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Darling C, Kumar S, Alexandrov Y, de Faye J, Almagro Santiago J, Rýdlová A, Bugeon L, Dallman MJ, Behrens AJ, French PMW, McGinty J. Optical projection tomography implemented for accessibility and low cost ( OPTImAL). PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2024; 382:20230101. [PMID: 38826047 DOI: 10.1098/rsta.2023.0101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/21/2024] [Indexed: 06/04/2024]
Abstract
Optical projection tomography (OPT) is a three-dimensional mesoscopic imaging modality that can use absorption or fluorescence contrast, and is widely applied to fixed and live samples in the mm-cm scale. For fluorescence OPT, we present OPT implemented for accessibility and low cost, an open-source research-grade implementation of modular OPT hardware and software that has been designed to be widely accessible by using low-cost components, including light-emitting diode (LED) excitation and cooled complementary metal-oxide-semiconductor (CMOS) cameras. Both the hardware and software are modular and flexible in their implementation, enabling rapid switching between sample size scales and supporting compressive sensing to reconstruct images from undersampled sparse OPT data, e.g. to facilitate rapid imaging with low photobleaching/phototoxicity. We also explore a simple implementation of focal scanning OPT to achieve higher resolution, which entails the use of a fan-beam geometry reconstruction method to account for variation in magnification. This article is part of the Theo Murphy meeting issue 'Open, reproducible hardware for microscopy'.
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Affiliation(s)
- C Darling
- Physics Department, Imperial College London , London SW7 2AZ, UK
| | - S Kumar
- Physics Department, Imperial College London , London SW7 2AZ, UK
- Francis Crick Institute , London NW1 1AT, UK
| | - Y Alexandrov
- Physics Department, Imperial College London , London SW7 2AZ, UK
- Francis Crick Institute , London NW1 1AT, UK
| | - J de Faye
- Cancer Stem Cell Laboratory, Institute of Cancer Research , London SW7 3RP, UK
| | - J Almagro Santiago
- Cancer Stem Cell Laboratory, Institute of Cancer Research , London SW7 3RP, UK
| | - A Rýdlová
- Department of Life Sciences, Imperial College London , London SW7 2AZ, UK
| | - L Bugeon
- Department of Life Sciences, Imperial College London , London SW7 2AZ, UK
| | - M J Dallman
- Department of Life Sciences, Imperial College London , London SW7 2AZ, UK
| | - A J Behrens
- Cancer Stem Cell Laboratory, Institute of Cancer Research , London SW7 3RP, UK
- CRUK Convergence Science Centre & Division of Cancer, Department of Surgery and Cancer, Imperial College , London, UK
| | - P M W French
- Physics Department, Imperial College London , London SW7 2AZ, UK
- Francis Crick Institute , London NW1 1AT, UK
| | - J McGinty
- Physics Department, Imperial College London , London SW7 2AZ, UK
- Francis Crick Institute , London NW1 1AT, UK
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2
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Sun J, Zhao F, Zhu L, Liu B, Fei P. Optical projection tomography reconstruction with few views using highly-generalizable deep learning at sinogram domain. BIOMEDICAL OPTICS EXPRESS 2023; 14:6260-6270. [PMID: 38420331 PMCID: PMC10898583 DOI: 10.1364/boe.500152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 10/31/2023] [Accepted: 10/31/2023] [Indexed: 03/02/2024]
Abstract
Optical projection tomography (OPT) reconstruction using a minimal number of measured views offers the potential to significantly reduce excitation dosage and greatly enhance temporal resolution in biomedical imaging. However, traditional algorithms for tomographic reconstruction exhibit severe quality degradation, e.g., presence of streak artifacts, when the number of views is reduced. In this study, we introduce a novel domain evaluation method which can evaluate the domain complexity, and thereby validate that the sinogram domain exhibits lower complexity as compared to the conventional spatial domain. Then we achieve robust deep-learning-based reconstruction with a feedback-based data initialization method at sinogram domain, which shows strong generalization ability that notably improves the overall performance for OPT image reconstruction. This learning-based approach, termed SinNet, enables 4-view OPT reconstructions of diverse biological samples showing robust generalization ability. It surpasses the conventional OPT reconstruction approaches in terms of peak-signal-to-noise ratio (PSNR) and structural similarity (SSIM) metrics, showing its potential for the augment of widely-used OPT techniques.
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Affiliation(s)
- Jiahao Sun
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Fang Zhao
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Lanxin Zhu
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - BinBing Liu
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Peng Fei
- School of Optical and Electronic Information-Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
- Advanced Biomedical Imaging Facility, Huazhong University of Science and Technology, Wuhan, 430074, China
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3
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Darling C, Davis SPX, Kumar S, French PMW, McGinty J. Single-shot optical projection tomography for high-speed volumetric imaging of dynamic biological samples. JOURNAL OF BIOPHOTONICS 2023; 16:e202200232. [PMID: 36087031 DOI: 10.1002/jbio.202200232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 09/07/2022] [Accepted: 09/08/2022] [Indexed: 06/15/2023]
Abstract
A single-shot adaptation of Optical Projection Tomography (OPT) for high-speed volumetric snapshot imaging of dynamic mesoscopic biological samples is presented. Conventional OPT has been applied to in vivo imaging of animal models such as D. rerio, but the sequential acquisition of projection images typically requires samples to be immobilized during the acquisition. A proof-of-principle system capable of single-shot tomography of a ~1 mm3 volume is presented, demonstrating camera-limited rates of up to 62.5 volumes/s, which has been applied to 3D imaging of a freely swimming zebrafish embryo. This is achieved by recording eight projection views simultaneously on four low-cost CMOS cameras. With no stage required to rotate the sample, this single-shot OPT system can be implemented with a component cost of under £5000. The system design can be adapted to different sized fields of view and may be applied to a broad range of dynamic samples, including high throughput flow cytometry applied to model organisms and fluid dynamics studies.
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Affiliation(s)
- Connor Darling
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Samuel P X Davis
- Photonics Group, Department of Physics, Imperial College London, London, UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - Paul M W French
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, London, UK
- Francis Crick Institute, London, UK
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4
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Wang S, Larina IV, Larin KV. Label-free optical imaging in developmental biology [Invited]. BIOMEDICAL OPTICS EXPRESS 2020; 11:2017-2040. [PMID: 32341864 PMCID: PMC7173889 DOI: 10.1364/boe.381359] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/30/2020] [Accepted: 02/25/2020] [Indexed: 05/03/2023]
Abstract
Application of optical imaging in developmental biology marks an exciting frontier in biomedical optics. Optical resolution and imaging depth allow for investigation of growing embryos at subcellular, cellular, and whole organism levels, while the complexity and variety of embryonic processes set multiple challenges stimulating the development of various live dynamic embryonic imaging approaches. Among other optical methods, label-free optical techniques attract an increasing interest as they allow investigation of developmental mechanisms without application of exogenous markers or fluorescent reporters. There has been a boost in development of label-free optical imaging techniques for studying embryonic development in animal models over the last decade, which revealed new information about early development and created new areas for investigation. Here, we review the recent progress in label-free optical embryonic imaging, discuss specific applications, and comment on future developments at the interface of photonics, engineering, and developmental biology.
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Affiliation(s)
- Shang Wang
- Department of Biomedical Engineering, Stevens Institute of Technology, 1 Castle Point Terrace, Hoboken, NJ 07030, USA
| | - Irina V. Larina
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
| | - Kirill V. Larin
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX 77030, USA
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, TX 77204, USA
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5
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Vallejo Ramirez PP, Zammit J, Vanderpoorten O, Riche F, Blé FX, Zhou XH, Spiridon B, Valentine C, Spasov SE, Oluwasanya PW, Goodfellow G, Fantham MJ, Siddiqui O, Alimagham F, Robbins M, Stretton A, Simatos D, Hadeler O, Rees EJ, Ströhl F, Laine RF, Kaminski CF. OptiJ: Open-source optical projection tomography of large organ samples. Sci Rep 2019; 9:15693. [PMID: 31666606 PMCID: PMC6821862 DOI: 10.1038/s41598-019-52065-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 10/09/2019] [Indexed: 12/20/2022] Open
Abstract
The three-dimensional imaging of mesoscopic samples with Optical Projection Tomography (OPT) has become a powerful tool for biomedical phenotyping studies. OPT uses visible light to visualize the 3D morphology of large transparent samples. To enable a wider application of OPT, we present OptiJ, a low-cost, fully open-source OPT system capable of imaging large transparent specimens up to 13 mm tall and 8 mm deep with 50 µm resolution. OptiJ is based on off-the-shelf, easy-to-assemble optical components and an ImageJ plugin library for OPT data reconstruction. The software includes novel correction routines for uneven illumination and sample jitter in addition to CPU/GPU accelerated reconstruction for large datasets. We demonstrate the use of OptiJ to image and reconstruct cleared lung lobes from adult mice. We provide a detailed set of instructions to set up and use the OptiJ framework. Our hardware and software design are modular and easy to implement, allowing for further open microscopy developments for imaging large organ samples.
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Affiliation(s)
- Pedro P Vallejo Ramirez
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Joseph Zammit
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Oliver Vanderpoorten
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Fergus Riche
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Francois-Xavier Blé
- Clinical Discovery Unit, Early Clinical Development, IMED Biotech Unit, AstraZeneca, Cambridge, UK
| | - Xiao-Hong Zhou
- Bioscience, Respiratory, Inflammation and Autoimmunity, IMED Biotech Unit, AstraZeneca, Gothenburg, Sweden
| | - Bogdan Spiridon
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | | | - Simeon E Spasov
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | | | - Gemma Goodfellow
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Marcus J Fantham
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Omid Siddiqui
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Farah Alimagham
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Miranda Robbins
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Andrew Stretton
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Dimitrios Simatos
- Sensor CDT 2015-2016 student cohort, University of Cambridge, Cambridge, UK
| | - Oliver Hadeler
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Eric J Rees
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
| | - Florian Ströhl
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037, Tromsø, Norway
| | - Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory for Molecular Cell Biology (LMCB), University College London, Gower Street, London, WC1E 6BT, UK
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge, UK.
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6
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Valle AF, Seelig JD. Two-photon Bessel beam tomography for fast volume imaging. OPTICS EXPRESS 2019; 27:12147-12162. [PMID: 31052759 DOI: 10.1364/oe.27.012147] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 04/01/2019] [Indexed: 06/09/2023]
Abstract
Light microscopy on dynamic samples, for example neural activity in the brain, often requires imaging volumes that extend over several 100 µm in axial direction at a rate of at least several tens of Hertz. Here, we develop a tomography approach for scanning fluorescence microscopy which allows recording a volume image in a single frame scan. Volumes are imaged by simultaneously recording four independent projections at different angles using temporally multiplexed, tilted Bessel beams. From the resulting projections, three-dimensional images are reconstructed using inverse Radon transforms combined with convolutional neural networks (U-net).
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7
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Cao B, Shetty R, Smith D, Kelbauskas L, Meldrum DR. Integrating fluorescence computed tomography with optical sheet illumination for imaging of live single cells. OPTICS EXPRESS 2018; 26:24020-24030. [PMID: 30184895 DOI: 10.1364/oe.26.024020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 08/12/2018] [Indexed: 05/24/2023]
Abstract
We present a new approach for three-dimensional (3D) live single-cell imaging with isotropic sub-micron spatial resolution using fluorescence computed tomography (fCT). A thin, highly inclined and laminated optical (HILO) sheet of light is used for fluorescence excitation in live single cells that are rotated around an axis perpendicular to the optical axis. During a full rotation, 400-500 two-dimensional (2D) projection images of the cell are acquired from multiple viewing perspectives by rapidly scanning the HILO light sheet along the optical axis. We report technical characteristics of the HILO approach and the results of a quantitative comparison with conventional epi fCT, demonstrating that HILO fCT offers significantly (about 17 times) reduced photobleaching and a two-fold improvement in 3D imaging contrast. We discuss potential application areas of the method for cell structure studies in live single cells with isotropic 3D spatial resolution.
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8
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Ancora D, Di Battista D, Giasafaki G, Psycharakis SE, Liapis E, Ripoll J, Zacharakis G. Optical projection tomography via phase retrieval algorithms. Methods 2017; 136:81-89. [PMID: 29080740 DOI: 10.1016/j.ymeth.2017.10.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Revised: 10/15/2017] [Accepted: 10/17/2017] [Indexed: 11/16/2022] Open
Abstract
We describe a computational method for accurate, quantitative tomographic reconstructions in Optical Projection Tomography, based on phase retrieval algorithms. Our method overcomes limitations imposed by light scattering in opaque tissue samples under the memory effect regime, as well as reduces artifacts due to mechanical movements, misalignments or vibrations. We make use of Gerchberg-Saxton algorithms, calculating first the autocorrelation of the object and then retrieving the associated phase under four numerically simulated measurement conditions. By approaching the task in such a way, we avoid the projection alignment procedure, exploiting the fact that the autocorrelation sinogram is always aligned and centered. We thus propose two new, projection-based, tomographic imaging flowcharts that allow registration-free imaging of opaque biological specimens and unlock three-dimensional tomographic imaging of hidden objects. Two main reconstruction approaches are discussed in the text, focusing on their efficiency in the tomographic retrieval and discussing their applicability under four different numerical experiments.
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Affiliation(s)
- Daniele Ancora
- Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, 70013 Heraklion, Greece; Department of Materials Science and Technology, University of Crete, 71003 Heraklion, Greece
| | - Diego Di Battista
- Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, 70013 Heraklion, Greece; Assing S.p.A, Monterotondo, 00015 Rome, Italy
| | - Georgia Giasafaki
- Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, 70013 Heraklion, Greece
| | - Stylianos E Psycharakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, 70013 Heraklion, Greece; School of Medicine, University of Crete, 71003 Heraklion, Greece
| | - Evangelos Liapis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, 70013 Heraklion, Greece
| | - Jorge Ripoll
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III de Madrid, 28911 Madrid, Spain; Instituto de Investigación Sanitaria del Hospital Gregorio Marañón, 28007 Madrid, Spain
| | - Giannis Zacharakis
- Institute of Electronic Structure and Laser, Foundation for Research and Technology - Hellas, 70013 Heraklion, Greece.
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9
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Phase-Retrieved Tomography enables Mesoscopic imaging of Opaque Tumor Spheroids. Sci Rep 2017; 7:11854. [PMID: 28928445 PMCID: PMC5605697 DOI: 10.1038/s41598-017-12193-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 09/06/2017] [Indexed: 12/03/2022] Open
Abstract
We present a new Phase-Retrieved Tomography (PRT) method to radically improve mesoscopic imaging at regimes beyond one transport mean-free-path and achieve high resolution, uniformly throughout the volume of opaque samples. The method exploits multi-view acquisition in a hybrid Selective Plane Illumination Microscope (SPIM) and Optical Projection Tomography (OPT) setup and a three-dimensional Gerchberg-Saxton phase-retrieval algorithm applied in 3D through the autocorrelation sinogram. We have successfully applied this innovative protocol to image optically dense 3D cell cultures in the form of tumor spheroids, highly versatile models to study cancer behavior and response to chemotherapy. We have thus achieved a significant improvement of resolution in depths not yet accessible with the currently used methods in SPIM/OPT, while overcoming all registration and alignment problems inherent to these techniques.
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10
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Coquoz S, Marchand PJ, Bouwens A, Mouchiroud L, Sorrentino V, Szlag D, Auwerx J, Lasser T. Label-free three-dimensional imaging of Caenorhabditis elegans with visible optical coherence microscopy. PLoS One 2017; 12:e0181676. [PMID: 28727813 PMCID: PMC5519216 DOI: 10.1371/journal.pone.0181676] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Accepted: 07/05/2017] [Indexed: 12/26/2022] Open
Abstract
Fast, label-free, high-resolution, three-dimensional imaging platforms are crucial for high-throughput in vivo time-lapse studies of the anatomy of Caenorhabditis elegans, one of the most commonly used model organisms in biomedical research. Despite the needs, methods combining all these characteristics have been lacking. Here, we present label-free imaging of live Caenorhabditis elegans with three-dimensional sub-micrometer resolution using visible optical coherence microscopy (visOCM). visOCM is a versatile optical imaging method which we introduced recently for tomography of cell cultures and tissue samples. Our method is based on Fourier domain optical coherence tomography, an interferometric technique that provides three-dimensional images with high sensitivity, high acquisition rate and micrometer-scale resolution. By operating in the visible wavelength range and using a high NA objective, visOCM attains lateral and axial resolutions below 1 μm. Additionally, we use a Bessel illumination offering an extended depth of field of approximately 40 μm. We demonstrate that visOCM’s imaging properties allow rapid imaging of full sized living Caenorhabditis elegans down to the sub-cellular level. Our system opens the door to many applications such as the study of phenotypic changes related to developmental or ageing processes.
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Affiliation(s)
- Séverine Coquoz
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
- * E-mail:
| | - Paul J. Marchand
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Arno Bouwens
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Laurent Mouchiroud
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Vincenzo Sorrentino
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Daniel Szlag
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Johan Auwerx
- Laboratory of Integrative and Systems Physiology, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
| | - Theo Lasser
- Laboratoire d’Optique Biomédicale, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland
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11
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Singh M, Wu C, Mayerich D, Dickinson ME, Larina IV, Larin KV. Multimodal embryonic imaging using optical coherence tomography, selective plane illumination microscopy, and optical projection tomography. ANNUAL INTERNATIONAL CONFERENCE OF THE IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. IEEE ENGINEERING IN MEDICINE AND BIOLOGY SOCIETY. ANNUAL INTERNATIONAL CONFERENCE 2017; 2016:3922-3925. [PMID: 28269143 DOI: 10.1109/embc.2016.7591585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The murine model is commonly utilized for studying developmental diseases. Different optical techniques have been developed to image mouse embryos, but each has its own set of limitations and restrictions. In this study, we compare the performance of the well-established technique of optical coherence tomography (OCT) to the relatively new methods of selective plane illumination microscopy (SPIM) and optical projection tomography (OPT) to assess murine embryonic development. OCT can provide label free high resolution images of the mouse embryo, but suffers from light attenuation that limits visualization of deeper structures. SPIM is able to image shallow regions with great detail utilizing fluorescent contrast. OPT can provide superior imaging depth, and can also use fluorescence labels but, it requires samples to be fixed and cleared before imaging. OCT requires no modification of the embryo, and thus, can be used in vivo and in utero. In this study, we compare the efficacy of OCT, SPIM, and OPT for imaging murine embryonic development. The data demonstrate the superior capability of SPIM and OPT for imaging fine structures with high resolution while only OCT can provide structural and functional imaging of live embryos with micrometer scale resolution.
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12
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Lee KJI, Calder GM, Hindle CR, Newman JL, Robinson SN, Avondo JJHY, Coen ES. Macro optical projection tomography for large scale 3D imaging of plant structures and gene activity. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:527-538. [PMID: 28025317 PMCID: PMC5441912 DOI: 10.1093/jxb/erw452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Optical projection tomography (OPT) is a well-established method for visualising gene activity in plants and animals. However, a limitation of conventional OPT is that the specimen upper size limit precludes its application to larger structures. To address this problem we constructed a macro version called Macro OPT (M-OPT). We apply M-OPT to 3D live imaging of gene activity in growing whole plants and to visualise structural morphology in large optically cleared plant and insect specimens up to 60 mm tall and 45 mm deep. We also show how M-OPT can be used to image gene expression domains in 3D within fixed tissue and to visualise gene activity in 3D in clones of growing young whole Arabidopsis plants. A further application of M-OPT is to visualise plant-insect interactions. Thus M-OPT provides an effective 3D imaging platform that allows the study of gene activity, internal plant structures and plant-insect interactions at a macroscopic scale.
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Affiliation(s)
- Karen J I Lee
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Grant M Calder
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | | | - Jacob L Newman
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | - Simon N Robinson
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
| | | | - Enrico S Coen
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, UK
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13
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Ardeshiri R, Mulcahy B, Zhen M, Rezai P. A hybrid microfluidic device for on-demand orientation and multidirectional imaging of C. elegans organs and neurons. BIOMICROFLUIDICS 2016; 10:064111. [PMID: 27990213 PMCID: PMC5135714 DOI: 10.1063/1.4971157] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 11/16/2016] [Indexed: 05/06/2023]
Abstract
C. elegans is a well-known model organism in biology and neuroscience with a simple cellular (959 cells) and nervous (302 neurons) system and a relatively homologous (40%) genome to humans. Lateral and longitudinal manipulation of C. elegans to a favorable orientation is important in many applications such as neural and cellular imaging, laser ablation, microinjection, and electrophysiology. In this paper, we describe a micro-electro-fluidic device for on-demand manipulation of C. elegans and demonstrate its application in imaging of organs and neurons that cannot be visualized efficiently under natural orientation. To achieve this, we have used the electrotaxis technique to longitudinally orient the worm in a microchannel and then insert it into an orientation and imaging channel in which we integrated a rotatable glass capillary for orientation of the worm in any desired direction. The success rates of longitudinal and lateral orientations were 76% and 100%, respectively. We have demonstrated the application of our device in optical and fluorescent imaging of vulva, uterine-vulval cell (uv1), vulB1\2 (adult vulval toroid cells), and ventral nerve cord of wild-type and mutant worms. In comparison to existing methods, the developed technique is capable of orienting the worm at any desired angle and maintaining the orientation while providing access to the worm for potential post-manipulation assays. This versatile tool can be potentially used in various applications such as neurobehavioral imaging, neuronal ablation, microinjection, and electrophysiology.
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Affiliation(s)
- Ramtin Ardeshiri
- Department of Mechanical Engineering, York University , Toronto, Ontario M3J 1P3, Canada
| | - Ben Mulcahy
- Lunenfeld-Tanenbaum Research Institute , Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | | | - Pouya Rezai
- Department of Mechanical Engineering, York University , Toronto, Ontario M3J 1P3, Canada
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14
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Rieckher M. Light Sheet Microscopy to Measure Protein Dynamics. J Cell Physiol 2016; 232:27-35. [DOI: 10.1002/jcp.25451] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Accepted: 06/07/2016] [Indexed: 12/26/2022]
Affiliation(s)
- Matthias Rieckher
- Institute for Genome Stability in Ageing and Disease; Cologne Cluster of Excellence in Cellular Stress Responses in Aging-Associated Diseases (CECAD); University of Cologne; Cologne Germany
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15
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Singh M, Raghunathan R, Piazza V, Davis-Loiacono AM, Cable A, Vedakkan TJ, Janecek T, Frazier MV, Nair A, Wu C, Larina IV, Dickinson ME, Larin KV. Applicability, usability, and limitations of murine embryonic imaging with optical coherence tomography and optical projection tomography. BIOMEDICAL OPTICS EXPRESS 2016; 7:2295-310. [PMID: 27375945 PMCID: PMC4918583 DOI: 10.1364/boe.7.002295] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2016] [Revised: 05/09/2016] [Accepted: 05/10/2016] [Indexed: 05/17/2023]
Abstract
We present an analysis of imaging murine embryos at various embryonic developmental stages (embryonic day 9.5, 11.5, and 13.5) by optical coherence tomography (OCT) and optical projection tomography (OPT). We demonstrate that while OCT was capable of rapid high-resolution live 3D imaging, its limited penetration depth prevented visualization of deeper structures, particularly in later stage embryos. In contrast, OPT was able to image the whole embryos, but could not be used in vivo because the embryos must be fixed and cleared. Moreover, the fixation process significantly altered the embryo morphology, which was quantified by the volume of the eye-globes before and after fixation. All of these factors should be weighed when determining which imaging modality one should use to achieve particular goals of a study.
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Affiliation(s)
- Manmohan Singh
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, 77204, USA
| | - Raksha Raghunathan
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, 77204, USA
| | - Victor Piazza
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, 77584, USA
| | | | - Alex Cable
- Thorlabs, Inc., 56 Sparta Ave., Newton, 07860, USA
| | - Tegy J. Vedakkan
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, 77584, USA
| | - Trevor Janecek
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, 77204, USA
| | - Michael V. Frazier
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, 77204, USA
| | - Achuth Nair
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, 77204, USA
| | - Chen Wu
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, 77204, USA
| | - Irina V. Larina
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, 77584, USA
| | - Mary E. Dickinson
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, 77584, USA
| | - Kirill V. Larin
- Department of Biomedical Engineering, University of Houston, 3605 Cullen Boulevard, Houston, 77204, USA
- Molecular Physiology and Biophysics, Baylor College of Medicine, One Baylor Plaza, Houston, 77584, USA
- Department of Electrical Engineering, Samara National Research University, Samara, 34 Moskovskoye sh., 443086, Russia
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16
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Soto AM, Koivisto JT, Parraga JE, Silva-Correia J, Oliveira JM, Reis RL, Kellomäki M, Hyttinen J, Figueiras E. Optical Projection Tomography Technique for Image Texture and Mass Transport Studies in Hydrogels Based on Gellan Gum. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2016; 32:5173-5182. [PMID: 27138138 DOI: 10.1021/acs.langmuir.6b00554] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
The microstructure and permeability are crucial factors for the development of hydrogels for tissue engineering, since they influence cell nutrition, penetration, and proliferation. The currently available imaging methods able to characterize hydrogels have many limitations. They often require sample drying and other destructive processing, which can change hydrogel structure, or they have limited imaging penetration depth. In this work, we show for the first time an alternative nondestructive method, based on optical projection tomography (OPT) imaging, to characterize hydrated hydrogels without the need of sample processing. As proof of concept, we used gellan gum (GG) hydrogels obtained by several cross-linking methods. Transmission mode OPT was used to analyze image microtextures, and emission mode OPT to study mass transport. Differences in hydrogel structure related to different types of cross-linking and between modified and native GG were found through the acquired Haralick's image texture features followed by multiple discriminant analysis (MDA). In mass transport studies, the mobility of FITC-dextran (MW 20, 150, 2000 kDa) was analyzed through the macroscopic hydrogel. The FITC-dextran velocities were found to be inversely proportional to the size of the dextran as expected. Furthermore, the threshold size in which the transport is affected by the hydrogel mesh was found to be 150 kDa (Stokes' radii between 69 and 95 Å). On the other hand, the mass transport study allowed us to define an index of homogeneity to assess the cross-linking distribution, structure inside the hydrogel, and repeatability of hydrogel production. As a conclusion, we showed that the set of OPT imaging based material characterization methods presented here are useful for screening many characteristics of hydrogel compositions in relatively short time in an inexpensive manner, providing tools for improving the process of designing hydrogels for tissue engineering and drugs/cells delivery applications.
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Affiliation(s)
- Ana M Soto
- Computational Biophysics and Imaging Group, ELT Department, Tampere University of Technology , 33720 Tampere, Finland
- BioMediTech - Institute of Biosciences and Medical Technology,33720 Tampere, Finland
| | - Janne T Koivisto
- BioMediTech - Institute of Biosciences and Medical Technology,33720 Tampere, Finland
- Biomaterials and Tissue Engineering Group, ELT Department, Tampere University of Technology , 33720 Tampere, Finland
- Heart Group, BioMediTech, University of Tampere , 33720 Tampere, Finland
| | - Jenny E Parraga
- BioMediTech - Institute of Biosciences and Medical Technology,33720 Tampere, Finland
- Biomaterials and Tissue Engineering Group, ELT Department, Tampere University of Technology , 33720 Tampere, Finland
| | - Joana Silva-Correia
- 3B's Research Group, Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine Barco GMR, 4704-553 Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Joaquim M Oliveira
- 3B's Research Group, Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine Barco GMR, 4704-553 Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Rui L Reis
- 3B's Research Group, Biomaterials, Biodegradables and Biomimetics, University of Minho, Headquarters of the European Institute of Excellence on Tissue Engineering and Regenerative Medicine Barco GMR, 4704-553 Braga, Portugal
- ICVS/3B's - PT Government Associate Laboratory, 4710-057 Braga/Guimarães, Portugal
| | - Minna Kellomäki
- BioMediTech - Institute of Biosciences and Medical Technology,33720 Tampere, Finland
- Biomaterials and Tissue Engineering Group, ELT Department, Tampere University of Technology , 33720 Tampere, Finland
| | - Jari Hyttinen
- Computational Biophysics and Imaging Group, ELT Department, Tampere University of Technology , 33720 Tampere, Finland
- BioMediTech - Institute of Biosciences and Medical Technology,33720 Tampere, Finland
| | - Edite Figueiras
- Computational Biophysics and Imaging Group, ELT Department, Tampere University of Technology , 33720 Tampere, Finland
- BioMediTech - Institute of Biosciences and Medical Technology,33720 Tampere, Finland
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17
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Hejazi SM, Sarkar S, Darezereshki Z. Fast multislice fluorescence molecular tomography using sparsity-inducing regularization. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:26012. [PMID: 26927222 DOI: 10.1117/1.jbo.21.2.026012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 02/04/2016] [Indexed: 05/05/2023]
Abstract
Fluorescence molecular tomography (FMT) is a rapidly growing imaging method that facilitates the recovery of small fluorescent targets within biological tissue. The major challenge facing the FMT reconstruction method is the ill-posed nature of the inverse problem. In order to overcome this problem, the acquisition of large FMT datasets and the utilization of a fast FMT reconstruction algorithm with sparsity regularization have been suggested recently. Therefore, the use of a joint L1/total-variation (TV) regularization as a means of solving the ill-posed FMT inverse problem is proposed. A comparative quantified analysis of regularization methods based on L1-norm and TV are performed using simulated datasets, and the results show that the fast composite splitting algorithm regularization method can ensure the accuracy and robustness of the FMT reconstruction. The feasibility of the proposed method is evaluated in an in vivo scenario for the subcutaneous implantation of a fluorescent-dye-filled capillary tube in a mouse, and also using hybrid FMT and x-ray computed tomography data. The results show that the proposed regularization overcomes the difficulties created by the ill-posed inverse problem.
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Affiliation(s)
- Sedigheh Marjaneh Hejazi
- Tehran University of Medical Sciences, Medical Physics and Biomedical Engineering Department, School of Medicine, Tehran 1417613151, IranbTehran University of Medical Sciences, Research Center for Molecular and Cellular in Imaging, Bio-optical Imaging Gro
| | - Saeed Sarkar
- Tehran University of Medical Sciences, Medical Physics and Biomedical Engineering Department, School of Medicine, Tehran 1417613151, IrancTehran University of Medical Sciences, Research Center for Science and Technology in Medicine, Imam Khomeini Hospital
| | - Ziba Darezereshki
- Tehran University of Medical Sciences, Medical Physics and Biomedical Engineering Department, School of Medicine, Tehran 1417613151, Iran
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18
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Unleashing Optics and Optoacoustics for Developmental Biology. Trends Biotechnol 2015; 33:679-691. [PMID: 26435161 DOI: 10.1016/j.tibtech.2015.08.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 08/11/2015] [Accepted: 08/18/2015] [Indexed: 01/23/2023]
Abstract
The past decade marked an optical revolution in biology: an unprecedented number of optical techniques were developed and adopted for biological exploration, demonstrating increasing interest in optical imaging and in vivo interrogations. Optical methods have become faster and have reached nanoscale resolution, and are now complemented by optoacoustic (photoacoustic) methods capable of imaging whole specimens in vivo. Never before were so many optical imaging barriers broken in such a short time-frame: with new approaches to optical microscopy and mesoscopy came an increased ability to image biology at unprecedented speed, resolution, and depth. This review covers the most relevant techniques for imaging in developmental biology, and offers an outlook on the next steps for these technologies and their applications.
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19
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Accelerated Optical Projection Tomography Applied to In Vivo Imaging of Zebrafish. PLoS One 2015; 10:e0136213. [PMID: 26308086 PMCID: PMC4550250 DOI: 10.1371/journal.pone.0136213] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2015] [Accepted: 07/31/2015] [Indexed: 11/19/2022] Open
Abstract
Optical projection tomography (OPT) provides a non-invasive 3-D imaging modality that can be applied to longitudinal studies of live disease models, including in zebrafish. Current limitations include the requirement of a minimum number of angular projections for reconstruction of reasonable OPT images using filtered back projection (FBP), which is typically several hundred, leading to acquisition times of several minutes. It is highly desirable to decrease the number of required angular projections to decrease both the total acquisition time and the light dose to the sample. This is particularly important to enable longitudinal studies, which involve measurements of the same fish at different time points. In this work, we demonstrate that the use of an iterative algorithm to reconstruct sparsely sampled OPT data sets can provide useful 3-D images with 50 or fewer projections, thereby significantly decreasing the minimum acquisition time and light dose while maintaining image quality. A transgenic zebrafish embryo with fluorescent labelling of the vasculature was imaged to acquire densely sampled (800 projections) and under-sampled data sets of transmitted and fluorescence projection images. The under-sampled OPT data sets were reconstructed using an iterative total variation-based image reconstruction algorithm and compared against FBP reconstructions of the densely sampled data sets. To illustrate the potential for quantitative analysis following rapid OPT data acquisition, a Hessian-based method was applied to automatically segment the reconstructed images to select the vasculature network. Results showed that 3-D images of the zebrafish embryo and its vasculature of sufficient visual quality for quantitative analysis can be reconstructed using the iterative algorithm from only 32 projections—achieving up to 28 times improvement in imaging speed and leading to total acquisition times of a few seconds.
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20
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A customized light sheet microscope to measure spatio-temporal protein dynamics in small model organisms. PLoS One 2015; 10:e0127869. [PMID: 26000610 PMCID: PMC4441442 DOI: 10.1371/journal.pone.0127869] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2014] [Accepted: 04/20/2015] [Indexed: 12/24/2022] Open
Abstract
We describe a customizable and cost-effective light sheet microscopy (LSM) platform for rapid three-dimensional imaging of protein dynamics in small model organisms. The system is designed for high acquisition speeds and enables extended time-lapse in vivo experiments when using fluorescently labeled specimens. We demonstrate the capability of the setup to monitor gene expression and protein localization during ageing and upon starvation stress in longitudinal studies in individual or small groups of adult Caenorhabditis elegans nematodes. The system is equipped to readily perform fluorescence recovery after photobleaching (FRAP), which allows monitoring protein recovery and distribution under low photobleaching conditions. Our imaging platform is designed to easily switch between light sheet microscopy and optical projection tomography (OPT) modalities. The setup permits monitoring of spatio-temporal expression and localization of ageing biomarkers of subcellular size and can be conveniently adapted to image a wide range of small model organisms and tissue samples.
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21
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In-vivo optical tomography of small scattering specimens: time-lapse 3D imaging of the head eversion process in Drosophila melanogaster. Sci Rep 2014; 4:7325. [PMID: 25471694 PMCID: PMC4255187 DOI: 10.1038/srep07325] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2014] [Accepted: 11/18/2014] [Indexed: 02/02/2023] Open
Abstract
Even though in vivo imaging approaches have witnessed several new and important developments, specimens that exhibit high light scattering properties such as Drosophila melanogaster pupae are still not easily accessible with current optical imaging techniques, obtaining images only from subsurface features. This means that in order to obtain 3D volumetric information these specimens need to be studied either after fixation and a chemical clearing process, through an imaging window - thus perturbing physiological development -, or during early stages of development when the scattering contribution is negligible. In this paper we showcase how Optical Projection Tomography may be used to obtain volumetric images of the head eversion process in vivo in Drosophila melanogaster pupae, both in control and headless mutant specimens. Additionally, we demonstrate the use of Helical Optical Projection Tomography (hOPT) as a tool for high throughput 4D-imaging of several specimens simultaneously.
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22
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Abstract
A new method to obtain the three-dimensional localization of fluorochrome distributions in micrometric samples is presented. It uses a microlens array coupled to the image port of a standard microscope to obtain tomographic data by a filtered back-projection algorithm. Scanning of the microlens array is proposed to obtain a dense data set for reconstruction. Simulation and experimental results are shown and the implications of this approach in fast 3D imaging are discussed.
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23
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Arranz A, Dong D, Zhu S, Rudin M, Tsatsanis C, Tian J, Ripoll J. Helical optical projection tomography. OPTICS EXPRESS 2013; 21:25912-25. [PMID: 24216818 DOI: 10.1364/oe.21.025912] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
A new technique termed Helical Optical Projection Tomography (hOPT) has been developed with the aim to overcome some of the limitations of current 3D optical imaging techniques. hOPT is based on Optical Projection Tomography (OPT) with the major difference that there is a translation of the sample in the vertical direction during the image acquisition process, requiring a new approach to image reconstruction. Contrary to OPT, hOPT makes possible to obtain 3D-optical images of intact long samples without imposing limits on the sample length. This has been tested using hOPT to image long murine tissue samples such as spinal cords and large intestines. Moreover, 3D-reconstructed images of the colon of DSS-treated mice, a model for Inflammatory Bowel Disease, allowed the identification of the structural alterations. Finally, the geometry of the hOPT device facilitates the addition of a Selective Plane Illumination Microscopy (SPIM) arm, providing the possibility of delivering high resolution images of selected areas together with complete volumetric information.
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24
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Wong MD, Dazai J, Walls JR, Gale NW, Henkelman RM. Design and implementation of a custom built optical projection tomography system. PLoS One 2013; 8:e73491. [PMID: 24023880 PMCID: PMC3762719 DOI: 10.1371/journal.pone.0073491] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2013] [Accepted: 07/23/2013] [Indexed: 11/18/2022] Open
Abstract
Optical projection tomography (OPT) is an imaging modality that has, in the last decade, answered numerous biological questions owing to its ability to view gene expression in 3 dimensions (3D) at high resolution for samples up to several cm3. This has increased demand for a cabinet OPT system, especially for mouse embryo phenotyping, for which OPT was primarily designed for. The Medical Research Council (MRC) Technology group (UK) released a commercial OPT system, constructed by Skyscan, called the Bioptonics OPT 3001 scanner that was installed in a limited number of locations. The Bioptonics system has been discontinued and currently there is no commercial OPT system available. Therefore, a few research institutions have built their own OPT system, choosing parts and a design specific to their biological applications. Some of these custom built OPT systems are preferred over the commercial Bioptonics system, as they provide improved performance based on stable translation and rotation stages and up to date CCD cameras coupled with objective lenses of high numerical aperture, increasing the resolution of the images. Here, we present a detailed description of a custom built OPT system that is robust and easy to build and install. Included is a hardware parts list, instructions for assembly, a description of the acquisition software and a free download site, and methods for calibration. The described OPT system can acquire a full 3D data set in 10 minutes at 6.7 micron isotropic resolution. The presented guide will hopefully increase adoption of OPT throughout the research community, for the OPT system described can be implemented by personnel with minimal expertise in optics or engineering who have access to a machine shop.
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Affiliation(s)
- Michael D. Wong
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario, Canada
- * E-mail:
| | - Jun Dazai
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario, Canada
| | - Johnathon R. Walls
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - Nicholas W. Gale
- Regeneron Pharmaceuticals, Tarrytown, New York, United States of America
| | - R. Mark Henkelman
- Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada
- Mouse Imaging Centre (MICe), Hospital for Sick Children, Toronto, Ontario, Canada
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25
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Feng G, Chen J, Lu X, Han D, Zeng Y. Laser speckle projection tomography. OPTICS LETTERS 2013; 38:2654-6. [PMID: 23903102 DOI: 10.1364/ol.38.002654] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We propose a laser speckle projection tomography (LSPT) method to obtain a three-dimensional (3D) flowing image. The method combines the advantages of optical projection tomography and laser speckle imaging to reconstruct the visualization of 3D flowing structure. With LSPT, the flowing signal is extracted by laser speckle contrast method and the 3D flowing image is reconstructed by the filtered back-projection algorithm. A phantom experiment is performed to demonstrate that LSPT is able to obtain 3D flowing structure, influenced by concentration and the flow speed.
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Affiliation(s)
- Guanping Feng
- Department of Photoelectric Technology, Foshan University, Guangdong, China
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26
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Leahy C, Radhakrishnan H, Srinivasan VJ. Volumetric imaging and quantification of cytoarchitecture and myeloarchitecture with intrinsic scattering contrast. BIOMEDICAL OPTICS EXPRESS 2013; 4:1978-90. [PMID: 24156058 PMCID: PMC3799660 DOI: 10.1364/boe.4.001978] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2013] [Revised: 08/21/2013] [Accepted: 08/22/2013] [Indexed: 05/18/2023]
Abstract
We present volumetric imaging and computational techniques to quantify neuronal and myelin architecture with intrinsic scattering contrast. Using spectral / Fourier domain Optical Coherence Microscopy (OCM) and software focus-tracking we validate imaging of neuronal cytoarchitecture and demonstrate quantification in the rodent cortex in vivo. Additionally, by ex vivo imaging in conjunction with optical clearing techniques, we demonstrate that intrinsic scattering contrast is preserved in the brain, even after sacrifice and fixation. We volumetrically image cytoarchitecture and myeloarchitecture ex vivo across the entire depth of the rodent cortex. Cellular-level imaging up to the working distance of our objective (~3 mm) is demonstrated ex vivo. Architectonic features show the expected laminar characteristics; moreover, changes in contrast after the application of acetic acid suggest that entire neuronal cell bodies are responsible for the "negative contrast" present in the images. Clearing and imaging techniques that preserve tissue architectural integrity have the potential to enable non-invasive studies of the brain during development, disease, and remodeling, even in samples where exogenous labeling is impractical.
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27
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Dong D, Zhu S, Qin C, Kumar V, Stein JV, Oehler S, Savakis C, Tian J, Ripoll J. Automated recovery of the center of rotation in optical projection tomography in the presence of scattering. IEEE J Biomed Health Inform 2012; 17:198-204. [PMID: 23008264 DOI: 10.1109/titb.2012.2219588] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Finding the center of rotation is an essential step for accurate three-dimensional reconstruction in optical projection tomography (OPT). Unfortunately current methods are not convenient since they require either prior scanning of a reference phantom, small structures of high intensity existing in the specimen, or active participation during the centering procedure. To solve these problems this paper proposes a fast and automatic center of rotation search method making use of parallel programming in graphics processing units (GPUs). Our method is based on a two step search approach making use only of those sections of the image with high signal to noise ratio. We have tested this method both in non-scattering ex vivo samples and in in vivo specimens with a considerable contribution of scattering such as Drosophila melanogaster pupae, recovering in all cases the center of rotation with a precision 1/4 pixel or less.
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28
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Zhu S, Dong D, Birk UJ, Rieckher M, Tavernarakis N, Qu X, Liang J, Tian J, Ripoll J. Automated motion correction for in vivo optical projection tomography. IEEE TRANSACTIONS ON MEDICAL IMAGING 2012; 31:1358-1371. [PMID: 22374352 DOI: 10.1109/tmi.2012.2188836] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
In in vivo optical projection tomography (OPT), object motion will significantly reduce the quality and resolution of the reconstructed image. Based on the well-known Helgason-Ludwig consistency condition (HLCC), we propose a novel method for motion correction in OPT under parallel beam illumination. The method estimates object motion from projection data directly and does not require any other additional information, which results in a straightforward implementation. We decompose object movement into translation and rotation, and discuss how to correct for both translation and general motion simultaneously. Since finding the center of rotation accurately is critical in OPT, we also point out that the system's geometrical offset can be considered as object translation and therefore also calibrated through the translation estimation method. In order to verify the algorithm effectiveness, both simulated and in vivo OPT experiments are performed. Our results demonstrate that the proposed approach is capable of decreasing movement artifacts significantly thus providing high quality reconstructed images in the presence of object motion.
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Affiliation(s)
- Shouping Zhu
- School of Life Sciences and Technology, Xidian University, Xi’an, Shaanxi, China
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29
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30
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Soloviev VY, Zacharakis G, Spiliopoulos G, Favicchio R, Correia T, Arridge SR, Ripoll J. Tomographic imaging with polarized light. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2012; 29:980-8. [PMID: 22673429 DOI: 10.1364/josaa.29.000980] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
We report three-dimensional tomographic reconstruction of optical parameters for the mesoscopic light scattering regime from experimentally obtained datasets by using polarized light. We present a numerically inexpensive approximation to the radiative transfer equation governing the polarized light transport. This approximation is employed in the reconstruction algorithm, which computes two optical parameters by using parallel and perpendicular polarizations of transmitted light. Datasets were obtained by imaging a scattering phantom embedding highly absorbing inclusions. Reconstruction results are presented and discussed.
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Affiliation(s)
- Vadim Y Soloviev
- Department of Computer Science, University College London, London, UK.
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31
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Fei P, Yu Z, Wang X, Lu PJ, Fu Y, He Z, Xiong J, Huang Y. High dynamic range optical projection tomography (HDR-OPT). OPTICS EXPRESS 2012; 20:8824-8836. [PMID: 22513593 DOI: 10.1364/oe.20.008824] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Traditional optical projection tomography (OPT) acquires a single image at each rotation angle, thereby suffering from limitations in CCD dynamic range; this conventional usage cannot resolve features in samples with highly heterogeneous absorption, such as in small animals with organs of varying size. We present a novel technique, applying multiple-exposure high dynamic range (HDR) imaging to OPT, and demonstrate its ability to resolve fine details in zebrafish embryos, without complicated chemical clearing. We implement the tomographic reconstruction algorithm on the GPU, yielding a performance increase of two orders of magnitude. These features give our method potential application in high-throughput, high-resolution in vivo 3D imaging.
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Affiliation(s)
- Peng Fei
- Biodynamic Optical Imaging Center (BIOPIC), Peking University, Beijing 100871, China
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32
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Heidrich M, Kühnel MP, Kellner M, Lorbeer RA, Lange T, Winkel A, Stiesch M, Meyer H, Heisterkamp A. 3D imaging of biofilms on implants by detection of scattered light with a scanning laser optical tomograph. BIOMEDICAL OPTICS EXPRESS 2011; 2:2982-94. [PMID: 22076261 PMCID: PMC3207369 DOI: 10.1364/boe.2.002982] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2011] [Revised: 09/02/2011] [Accepted: 09/02/2011] [Indexed: 05/13/2023]
Abstract
Biofilms - communities of microorganisms attached to surfaces - are a constant threat for long-term success in modern implantology. The application of laser scanning microscopy (LSM) has increased the knowledge about microscopic properties of biofilms, whereas a 3D imaging technique for the large scale visualization of bacterial growth and migration on curved and non-transparent surfaces is not realized so far.Towards this goal, we built a scanning laser optical tomography (SLOT) setup detecting scattered laser light to image biofilm on dental implant surfaces. SLOT enables the visualization of living biofilms in 3D by detecting the wavelength-dependent absorption of non-fluorescent stains like e.g. reduced triphenyltetrazolium chloride (TTC) accumulated within metabolically active bacterial cells. Thus, the presented system allows the large scale investigation of vital biofilm structure and in vitro development on cylindrical and non-transparent objects without the need for fluorescent vital staining. We suggest SLOT to be a valuable tool for the structural and volumetric investigation of biofilm formation on implants with sizes up to several millimeters.
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Affiliation(s)
- Marko Heidrich
- Biomedical Optics Department, Laser Zentrum Hannover e.V., Hollerithallee 8, D-30419 Hannover,
Germany
- Institute of Quantum Optics, Gottfried Wilhelm Leibniz Universität Hannover, Welfengarten1, D-30167 Hannover,
Germany
| | - Mark P. Kühnel
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neubergstr.1, D-30625 Hannover,
Germany
| | - Manuela Kellner
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neubergstr.1, D-30625 Hannover,
Germany
| | - Raoul-Amadeus Lorbeer
- Biomedical Optics Department, Laser Zentrum Hannover e.V., Hollerithallee 8, D-30419 Hannover,
Germany
| | - Tineke Lange
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neubergstr.1, D-30625 Hannover,
Germany
| | - Andreas Winkel
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neubergstr.1, D-30625 Hannover,
Germany
- CrossBIT Verbundzentrum für Biokompatibilität und Implantatimmunologie in der Medizintechnik, Feodor-Lynen-Straße 31, D-30625 Hannover,
Germany
| | - Meike Stiesch
- Department of Prosthetic Dentistry and Biomedical Materials Science, Hannover Medical School, Carl-Neubergstr.1, D-30625 Hannover,
Germany
| | - Heiko Meyer
- Biomedical Optics Department, Laser Zentrum Hannover e.V., Hollerithallee 8, D-30419 Hannover,
Germany
- Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, Carl-Neubergstr.1, D-30625 Hannover,
Germany
| | - Alexander Heisterkamp
- Biomedical Optics Department, Laser Zentrum Hannover e.V., Hollerithallee 8, D-30419 Hannover,
Germany
- Institute of Quantum Optics, Gottfried Wilhelm Leibniz Universität Hannover, Welfengarten1, D-30167 Hannover,
Germany
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33
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Sinkó J, Dudás L, Gajdátsy G, Erdélyi M, Szabó G. Map-free line-scanning tomographic optical microscope. OPTICS LETTERS 2011; 36:4011-4013. [PMID: 22002369 DOI: 10.1364/ol.36.004011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Line-scanning tomographic optical microscopy (LSTOM) requires precise rotation of the scanning line. We demonstrate a method that applies translation-invariant optical elements (polarizer and birefringent plate) to minimize the rotation error. An astigmatic line produced by means of a focused beam through a birefringent plate is used as line illumination. A comparative theoretical and experimental study is presented using an LSTOM system.
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Affiliation(s)
- József Sinkó
- Department of Optics and Quantum Electronics, University of Szeged, Szeged, Hungary
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34
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Bassi A, Fieramonti L, D'Andrea C, Mione M, Valentini G. In vivo label-free three-dimensional imaging of zebrafish vasculature with optical projection tomography. JOURNAL OF BIOMEDICAL OPTICS 2011; 16:100502. [PMID: 22029341 DOI: 10.1117/1.3640808] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
We introduce flow optical projection tomography, an imaging technique capable of visualizing the vasculature of living specimens in 3-D. The method detects the movement of cells in the bloodstream and creates flow maps using a motion-analysis procedure. Then, flow maps obtained from projection taken at several angles are used to reconstruct sections of the circulatory system of the specimen. We therefore demonstrate an in vivo, 3-D optical imaging technique that, without the use of any labeling, is able to reconstruct and visualize the vascular network of transparent and weakly scattering living specimens.
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Affiliation(s)
- Andrea Bassi
- Politecnico di Milano, Dipartimento di Fisica, Piazza Leonardo da Vinci 32, Milan, 20133, Italy.
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