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Branning JM, Faughnan KA, Tomson AA, Bell GJ, Isbell SM, DeGroot A, Jameson L, Kilroy K, Smith M, Smith R, Mottel L, Branning EG, Worrall Z, Anderson F, Panditaradyula A, Yang W, Abdelmalek J, Brake J, Cash KJ. Multifunction fluorescence open source in vivo/in vitro imaging system (openIVIS). PLoS One 2024; 19:e0299875. [PMID: 38498588 PMCID: PMC10947658 DOI: 10.1371/journal.pone.0299875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 02/18/2024] [Indexed: 03/20/2024] Open
Abstract
The widespread availability and diversity of open-source microcontrollers paired with off-the-shelf electronics and 3D printed technology has led to the creation of a wide range of low-cost scientific instruments, including microscopes, spectrometers, sensors, data loggers, and other tools that can be used for research, education, and experimentation. These devices can be used to explore a wide range of scientific topics, from biology and chemistry to physics and engineering. In this study, we designed and built a multifunction fluorescent open source in vivo/in vitro imaging system (openIVIS) system that integrates a Raspberry Pi with commercial cameras and LEDs with 3D printed structures combined with an acrylic housing. Our openIVIS provides three excitation wavelengths of 460 nm, 520 nm, and 630 nm integrated with Python control software to enable fluorescent measurements across the full visible light spectrum. To demonstrate the potential applications of our system, we tested its performance against a diverse set of experiments including laboratory assays (measuring fluorescent dyes, using optical nanosensors, and DNA gel electrophoresis) to potentially fieldable applications (plant and mineral imaging). We also tested the potential use for a high school biology environment by imaging small animals and tracking their development over the course of ten days. Our system demonstrated its ability to measure a wide dynamic range fluorescent response from millimolar to picomolar concentrations in the same sample while measuring responses across visible wavelengths. These results demonstrate the power and flexibility of open-source hardware and software and how it can be integrated with customizable manufacturing to create low-cost scientific instruments with a wide range of applications. Our study provides a promising model for the development of low-cost instruments that can be used in both research and education.
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Affiliation(s)
- John M. Branning
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, Colorado, United States of America
- The MITRE Corporation, Bedford, Massachusetts, United States of America
| | - Kealy A. Faughnan
- Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado, United States of America
| | - Austin A. Tomson
- Mechanical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Grant J. Bell
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Sydney M. Isbell
- Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado, United States of America
| | - Allen DeGroot
- Electrical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Lydia Jameson
- Electrical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Kramer Kilroy
- Mechanical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Michael Smith
- Mechanical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Robert Smith
- Electrical Engineering, Colorado School of Mines, Golden, Colorado, United States of America
| | - Landon Mottel
- Arvada West High School, Arvada, Colorado, United States of America
| | - Elizabeth G. Branning
- Colorado Early Colleges Castle Rock, Castle Rock, Colorado, United States of America
| | - Zoe Worrall
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Frances Anderson
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Ashrit Panditaradyula
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - William Yang
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Joseph Abdelmalek
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Joshua Brake
- Department of Engineering, Harvey Mudd College, Claremont, California, United States of America
| | - Kevin J. Cash
- Quantitative Biosciences and Engineering, Colorado School of Mines, Golden, Colorado, United States of America
- Chemical and Biological Engineering Department, Colorado School of Mines, Golden, Colorado, United States of America
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2
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Three-Dimensional Culture of Rhipicephalus ( Boophilus) microplus BmVIII-SCC Cells on Multiple Synthetic Scaffold Systems and in Rotating Bioreactors. INSECTS 2021; 12:insects12080747. [PMID: 34442313 PMCID: PMC8396921 DOI: 10.3390/insects12080747] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Revised: 08/10/2021] [Accepted: 08/14/2021] [Indexed: 12/12/2022]
Abstract
Tick cell culture facilitates research on the biology of ticks and their role as vectors of pathogens that affect humans, domestic animals, and wildlife. Because two-dimensional cell culture doesn't promote the development of multicellular tissue-like composites, we hypothesized that culturing tick cells in a three-dimensional (3-D) configuration would form spheroids or tissue-like organoids. In this study, the cell line BmVIII-SCC obtained from the cattle fever tick, Rhipicephalus (Boophilus) microplus (Canestrini, 1888), was cultured in different synthetic scaffold systems. Growth of the tick cells on macrogelatinous beads in rotating continuous culture system bioreactors enabled cellular attachment, organization, and development into spheroid-like aggregates, with evidence of tight cellular junctions between adjacent cells and secretion of an extracellular matrix. At least three cell morphologies were identified within the aggregates: fibroblast-like cells, small endothelial-like cells, and larger cells exhibiting multiple cytoplasmic endosomes and granular vesicles. These observations suggest that BmVIII-SCC cells adapted to 3-D culture retain pluripotency. Additional studies involving genomic analyses are needed to determine if BmVIII-SCC cells in 3-D culture mimic tick organs. Applications of 3-D culture to cattle fever tick research are discussed.
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Three-dimensional bright-field microscopy with isotropic resolution based on multi-view acquisition and image fusion reconstruction. Sci Rep 2020; 10:12771. [PMID: 32728161 PMCID: PMC7392767 DOI: 10.1038/s41598-020-69730-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/30/2020] [Indexed: 11/08/2022] Open
Abstract
Optical Projection Tomography (OPT) is a powerful three-dimensional imaging technique used for the observation of millimeter-scaled biological samples, compatible with bright-field and fluorescence contrast. OPT is affected by spatially variant artifacts caused by the fact that light diffraction is not taken into account by the straight-light propagation models used for reconstruction. These artifacts hinder high-resolution imaging with OPT. In this work we show that, by using a multiview imaging approach, a 3D reconstruction of the bright-field contrast can be obtained without the diffraction artifacts typical of OPT, drastically reducing the amount of acquired data, compared to previously reported approaches. The method, purely based on bright-field contrast of the unstained sample, provides a comprehensive picture of the sample anatomy, as demonstrated in vivo on Arabidopsis thaliana and zebrafish embryos. Furthermore, this bright-field reconstruction can be implemented on practically any multi-view light-sheet fluorescence microscope without complex hardware modifications or calibrations, complementing the fluorescence information with tissue anatomy.
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4
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Iafrate M, Fruhwirth GO. How Non-invasive in vivo Cell Tracking Supports the Development and Translation of Cancer Immunotherapies. Front Physiol 2020; 11:154. [PMID: 32327996 PMCID: PMC7152671 DOI: 10.3389/fphys.2020.00154] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 02/12/2020] [Indexed: 12/26/2022] Open
Abstract
Immunotherapy is a relatively new treatment regimen for cancer, and it is based on the modulation of the immune system to battle cancer. Immunotherapies can be classified as either molecular or cell-based immunotherapies, and both types have demonstrated promising results in a growing number of cancers. Indeed, several immunotherapies representing both classes are already approved for clinical use in oncology. While spectacular treatment successes have been reported, particularly for so-called immune checkpoint inhibitors and certain cell-based immunotherapies, they have also been accompanied by a variety of severe, sometimes life-threatening side effects. Furthermore, not all patients respond to immunotherapy. Hence, there is the need for more research to render these promising therapeutics more efficacious, more widely applicable, and safer to use. Whole-body in vivo imaging technologies that can interrogate cancers and/or immunotherapies are highly beneficial tools for immunotherapy development and translation to the clinic. In this review, we explain how in vivo imaging can aid the development of molecular and cell-based anti-cancer immunotherapies. We describe the principles of imaging host T-cells and adoptively transferred therapeutic T-cells as well as the value of traceable cancer cell models in immunotherapy development. Our emphasis is on in vivo cell tracking methodology, including important aspects and caveats specific to immunotherapies. We discuss a variety of associated experimental design aspects including parameters such as cell type, observation times/intervals, and detection sensitivity. The focus is on non-invasive 3D cell tracking on the whole-body level including aspects relevant for both preclinical experimentation and clinical translatability of the underlying methodologies.
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Affiliation(s)
| | - Gilbert O. Fruhwirth
- Imaging Therapy and Cancer Group, Department of Imaging Chemistry and Biology, School of Biomedical Engineering & Imaging Sciences, King’s College London, London, United Kingdom
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5
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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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6
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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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7
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Koskela O, Montonen T, Belay B, Figueiras E, Pursiainen S, Hyttinen J. Gaussian Light Model in Brightfield Optical Projection Tomography. Sci Rep 2019; 9:13934. [PMID: 31558755 PMCID: PMC6763473 DOI: 10.1038/s41598-019-50469-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 09/12/2019] [Indexed: 01/27/2023] Open
Abstract
This study focuses on improving the reconstruction process of the brightfield optical projection tomography (OPT). OPT is often described as the optical equivalent of X-ray computed tomography, but based on visible light. The detection optics used to collect light in OPT focus on a certain distance and induce blurring in those features out of focus. However, the conventionally used inverse Radon transform assumes an absolute focus throughout the propagation axis. In this study, we model the focusing properties of the detection by coupling Gaussian beam model (GBM) with the Radon transform. The GBM enables the construction of a projection operator that includes modeling of the blurring caused by the light beam. We also introduce the concept of a stretched GBM (SGBM) in which the Gaussian beam is scaled in order to avoid the modeling errors related to the determination of the focal plane. Furthermore, a thresholding approach is used to compress memory usage. We tested the GBM and SGBM approaches using simulated and experimental data in mono- and multifocal modes. When compared with the traditionally used filtered backprojection algorithm, the iteratively computed reconstructions, including the Gaussian models GBM and SGBM, provided smoother images with higher contrast.
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Affiliation(s)
- Olli Koskela
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland.
- HAMK Smart Research Unit, Häme University of Applied Sciences, Hämeenlinna, 13100, Finland.
| | - Toni Montonen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Birhanu Belay
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
| | - Edite Figueiras
- Champalimaud Research, Champalimaud Foundation, Lisbon, 1400-038, Portugal
| | - Sampsa Pursiainen
- Faculty of Information Technology and Communication Sciences, Tampere University, Tampere, 33014, Finland
| | - Jari Hyttinen
- Faculty of Medicine and Health Technology and BioMediTech Institute, Tampere University, Tampere, 33014, Finland
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8
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Kerstens A, Corthout N, Pavie B, Huang Z, Vernaillen F, Vande Velde G, Munck S. A Label-free Multicolor Optical Surface Tomography (ALMOST) imaging method for nontransparent 3D samples. BMC Biol 2019; 17:1. [PMID: 30616566 PMCID: PMC6323867 DOI: 10.1186/s12915-018-0614-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2018] [Accepted: 11/26/2018] [Indexed: 12/22/2022] Open
Abstract
Background Current mesoscale 3D imaging techniques are limited to transparent or cleared samples or require the use of X-rays. This is a severe limitation for many research areas, as the 3D color surface morphology of opaque samples—for example, intact adult Drosophila, Xenopus embryos, and other non-transparent samples—cannot be assessed. We have developed “ALMOST,” a novel optical method for 3D surface imaging of reflective opaque objects utilizing an optical projection tomography device in combination with oblique illumination and optical filters. Results As well as demonstrating image formation, we provide background information and explain the reconstruction—and consequent rendering—using a standard filtered back projection algorithm and 3D software. We expanded our approach to fluorescence and multi-channel spectral imaging, validating our results with micro-computed tomography. Different biological and inorganic test samples were used to highlight the versatility of our approach. To further demonstrate the applicability of ALMOST, we explored the muscle-induced form change of the Drosophila larva, imaged adult Drosophila, dynamically visualized the closure of neural folds during neurulation of live Xenopus embryos, and showed the complementarity of our approach by comparison with transmitted light and fluorescence OPT imaging of a Xenopus tadpole. Conclusion Thus, our new modality for spectral/color, macro/mesoscopic 3D imaging can be applied to a variety of model organisms and enables the longitudinal surface dynamics during development to be revealed. Electronic supplementary material The online version of this article (10.1186/s12915-018-0614-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Axelle Kerstens
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Nikky Corthout
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Benjamin Pavie
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Zengjin Huang
- VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.,Neuronal Wiring Lab, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium
| | - Frank Vernaillen
- VIB BioInformatics Core, Rijvisschestraat 126 3R, 9052, Ghent, Belgium
| | - Greetje Vande Velde
- Department of Imaging and Pathology, KU Leuven - University of Leuven, Herestraat 49, Box 505, 3000, Leuven, Belgium
| | - Sebastian Munck
- VIB Bio Imaging Core, Herestraat 49, Box 602, 3000, Leuven, Belgium. .,Research Group Molecular Neurobiology, Department of Neuroscience, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium. .,VIB Center for Brain and Disease Research, KU Leuven, Herestraat 49, Box 602, 3000, Leuven, Belgium.
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9
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Pende M, Becker K, Wanis M, Saghafi S, Kaur R, Hahn C, Pende N, Foroughipour M, Hummel T, Dodt HU. High-resolution ultramicroscopy of the developing and adult nervous system in optically cleared Drosophila melanogaster. Nat Commun 2018; 9:4731. [PMID: 30413688 PMCID: PMC6226481 DOI: 10.1038/s41467-018-07192-z] [Citation(s) in RCA: 44] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 10/13/2018] [Indexed: 11/21/2022] Open
Abstract
The fruit fly, Drosophila melanogaster, is an important experimental model to address central questions in neuroscience at an organismic level. However, imaging of neural circuits in intact fruit flies is limited due to structural properties of the cuticle. Here we present a novel approach combining tissue clearing, ultramicroscopy, and data analysis that enables the visualisation of neuronal networks with single-cell resolution from the larval stage up to the adult Drosophila. FlyClear, the signal preserving clearing technique we developed, stabilises tissue integrity and fluorescence signal intensity for over a month and efficiently removes the overall pigmentation. An aspheric ultramicroscope set-up utilising an improved light-sheet generator allows us to visualise long-range connections of peripheral sensory and central neurons in the visual and olfactory system. High-resolution 3D reconstructions with isotropic resolution from entire GFP-expressing flies are obtained by applying image fusion from orthogonal directions. This methodological integration of novel chemical, optical, and computational techniques allows a major advance in the analysis of global neural circuit organisation.
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Affiliation(s)
- Marko Pende
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria.
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria.
| | - Klaus Becker
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Martina Wanis
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Saiedeh Saghafi
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
| | - Rashmit Kaur
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Christian Hahn
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Nika Pende
- Department of Ecogenomics and Systems Biology, Archaeal Biology and Ecogenomics Division, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Massih Foroughipour
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria
| | - Thomas Hummel
- Department of Neurobiology, University of Vienna, Althanstrasse 14, 1090, Vienna, Austria
| | - Hans-Ulrich Dodt
- Department for Bioelectronics, FKE, Vienna University of Technology, Gußhausstraße 25-25A, Building CH, 1040, Vienna, Austria.
- Section of Bioelectronics, Center for Brain Research, Medical University of Vienna, Spitalgasse 4, 1090, Vienna, Austria.
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10
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Volpe A, Kurtys E, Fruhwirth GO. Cousins at work: How combining medical with optical imaging enhances in vivo cell tracking. Int J Biochem Cell Biol 2018; 102:40-50. [PMID: 29960079 PMCID: PMC6593261 DOI: 10.1016/j.biocel.2018.06.008] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2018] [Revised: 06/25/2018] [Accepted: 06/26/2018] [Indexed: 12/11/2022]
Abstract
Microscopy and medical imaging are related in their exploitation of electromagnetic waves, but were developed to satisfy differing needs, namely to observe small objects or to look inside subjects/objects, respectively. Together, these techniques can help elucidate complex biological processes and better understand health and disease. A current major challenge is to delineate mechanisms governing cell migration and tissue invasion in organismal development, the immune system and in human diseases such as cancer where the spatiotemporal tracking of small cell numbers in live animal models is extremely challenging. Multi-modal multi-scale in vivo cell tracking integrates medical and optical imaging. Fuelled by basic research in cancer biology and cell-based therapeutics, it has been enabled by technological advances providing enhanced resolution, sensitivity and multiplexing capabilities. Here, we review which imaging modalities have been successfully used for in vivo cell tracking and how this challenging task has benefitted from combining macroscopic with microscopic techniques.
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Affiliation(s)
- Alessia Volpe
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, SE1 7EH, London, UK
| | - Ewelina Kurtys
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, SE1 7EH, London, UK
| | - Gilbert O Fruhwirth
- Department of Imaging Chemistry and Biology, School of Biomedical Engineering and Imaging Sciences, King's College London, SE1 7EH, London, UK.
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11
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Chatterjee K, Pratiwi FW, Wu FCM, Chen P, Chen BC. Recent Progress in Light Sheet Microscopy for Biological Applications. APPLIED SPECTROSCOPY 2018; 72:1137-1169. [PMID: 29926744 DOI: 10.1177/0003702818778851] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The introduction of light sheet fluorescence microscopy (LSFM) has overcome the challenges in conventional optical microscopy. Among the recent breakthroughs in fluorescence microscopy, LSFM had been proven to provide a high three-dimensional spatial resolution, high signal-to-noise ratio, fast imaging acquisition rate, and minuscule levels of phototoxic and photodamage effects. The aforementioned auspicious properties are crucial in the biomedical and clinical research fields, covering a broad range of applications: from the super-resolution imaging of intracellular dynamics in a single cell to the high spatiotemporal resolution imaging of developmental dynamics in an entirely large organism. In this review, we provided a systematic outline of the historical development of LSFM, detailed discussion on the variants and improvements of LSFM, and delineation on the most recent technological advancements of LSFM and its potential applications in single molecule/particle detection, single-molecule super-resolution imaging, imaging intracellular dynamics of a single cell, multicellular imaging: cell-cell and cell-matrix interactions, plant developmental biology, and brain imaging and developmental biology.
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Affiliation(s)
- Krishnendu Chatterjee
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 3 Department of Engineering and System Science, National Tsing-Hua University, Hsinchu, Taiwan
| | - Feby Wijaya Pratiwi
- 1 Nanoscience and Technology Program, Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
- 4 Department of Chemistry, National Taiwan University, Taipei, Taiwan
| | | | - Peilin Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
| | - Bi-Chang Chen
- 2 Research Center for Applied Sciences, Academia Sinica, Taipei, Taiwan
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12
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Mayer J, Robert-Moreno A, Sharpe J, Swoger J. Attenuation artifacts in light sheet fluorescence microscopy corrected by OPTiSPIM. LIGHT, SCIENCE & APPLICATIONS 2018; 7:70. [PMID: 30302241 PMCID: PMC6168557 DOI: 10.1038/s41377-018-0068-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Revised: 08/30/2018] [Accepted: 08/30/2018] [Indexed: 05/18/2023]
Abstract
Light sheet fluorescence microscopy (LSFM) is rapidly becoming an essential technology for mesoscopic imaging of samples such as embryos and adult mouse organs. However, LSFM can suffer from optical artifacts for which there is no intrinsic solution. The attenuation of light due to absorbing material causes "shadow" artifacts along both the illumination and detection paths. Several approaches have been introduced to reduce this problem, including scanning illumination and multi-view imaging. However, neither of these approaches completely eliminates the problem. If the distribution of the absorbing material is complex, shadows cannot be avoided. We introduce a new approach that relies on multi-modal integration of two very different mesoscopic techniques. Unlike LSFM, optical projection tomography (OPT) can operate in transmission mode to create a voxel map of the 3D distribution of the sample's optical attenuation. Here, we demonstrate a hybrid instrument (OPTiSPIM) that can quantify this attenuation and use the information to correct the shadow artifacts of LSFM.
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Affiliation(s)
- Jürgen Mayer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Alexandre Robert-Moreno
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - James Sharpe
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Pg. Lluis Companys 23, 08010 Barcelona, Spain
| | - Jim Swoger
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, 08003 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Barcelona, Spain
- Present Address: European Molecular Biology Laboratory (EMBL), Dr. Aiguader 88, 08003 Barcelona, Spain
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13
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Rieckher M, Psycharakis SE, Ancora D, Liapis E, Zacharopoulos A, Ripoll J, Tavernarakis N, Zacharakis G. Demonstrating Improved Multiple Transport-Mean-Free-Path Imaging Capabilities of Light Sheet Microscopy in the Quantification of Fluorescence Dynamics. Biotechnol J 2017; 13. [DOI: 10.1002/biot.201700419] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Revised: 10/23/2017] [Indexed: 01/16/2023]
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 Hospital Cologne; Cologne 50931 Germany
| | - Stylianos E. Psycharakis
- Foundation for Research and Technology Hellas; Institute of Electronic Structure and Laser; N. Plastira 100 Heraklion GR-70013 Crete Greece
| | - Daniele Ancora
- Foundation for Research and Technology Hellas; Institute of Electronic Structure and Laser; N. Plastira 100 Heraklion GR-70013 Crete Greece
| | - Evangelos Liapis
- Foundation for Research and Technology Hellas; Institute of Electronic Structure and Laser; N. Plastira 100 Heraklion GR-70013 Crete Greece
| | - Athanasios Zacharopoulos
- Foundation for Research and Technology Hellas; Institute of Electronic Structure and Laser; N. Plastira 100 Heraklion GR-70013 Crete Greece
| | - Jorge Ripoll
- Department of Bioengineering and Aerospace Engineering; Universidad Carlos III de Madrid; Madrid 28911 Spain
| | - Nektarios Tavernarakis
- Foundation for Research and Technology Hellas; Institute of Molecular Biology and Biotechnology; N. Plastira 100 Heraklion GR-70013 Crete Greece
| | - Giannis Zacharakis
- Foundation for Research and Technology Hellas; Institute of Electronic Structure and Laser; N. Plastira 100 Heraklion GR-70013 Crete Greece
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14
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Nguyen D, Marchand PJ, Planchette AL, Nilsson J, Sison M, Extermann J, Lopez A, Sylwestrzak M, Sordet-Dessimoz J, Schmidt-Christensen A, Holmberg D, Van De Ville D, Lasser T. Optical projection tomography for rapid whole mouse brain imaging. BIOMEDICAL OPTICS EXPRESS 2017; 8:5637-5650. [PMID: 29296493 PMCID: PMC5745108 DOI: 10.1364/boe.8.005637] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Revised: 10/31/2017] [Accepted: 10/31/2017] [Indexed: 05/21/2023]
Abstract
In recent years, three-dimensional mesoscopic imaging has gained significant importance in life sciences for fundamental studies at the whole-organ level. In this manuscript, we present an optical projection tomography (OPT) method designed for imaging of the intact mouse brain. The system features an isotropic resolution of ~50 µm and an acquisition time of four to eight minutes, using a 3-day optimized clearing protocol. Imaging of the brain autofluorescence in 3D reveals details of the neuroanatomy, while the use of fluorescent labels displays the vascular network and amyloid deposition in 5xFAD mice, an important model of Alzheimer's disease (AD). Finally, the OPT images are compared with histological slices.
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Affiliation(s)
- David Nguyen
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Paul J. Marchand
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Arielle L. Planchette
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Julia Nilsson
- Autoimmunity, Department of Experimental Medical Sciences, Lund University Diabetes Centre, 20502 Malmö,
Sweden
| | - Miguel Sison
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Jérôme Extermann
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Antonio Lopez
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Marcin Sylwestrzak
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Jessica Sordet-Dessimoz
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
| | - Anja Schmidt-Christensen
- Autoimmunity, Department of Experimental Medical Sciences, Lund University Diabetes Centre, 20502 Malmö,
Sweden
| | - Dan Holmberg
- Autoimmunity, Department of Experimental Medical Sciences, Lund University Diabetes Centre, 20502 Malmö,
Sweden
| | - Dimitri Van De Ville
- Medical Image Processing Lab, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1202 Genève,
Switzerland
| | - Theo Lasser
- Laboratoire d’Optique Biomédicale, School of Engineering, École Polytechnique Fédérale de Lausanne, CH-1015 Lausanne,
Switzerland
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15
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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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16
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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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17
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Liang X, Zang Y, Dong D, Zhang L, Fang M, Yang X, Arranz A, Ripoll J, Hui H, Tian J. Stripe artifact elimination based on nonsubsampled contourlet transform for light sheet fluorescence microscopy. JOURNAL OF BIOMEDICAL OPTICS 2016; 21:106005. [PMID: 27784051 DOI: 10.1117/1.jbo.21.10.106005] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Accepted: 09/28/2016] [Indexed: 05/18/2023]
Abstract
Stripe artifacts, caused by high-absorption or high-scattering structures in the illumination light path, are a common drawback in both unidirectional and multidirectional light sheet fluorescence microscopy (LSFM), significantly deteriorating image quality. To circumvent this problem, we present an effective multidirectional stripe remover (MDSR) method based on nonsubsampled contourlet transform (NSCT), which can be used for both unidirectional and multidirectional LSFM. In MDSR, a fast Fourier transform (FFT) filter is designed in the NSCT domain to shrink the stripe components and eliminate the noise. Benefiting from the properties of being multiscale and multidirectional, MDSR succeeds in eliminating stripe artifacts in both unidirectional and multidirectional LSFM. To validate the method, MDSR has been tested on images from a custom-made unidirectional LSFM system and a commercial multidirectional LSFM system, clearly demonstrating that MDSR effectively removes most of the stripe artifacts. Moreover, we performed a comparative experiment with the variational stationary noise remover and the wavelet-FFT methods and quantitatively analyzed the results with a peak signal-to-noise ratio, showing an improved noise removal when using the MDSR method.
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Affiliation(s)
- Xiao Liang
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, ChinacUniversity of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China
| | - Yali Zang
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, ChinacUniversity of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China
| | - Di Dong
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, ChinacUniversity of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China
| | - Liwen Zhang
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, China
| | - Mengjie Fang
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, ChinacUniversity of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China
| | - Xin Yang
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, ChinacUniversity of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China
| | - Alicia Arranz
- Center for Molecular Biology "Severo Ochoa", Calle Nicolás Cabrera, 1, Madrid 28049, Spain
| | - Jorge Ripoll
- Universidad Carlos III of Madrid, Department of Bioengineering and Aerospace Engineering, Escuela Politécnica Superior, Avd. de la Universidad, 30, Madrid 28911, SpainfInstituto de Investigación Sanitaria del Hospital Gregorio Marañón, Experimental Medicine and Surgery Unit, Calle del Dr. Esquerdo, 46, Madrid 28007, Spain
| | - Hui Hui
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, ChinacUniversity of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China
| | - Jie Tian
- Chinese Academy of Sciences, Key Laboratory of Molecular Imaging, No. 95 Zhongguancun East Road, Beijing 100190, ChinabThe State Key Laboratory of Management and Control for Complex Systems, No. 95 Zhongguancun East Road, Beijing 100190, ChinacUniversity of Chinese Academy of Sciences, No. 80 Zhongguancun East Road, Beijing 100190, China
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18
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Liepe J, Sim A, Weavers H, Ward L, Martin P, Stumpf MPH. Accurate Reconstruction of Cell and Particle Tracks from 3D Live Imaging Data. Cell Syst 2016; 3:102-7. [PMID: 27453447 PMCID: PMC4963212 DOI: 10.1016/j.cels.2016.06.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2015] [Revised: 01/28/2016] [Accepted: 06/03/2016] [Indexed: 11/17/2022]
Abstract
Spatial structures often constrain the 3D movement of cells or particles in vivo, yet this information is obscured when microscopy data are analyzed using standard approaches. Here, we present methods, called unwrapping and Riemannian manifold learning, for mapping particle-tracking data along unseen and irregularly curved surfaces onto appropriate 2D representations. This is conceptually similar to the problem of reconstructing accurate geography from conventional Mercator maps, but our methods do not require prior knowledge of the environments' physical structure. Unwrapping and Riemannian manifold learning accurately recover the underlying 2D geometry from 3D imaging data without the need for fiducial marks. They outperform standard x-y projections, and unlike standard dimensionality reduction techniques, they also successfully detect both bias and persistence in cell migration modes. We demonstrate these features on simulated data and zebrafish and Drosophila in vivo immune cell trajectory datasets. Software packages that implement unwrapping and Riemannian manifold learning are provided.
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Affiliation(s)
- Juliane Liepe
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK; Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, SW72AZ, UK
| | - Aaron Sim
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK; Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, SW72AZ, UK
| | - Helen Weavers
- School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Laura Ward
- School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK
| | - Paul Martin
- School of Biochemistry, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK; School of Physiology, Pharmacology and Neuroscience, Biomedical Sciences, University of Bristol, Bristol, BS8 1TD, UK; School of Medicine, University of Cardiff, BS8 1TD, UK
| | - Michael P H Stumpf
- Department of Life Sciences, Imperial College London, London, SW7 2AZ, UK; Centre for Integrative Systems Biology and Bioinformatics, Imperial College London, SW72AZ, UK.
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19
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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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20
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Abe J, Ozga AJ, Swoger J, Sharpe J, Ripoll J, Stein JV. Light sheet fluorescence microscopy for in situ cell interaction analysis in mouse lymph nodes. J Immunol Methods 2016; 431:1-10. [DOI: 10.1016/j.jim.2016.01.015] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2015] [Revised: 01/29/2016] [Accepted: 01/29/2016] [Indexed: 11/25/2022]
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21
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Fang M, Dong D, Zeng C, Liang X, Yang X, Arranz A, Ripoll J, Hui H, Tian J. Polarization-sensitive optical projection tomography for muscle fiber imaging. Sci Rep 2016; 6:19241. [PMID: 26752330 PMCID: PMC4707546 DOI: 10.1038/srep19241] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2015] [Accepted: 12/07/2015] [Indexed: 01/22/2023] Open
Abstract
Optical projection tomography (OPT) is a tool used for three-dimensional imaging of millimeter-scale biological samples, with the advantage of exhibiting isotropic resolution typically in the micron range. OPT can be divided into two types: transmission OPT (tOPT) and emission OPT (eOPT). Compared with eOPT, tOPT discriminates different tissues based on their absorption coefficient, either intrinsic or after specific staining. However, it fails to distinguish muscle fibers whose absorption coefficients are similar to surrounding tissues. To circumvent this problem, in this article we demonstrate a polarization sensitive OPT system which improves the detection and 3D imaging of muscle fibers by using polarized light. We also developed image acquisition and processing protocols that, together with the system, enable the clear visualization of muscles. Experimental results show that the muscle fibers of diaphragm and stomach, difficult to be distinguished in regular tOPT, were clearly displayed in our system, proving its potential use. Moreover, polarization sensitive OPT was fused with tOPT to investigate the stomach tissue comprehensively. Future applications of polarization sensitive OPT could be imaging other fiber-like structures such as myocardium or other tissues presenting high optical anisotropy.
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Affiliation(s)
- Mengjie Fang
- Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.,Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China
| | - Di Dong
- Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.,Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China
| | - Chaoting Zeng
- Department of Hepatobiliary Surgery, Zhujiang Hospital, Southern Medical University, Guangdong 510282, China
| | - Xiao Liang
- Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.,Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China
| | - Xin Yang
- Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.,Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China
| | - Alicia Arranz
- Center for Molecular Biology "Severo Ochoa" (CSIC-UAM), Madrid 28049, Spain
| | - Jorge Ripoll
- Department of Bioengineering and Aerospace Engineering, Universidad Carlos III of Madrid, Madrid 28911, Spain
| | - Hui Hui
- Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.,Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China
| | - Jie Tian
- Key Laboratory of Molecular Imaging, Institute of Automation, Chinese Academy of Sciences, Beijing 100190, China.,Beijing Key Laboratory of Molecular Imaging, Beijing 100190, China
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22
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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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23
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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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