have evolved from static studies of embryo anatomy and into dynamic studies of the genetic and cellular mechanisms responsible for shaping the embryo anatomy. With the advancement of fluorescent protein fusions, the ability to visualize and comprehend how thousands to millions of cells interact with one another to form tissues and organs in three dimensions (xyz) over time (t) is just beginning to be realized and exploited. In this review, we explore recent advances utilizing confocal and multi-photon time-lapse microscopy to capture gene expression, cell behavior, and embryo development. From choosing the appropriate fluorophore, to labeling strategy, to experimental set-up, and data pipeline handling, this review covers the various aspects related to acquiring and analyzing multi-dimensional data sets. These innovative techniques in multi-dimensional imaging and analysis can be applied across a number of fields in time and space including protein dynamics to cell biology to morphogenesis.
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Affiliation(s)
- Christie A. Canaria
- California Institute of Technology, 1200 E. California Blvd, MC 139-74, Pasadena, CA 91125 USA
| | - Rusty Lansford
- California Institute of Technology, 1200 E. California Blvd, MC 139-74, Pasadena, CA 91125 USA
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Ritter JG, Veith R, Veenendaal A, Siebrasse JP, Kubitscheck U. Light sheet microscopy for single molecule tracking in living tissue. PLoS One 2010; 5:e11639. [PMID: 20668517 PMCID: PMC2909143 DOI: 10.1371/journal.pone.0011639] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 06/24/2010] [Indexed: 01/23/2023] Open
Abstract
Single molecule observation in cells and tissue allows the analysis of physiological processes with molecular detail, but it still represents a major methodological challenge. Here we introduce a microscopic technique that combines light sheet optical sectioning microscopy and ultra sensitive high-speed imaging. By this approach it is possible to observe single fluorescent biomolecules in solution, living cells and even tissue with an unprecedented speed and signal-to-noise ratio deep within the sample. Thereby we could directly observe and track small and large tracer molecules in aqueous solution. Furthermore, we demonstrated the feasibility to visualize the dynamics of single tracer molecules and native messenger ribonucleoprotein particles (mRNPs) in salivary gland cell nuclei of Chironomus tentans larvae up to 200 µm within the specimen with an excellent signal quality. Thus single molecule light sheet based fluorescence microscopy allows analyzing molecular diffusion and interactions in complex biological systems.
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Affiliation(s)
- Jörg Gerhard Ritter
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität, Bonn, Germany
| | - Roman Veith
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität, Bonn, Germany
| | - Andreas Veenendaal
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität, Bonn, Germany
| | - Jan Peter Siebrasse
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität, Bonn, Germany
| | - Ulrich Kubitscheck
- Institute of Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität, Bonn, Germany
- * E-mail:
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46
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Keller PJ, Stelzer EHK. Digital scanned laser light sheet fluorescence microscopy. Cold Spring Harb Protoc 2010; 2010:pdb.top78. [PMID: 20439423 DOI: 10.1101/pdb.top78] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Modern applications in the life sciences are frequently based on in vivo imaging of biological specimens, a domain for which light microscopy approaches are typically best suited. Often, quantitative information must be obtained from large multicellular organisms on the cellular or even subcellular level and with a good temporal resolution. However, this usually requires a combination of conflicting features: high imaging speed, low photobleaching, and low phototoxicity in the specimen, good three-dimensional (3D) resolution, an excellent signal-to-noise ratio, and multiple-view imaging capability. The latter feature refers to the capability of recording a specimen along multiple directions, which is crucial for the imaging of large specimens with strong light-scattering or light-absorbing tissue properties. An imaging technique that fulfills these requirements is essential for many key applications: For example, studying fast cellular processes over long periods of time, imaging entire embryos throughout development, or reconstructing the formation of morphological defects in mutants. Here, we discuss digital scanned laser light sheet fluorescence microscopy (DSLM) as a novel tool for quantitative in vivo imaging in the post-genomic era and show how this emerging technique relates to the currently most widely applied 3D microscopy techniques in biology: confocal fluorescence microscopy and two-photon microscopy.
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47
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Supatto W, McMahon A, Fraser SE, Stathopoulos A. Quantitative imaging of collective cell migration during Drosophila gastrulation: multiphoton microscopy and computational analysis. Nat Protoc 2009; 4:1397-412. [PMID: 19745822 DOI: 10.1038/nprot.2009.130] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This protocol describes imaging and computational tools to collect and analyze live imaging data of embryonic cell migration. Our five-step protocol requires a few weeks to move through embryo preparation and four-dimensional (4D) live imaging using multi-photon microscopy, to 3D cell tracking using image processing, registration of tracking data and their quantitative analysis using computational tools. It uses commercially available equipment and requires expertise in microscopy and programming that is appropriate for a biology laboratory. Custom-made scripts are provided, as well as sample datasets to permit readers without experimental data to carry out the analysis. The protocol has offered new insights into the genetic control of cell migration during Drosophila gastrulation. With simple modifications, this systematic analysis could be applied to any developing system to define cell positions in accordance with the body plan, to decompose complex 3D movements and to quantify the collective nature of cell migration.
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Affiliation(s)
- Willy Supatto
- Division of Biology and Beckman Institute, California Institute of Technology, Pasadena, California, USA
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48
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Meijering E, Dzyubachyk O, Smal I, van Cappellen WA. Tracking in cell and developmental biology. Semin Cell Dev Biol 2009; 20:894-902. [PMID: 19660567 DOI: 10.1016/j.semcdb.2009.07.004] [Citation(s) in RCA: 133] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2009] [Revised: 07/10/2009] [Accepted: 07/28/2009] [Indexed: 11/30/2022]
Abstract
The past decade has seen an unprecedented data explosion in biology. It has become evident that in order to take full advantage of the potential wealth of information hidden in the data produced by even a single experiment, visual inspection and manual analysis are no longer adequate. To ensure efficiency, consistency, and completeness in data processing and analysis, computational tools are essential. Of particular importance to many modern live-cell imaging experiments is the ability to automatically track and analyze the motion of objects in time-lapse microscopy images. This article surveys the recent literature in this area. Covering all scales of microscopic observation, from cells, down to molecules, and up to entire organisms, it discusses the latest trends and successes in the development and application of computerized tracking methods in cell and developmental biology.
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Affiliation(s)
- Erik Meijering
- Biomedical Imaging Group Rotterdam, Erasmus MC - University Medical Center Rotterdam, Department of Medical Informatics, P. O. Box 2040, 3000 CA Rotterdam, The Netherlands.
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49
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Quantitative in vivo imaging of entire embryos with Digital Scanned Laser Light Sheet Fluorescence Microscopy. Curr Opin Neurobiol 2008; 18:624-32. [DOI: 10.1016/j.conb.2009.03.008] [Citation(s) in RCA: 125] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2008] [Revised: 02/23/2009] [Accepted: 03/23/2009] [Indexed: 11/22/2022]
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50
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Supatto W, Fraser SE, Vermot J. An all-optical approach for probing microscopic flows in living embryos. Biophys J 2008. [PMID: 18556762 PMCID: PMC2907726 DOI: 10.1016/j.bpj.2009.02.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/30/2023] Open
Abstract
Living systems rely on fluid dynamics from embryonic development to adulthood. To visualize biological fluid flow, devising the proper labeling method compatible with both normal biology and in vivo imaging remains a major experimental challenge. Here, we describe a simple strategy for probing microscopic fluid flows in vivo that meets this challenge. An all-optical procedure combining femtosecond laser ablation, fast confocal microscopy and 3D-particle tracking was devised to label, image and quantify the flow. This approach is illustrated by studying the flow generated within a micrometer scale ciliated vesicle located deep inside the zebrafish embryo and involved in breaking left-right embryonic symmetry. By mapping the velocity field within the vesicle and surrounding a single beating cilium, we show this method can address the dynamics of cilia-driven flows at multiple length scales, and can validate the flow features as predicted from previous simulations. This approach provides new experimental access to questions of microscopic fluid dynamics in vivo.
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Affiliation(s)
- Willy Supatto
- Biological Imaging Center, Beckman Institute, California Institute of Technology, Pasadena, California, USA
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