1
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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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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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3
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Vacek E, Jacobsen C. Fast and noise-tolerant determination of the center of rotation in tomography. JOURNAL OF SYNCHROTRON RADIATION 2022; 29:488-495. [PMID: 35254313 PMCID: PMC8900868 DOI: 10.1107/s1600577521012777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
High-quality tomographic reconstruction is not possible without the accurate localization of the center of rotation. Poor localization leads to artifacts in the data and can even cause reconstructions to fail. There are many approaches to solving this problem, some of which involve the collection of full sinograms, or even provisional tomographic reconstructions, in order to determine the center of rotation. Here, a simple method based on the expected symmetry of the Fourier transform of summed projections approximately 180° apart is presented; unlike cross-correlation methods, it requires only a single Fourier transform to compute, and uses mainly low spatial frequency information which is less susceptible to noise. This approach is shown to be fast, and robust against poor signal-to-noise as well as to projection images acquired at angles that are not exactly 180° apart. This rapid method can be useful as a first step in the processing of tomographic data.
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Affiliation(s)
- Everett Vacek
- Applied Physics Program, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
| | - Chris Jacobsen
- Advanced Photon Source, Argonne National Laboratory, 9700 South Cass Avenue, Argonne, IL 60439, USA
- Department of Physics and Astronomy, Northwestern University, 2145 Sheridan Road, Evanston, IL 60208, USA
- Chemistry of Life Processes Institute, Northwestern University, 2170 Campus Drive, Evanston, IL 60208, USA
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4
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Zhang H, Waldmann L, Manuel R, Boije H, Haitina T, Allalou A. zOPT: an open source optical projection tomography system and methods for rapid 3D zebrafish imaging. BIOMEDICAL OPTICS EXPRESS 2020; 11:4290-4305. [PMID: 32923043 PMCID: PMC7449731 DOI: 10.1364/boe.393519] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 06/26/2020] [Accepted: 06/26/2020] [Indexed: 06/11/2023]
Abstract
Optical projection tomography (OPT) is a 3D imaging alternative to conventional microscopy which allows imaging of millimeter-sized object with isotropic micrometer resolution. The zebrafish is an established model organism and an important tool used in genetic and chemical screening. The size and optical transparency of the embryo and larva makes them well suited for imaging using OPT. Here, we present an open-source implementation of an OPT platform, built around a customized sample stage, 3D-printed parts and open source algorithms optimized for the system. We developed a versatile automated workflow including a two-step image processing approach for correcting the center of rotation and generating accurate 3D reconstructions. Our results demonstrate high-quality 3D reconstruction using synthetic data as well as real data of live and fixed zebrafish. The presented 3D-printable OPT platform represents a fully open design, low-cost and rapid loading and unloading of samples. Our system offers the opportunity for researchers with different backgrounds to setup and run OPT for large scale experiments, particularly in studies using zebrafish larvae as their key model organism.
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Affiliation(s)
- Hanqing Zhang
- Division of Visual Information and
Interaction, Department of Information Technology, Uppsala University,
S-75105 Uppsala, Sweden
- BioImage Informatics Facility at
SciLifeLab, S-75105 Uppsala, Sweden
| | - Laura Waldmann
- Department of Organismal Biology, Uppsala
University, S-75236 Uppsala, Sweden
| | - Remy Manuel
- Department of Neuroscience, Uppsala
University, S-75124 Uppsala, Sweden
| | - Henrik Boije
- Department of Neuroscience, Uppsala
University, S-75124 Uppsala, Sweden
| | - Tatjana Haitina
- Department of Organismal Biology, Uppsala
University, S-75236 Uppsala, Sweden
| | - Amin Allalou
- Division of Visual Information and
Interaction, Department of Information Technology, Uppsala University,
S-75105 Uppsala, Sweden
- BioImage Informatics Facility at
SciLifeLab, S-75105 Uppsala, Sweden
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5
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Optical Projection Tomography Using a Commercial Microfluidic System. MICROMACHINES 2020; 11:mi11030293. [PMID: 32168806 PMCID: PMC7142877 DOI: 10.3390/mi11030293] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 03/05/2020] [Accepted: 03/10/2020] [Indexed: 01/17/2023]
Abstract
Optical projection tomography (OPT) is the direct optical equivalent of X-ray computed tomography (CT). To obtain a larger depth of field, traditional OPT usually decreases the numerical aperture (NA) of the objective lens to decrease the resolution of the image. So, there is a trade-off between sample size and resolution. Commercial microfluidic systems can observe a sample in flow mode. In this paper, an OPT instrument is constructed to observe samples. The OPT instrument is combined with commercial microfluidic systems to obtain a three-dimensional and time (3D + T)/four-dimensional (4D) video of the sample. “Focal plane scanning” is also used to increase the images’ depth of field. A series of two-dimensional (2D) images in different focal planes was observed and compared with images simulated using our program. Our work dynamically monitors 3D OPT images. Commercial microfluidic systems simulate blood flow, which has potential application in blood monitoring and intelligent drug delivery platforms. We design an OPT adaptor to perform OPT on a commercial wide-field inverted microscope (Olympusix81). Images in different focal planes are observed and analyzed. Using a commercial microfluidic system, a video is also acquired to record motion pictures of samples at different flow rates. To our knowledge, this is the first time an OPT setup has been combined with a microfluidic system.
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Dou S, Liu J, Yang L. Dual-modality optical projection tomography reconstruction method from fewer views. JOURNAL OF BIOPHOTONICS 2019; 12:e201800407. [PMID: 30578626 DOI: 10.1002/jbio.201800407] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 12/04/2018] [Accepted: 12/05/2018] [Indexed: 06/09/2023]
Abstract
In optical projection tomography (OPT), for longitudinal living model studies, multiple measurements of the same sample are required at different time points. It is important to decrease both the total acquisition time and the light dose to the sample. We improved the ordered subsets expectation maximization reconstruction algorithm for OPT, which reduces the acquisition time and number of projections greatly compared with filtered back projection (FBP), and obtained satisfactory reconstructed images. Using zebrafish, in transmission and fluorescence mode, we demonstrate the capability of the method to reconstruct image from downsampled projection subsets. The result shows that the reconstruction image quality of the proposed method using 30 projections is comparable to that of FBP using 720 projections. The total acquisition procedure can be finished in a few seconds. The method also provides OPT with the remarkable capability to resist noises and artifacts. Projection image and fused image of zebrafish.
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Affiliation(s)
- Shaobin Dou
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, China
| | - Jinhuai Liu
- Institute of Intelligent Machines, Chinese Academy of Sciences, Hefei, China
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7
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Chan KG, Liebling M. Direct inversion algorithm for focal plane scanning optical projection tomography. BIOMEDICAL OPTICS EXPRESS 2017; 8:5349-5358. [PMID: 29188125 PMCID: PMC5695975 DOI: 10.1364/boe.8.005349] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Revised: 09/20/2017] [Accepted: 09/28/2017] [Indexed: 05/09/2023]
Abstract
To achieve approximately parallel projection geometry, traditional optical projection tomography (OPT) requires the use of low numerical aperture (NA) objectives, which have a long depth-of-field at the expense of poor lateral resolution. Particularly promising methods to improve spatial resolution include ad-hoc post-processing filters that limit the effect of the system's MTF and focal-plane-scanning OPT (FPS-OPT), an alternative acquisition procedure that allows the use of higher NA objectives by limiting the effect of their shallow depth of field yet still assumes parallel projection rays during reconstruction. Here, we provide a detailed derivation that establishes the existence of a direct inversion formula for FPS-OPT. Based on this formula, we propose a point spread function-aware algorithm that is similar in form and complexity to traditional filtered backprojection (FBP). With simulations, we demonstrate that our point-spread-function aware FBP for FPS-OPT leads to more accurate images than both traditional OPT with deconvolution and FPS-OPT with naive FBP reconstruction. We further illustrate the technique on experimental zebrafish data, which shows that our approach reduces out-of-focus blur compared to a direct FBP reconstruction with FPS-OPT.
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Affiliation(s)
- Kevin G. Chan
- Electrical & Computer Engineering Department, University of California, Santa Barbara, CA 93106,
USA
| | - Michael Liebling
- Electrical & Computer Engineering Department, University of California, Santa Barbara, CA 93106,
USA
- Idiap Research Institute, CH-1920 Martigny,
Switzerland
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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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Cremer C, Szczurek A, Schock F, Gourram A, Birk U. Super-resolution microscopy approaches to nuclear nanostructure imaging. Methods 2017; 123:11-32. [PMID: 28390838 DOI: 10.1016/j.ymeth.2017.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
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Affiliation(s)
- Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany. http://www.optics.imb-mainz.de
| | - Aleksander Szczurek
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Florian Schock
- Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Amine Gourram
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
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11
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Kumar S, Lockwood N, Ramel MC, Correia T, Ellis M, Alexandrov Y, Andrews N, Patel R, Bugeon L, Dallman MJ, Brandner S, Arridge S, Katan M, McGinty J, Frankel P, French PM. Quantitative in vivo optical tomography of cancer progression & vasculature development in adult zebrafish. Oncotarget 2016; 7:43939-43948. [PMID: 27259259 PMCID: PMC5190069 DOI: 10.18632/oncotarget.9756] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Accepted: 04/28/2016] [Indexed: 12/16/2022] Open
Abstract
We describe a novel approach to study tumour progression and vasculature development in vivo via global 3-D fluorescence imaging of live non-pigmented adult zebrafish utilising angularly multiplexed optical projection tomography with compressive sensing (CS-OPT). This "mesoscopic" imaging method bridges a gap between established ~μm resolution 3-D fluorescence microscopy techniques and ~mm-resolved whole body planar imaging and diffuse tomography. Implementing angular multiplexing with CS-OPT, we demonstrate the in vivo global imaging of an inducible fluorescently labelled genetic model of liver cancer in adult non-pigmented zebrafish that also present fluorescently labelled vasculature. In this disease model, addition of a chemical inducer (doxycycline) drives expression of eGFP tagged oncogenic K-RASV12 in the liver of immune competent animals. We show that our novel in vivo global imaging methodology enables non-invasive quantitative imaging of the development of tumour and vasculature throughout the progression of the disease, which we have validated against established methods of pathology including immunohistochemistry. We have also demonstrated its potential for longitudinal imaging through a study of vascular development in the same zebrafish from early embryo to adulthood. We believe that this instrument, together with its associated analysis and data management tools, constitute a new platform for in vivo cancer studies and drug discovery in zebrafish disease models.
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Affiliation(s)
- Sunil Kumar
- Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Nicola Lockwood
- Department of Physics, Imperial College London, London SW7 2AZ, UK
- Division of Medicine, University College London, London WC1E 6JF, UK
- CoMPLEX, University College London, London WC1E 6BT, UK
| | - Marie-Christine Ramel
- Division of Medicine, University College London, London WC1E 6JF, UK
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | - Teresa Correia
- Department of Computer Science, University College London, London WC1E 6BT, UK
| | - Matthew Ellis
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
| | - Yuriy Alexandrov
- Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Natalie Andrews
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
- Institute of Chemical Biology, Department of Chemistry, Imperial College, London SW7 2AZ, UK
| | - Rachel Patel
- Division of Medicine, University College London, London WC1E 6JF, UK
| | - Laurence Bugeon
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK
| | | | - Sebastian Brandner
- Department of Neurodegenerative Disease, UCL Institute of Neurology, London WC1N 3BG, UK
- Division of Neuropathology, The National Hospital for Neurology and Neurosurgery, University College London NHS Foundation Trust, London WC1N 3BG, UK
| | - Simon Arridge
- Department of Computer Science, University College London, London WC1E 6BT, UK
| | - Matilda Katan
- Division of Structural and Molecular Biology, University College London, London WC1E 6BT, UK
| | - James McGinty
- Department of Physics, Imperial College London, London SW7 2AZ, UK
| | - Paul Frankel
- Division of Medicine, University College London, London WC1E 6JF, UK
| | - Paul M.W. French
- Department of Physics, Imperial College London, London SW7 2AZ, UK
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12
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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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13
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Malek M, Khelfa H, Picart P, Mounier D, Poilâne C. Microtomography imaging of an isolated plant fiber: a digital holographic approach. APPLIED OPTICS 2016; 55:A111-A121. [PMID: 26835942 DOI: 10.1364/ao.55.00a111] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
This paper describes a method for optical projection tomography for the 3D in situ characterization of micrometric plant fibers. The proposed approach is based on digital holographic microscopy, the holographic capability being convenient to compensate for the runout of the fiber during rotations. The setup requires a telecentric alignment to prevent from the changes in the optical magnification, and calibration results show the very good experimental adjustment. Amplitude images are obtained from the set of recorded and digitally processed holograms. Refocusing of blurred images and correction of both runout and jitter are carried out to get appropriate amplitude images. The 3D data related to the plant fiber are computed from the set of images using a dedicated numerical processing. Experimental results exhibit the internal and external shapes of the plant fiber. These experimental results constitute the first attempt to obtain 3D data of flax fiber, about 12 μm×17 μm in apparent diameter, with a full-field optical tomography approach using light in the visible range.
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14
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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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15
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Guo J, Yang Y, Dong D, Shi L, Hui H, Xu M. A projection selection method to improve image quality in 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 2015; 2014:206-9. [PMID: 25569933 DOI: 10.1109/embc.2014.6943565] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Optical projection tomography (OPT) is a very important imaging tool for a mesoscopic-scale. It can provide three dimensional (3D) transmission and emission imaging. However, high-resolution OPT is limited in depth of field (DOF) due to a high numerical aperture, which causes a poor performance of OPT in imaging large samples. Moreover, it is difficult to tune the focus plane (FP) to a fixed position where OPT always has the best image quality in different directions. To address these problems, we developed a projection selection method to improve DOF in OPT. In each direction, our method automatically selects the best projection from several projections with different FP. Then, we use a series of selected projections for 3D reconstruction. The experimental results demonstrate that our method can improve the image quality comparing to a fixed FP. Moreover, our method is flexible to be used in other OPT setups by adding a linear stage.
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16
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Figueiras E, Soto AM, Jesus D, Lehti M, Koivisto J, Parraga JE, Silva-Correia J, Oliveira JM, Reis RL, Kellomäki M, Hyttinen J. Optical projection tomography as a tool for 3D imaging of hydrogels. BIOMEDICAL OPTICS EXPRESS 2014; 5:3443-9. [PMID: 25360363 PMCID: PMC4206315 DOI: 10.1364/boe.5.003443] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Revised: 08/15/2014] [Accepted: 08/29/2014] [Indexed: 05/22/2023]
Abstract
An Optical Projection Tomography (OPT) system was developed and optimized to image 3D tissue engineered products based in hydrogels. We develop pre-reconstruction algorithms to get the best result from the reconstruction procedure, which include correction of the illumination and determination of sample center of rotation (CoR). Existing methods for CoR determination based on the detection of the maximum variance of reconstructed slices failed, so we develop a new CoR search method based in the detection of the variance sharpest local maximum. We show the capabilities of the system to give quantitative information of different types of hydrogels that may be useful in its characterization.
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Affiliation(s)
- Edite Figueiras
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
| | - Ana M. Soto
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
| | - Danilo Jesus
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
| | - M. Lehti
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
| | - J. Koivisto
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
- University of Tampere, BioMediTech, Tampere, Finland
| | - J. E. Parraga
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
| | - J. Silva-Correia
- 3Bs- Research Group, Biomaterials, Biodegradables and Biomimetics, University of Minho, Guimarães, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - J. M. Oliveira
- 3Bs- Research Group, Biomaterials, Biodegradables and Biomimetics, University of Minho, Guimarães, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - R. L. Reis
- 3Bs- Research Group, Biomaterials, Biodegradables and Biomimetics, University of Minho, Guimarães, Portugal
- ICVS/3B’s - PT Government Associate Laboratory, Braga/Guimarães, Portugal
| | - M. Kellomäki
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
| | - J. Hyttinen
- Tampere University of Technology, ELT, BioMediTech, Tampere, Finland
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17
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Chen L, Kumar S, Kelly D, Andrews N, Dallman MJ, French PMW, McGinty J. Remote focal scanning optical projection tomography with an electrically tunable lens. BIOMEDICAL OPTICS EXPRESS 2014; 5:3367-75. [PMID: 25360356 PMCID: PMC4206308 DOI: 10.1364/boe.5.003367] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Revised: 07/08/2014] [Accepted: 07/23/2014] [Indexed: 05/04/2023]
Abstract
We describe a remote focal scanning technique for optical projection tomography (OPT) implemented with an electrically tunable lens (ETL) that removes the need to scan the specimen or objective lens. Using a 4× objective lens the average spatial resolution is improved by ∼46% and the light collection efficiency by a factor of ∼6.76, thereby enabling increased acquisition speed and reduced light dose. This convenient implementation is particularly appropriate for lower magnifications and larger sample diameters where axial objective scanning would encounter problems with speed and stability.
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Affiliation(s)
- Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
| | - Sunil Kumar
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
| | - Douglas Kelly
- Institute for Chemical Biology, Department of Chemistry, Imperial College London, SW7 2AZ,
UK
| | - Natalie Andrews
- Institute for Chemical Biology, Department of Chemistry, Imperial College London, SW7 2AZ,
UK
| | - Margaret J. Dallman
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, SW7 2AZ,
UK
- Centre for Integrative Systems Biology, Department of Life Sciences, Imperial College London, SW7 2AZ,
UK
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
| | - James McGinty
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ,
UK
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18
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Gualda E, Moreno N, Tomancak P, Martins GG. Going "open" with mesoscopy: a new dimension on multi-view imaging. PROTOPLASMA 2014; 251:363-372. [PMID: 24442669 DOI: 10.1007/s00709-013-0599-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Accepted: 12/12/2013] [Indexed: 06/03/2023]
Abstract
OpenSPIM and OpenSpinMicroscopy emerged as open access platforms for Light Sheet and Optical Projection Imaging, often called as optical mesoscopy techniques. Both projects can be easily reproduced using comprehensive online instructions that should foster the implementation and further development of optical imaging techniques with sample rotation control. This additional dimension in an open system offers the possibility to make multi-view microscopy easily modified and will complement the emerging commercial solutions. Furthermore, it is deeply based on other open platforms such as MicroManager and Arduino, enabling development of tailored setups for very specific biological questions. In our perspective, the open access principle of OpenSPIM and OpenSpinMicroscopy is a game-changer, helping the concepts of light sheet and optical projection tomography (OPT) to enter the mainstream of biological imaging.
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Affiliation(s)
- Emilio Gualda
- Instituto Gulbenkian de Ciência, Rua da Quinta Grande 6, 2780-156, Oeiras, Portugal
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19
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Chen L, Andrews N, Kumar S, Frankel P, McGinty J, French PMW. Simultaneous angular multiplexing optical projection tomography at shifted focal planes. OPTICS LETTERS 2013; 38:851-3. [PMID: 23503237 DOI: 10.1364/ol.38.000851] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
We describe an angular multiplexing technique for optical projection tomography that improves resolution, signal-to-noise ratio, and imaging speed by ameliorating the trade-off between spatial resolution and depth of field and improving the light collection efficiency. Here we demonstrate that imaging at two orthogonal angular projections simultaneously, focused on shifted planes in the sample, improves the average spatial resolution by ~20% and the light collection efficiency by a factor of ~4, thereby enabling increased acquisition speed and reduced light dose.
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Affiliation(s)
- Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, London, UK.
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20
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Dong D, Guo J, Yang Y, Shi L, Peng D, Liu Z, Ripoll J, Tian J. Analysis of the rotational center location method in 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 2013; 2013:3008-3011. [PMID: 24110360 DOI: 10.1109/embc.2013.6610173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
In Optical Projection Tomography (OPT), if the rotational center deviates from the central line of the image and this offset is not corrected during the reconstruction, serious blurring will happen in the final 3-dimensional (3D) result. Therefore, the high-precision rotational center location method is very important for OPT. However, existing methods are inconvenient because they need active participation during the location process. Thus, the automated and fast rotational center location method is in great demand. In preliminary work, we proposed an automated rotational center location method which consisted of a high Specimen Signal Intensity (SSI) sinogram selection and a coarse-fine search. Our method had an accuracy of about 1/4 pixel. However, further robustness analysis of our method is lacking. In this paper, we have investigated its location errors on sinograms with various SSIs and analyzed whether it was effective to use high SSI sinograms for rotational center location. Moreover, we have also discussed the relationship between location errors and the starting rotational angles. The experimental results showed that our coarse-fine method was robust under different starting angles. Meanwhile, the high SSI sinogram selection scheme improved the location precision.
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21
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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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22
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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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23
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Chen L, McGinty J, Taylor HB, Bugeon L, Lamb JR, Dallman MJ, French PMW. Incorporation of an experimentally determined MTF for spatial frequency filtering and deconvolution during optical projection tomography reconstruction. OPTICS EXPRESS 2012; 20:7323-37. [PMID: 22453413 DOI: 10.1364/oe.20.007323] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
We demonstrate two techniques to improve the quality of reconstructed optical projection tomography (OPT) images using the modulation transfer function (MTF) as a function of defocus experimentally determined from tilted knife-edge measurements. The first employs a 2-D binary filter based on the MTF frequency cut-off as an additional filter during back-projection reconstruction that restricts the high frequency information to the region around the focal plane and progressively decreases the spatial frequency bandwidth with defocus. This helps to suppress "streak" artifacts in OPT data acquired at reduced angular sampling, thereby facilitating faster OPT acquisitions. This method is shown to reduce the average background by approximately 72% for an NA of 0.09 and by approximately 38% for an NA of 0.07 compared to standard filtered back-projection. As a biological illustration, a Fli:GFP transgenic zebrafish embryo (3 days post-fertilisation) was imaged to demonstrate the improved imaging speed (a quarter of the acquisition time). The second method uses the MTF to produce an appropriate deconvolution filter that can be used to correct for the spatial frequency modulation applied by the imaging system.
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Affiliation(s)
- Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ, UK.
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24
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Cheddad A, Svensson C, Sharpe J, Georgsson F, Ahlgren U. Image processing assisted algorithms for optical projection tomography. IEEE TRANSACTIONS ON MEDICAL IMAGING 2012; 31:1-15. [PMID: 21768046 DOI: 10.1109/tmi.2011.2161590] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Since it was first presented in 2002, optical projection tomography (OPT) has emerged as a powerful tool for the study of biomedical specimen on the mm to cm scale. In this paper, we present computational tools to further improve OPT image acquisition and tomographic reconstruction. More specifically, these methods provide: semi-automatic and precise positioning of a sample at the axis of rotation and a fast and robust algorithm for determination of postalignment values throughout the specimen as compared to existing methods. These tools are easily integrated for use with current commercial OPT scanners and should also be possible to implement in "home made" or experimental setups for OPT imaging. They generally contribute to increase acquisition speed and quality of OPT data and thereby significantly simplify and improve a number of three-dimensional and quantitative OPT based assessments.
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Affiliation(s)
- Abbas Cheddad
- Umeå Centre for Molecular Medicine, Umeå University, S-901 87 Umeå, Sweden.
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25
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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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26
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Staier F, Eipel H, Matula P, Evsikov AV, Kozubek M, Cremer C, Hausmann M. Micro axial tomography: a miniaturized, versatile stage device to overcome resolution anisotropy in fluorescence light microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2011; 82:093701. [PMID: 21974588 PMCID: PMC3189255 DOI: 10.1063/1.3632115] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2011] [Accepted: 08/11/2011] [Indexed: 05/02/2023]
Abstract
With the development of novel fluorescence techniques, high resolution light microscopy has become a challenging technique for investigations of the three-dimensional (3D) micro-cosmos in cells and sub-cellular components. So far, all fluorescence microscopes applied for 3D imaging in biosciences show a spatially anisotropic point spread function resulting in an anisotropic optical resolution or point localization precision. To overcome this shortcoming, micro axial tomography was suggested which allows object tilting on the microscopic stage and leads to an improvement in localization precision and spatial resolution. Here, we present a miniaturized device which can be implemented in a motor driven microscope stage. The footprint of this device corresponds to a standard microscope slide. A special glass fiber can manually be adjusted in the object space of the microscope lens. A stepwise fiber rotation can be controlled by a miniaturized stepping motor incorporated into the device. By means of a special mounting device, test particles were fixed onto glass fibers, optically localized with high precision, and automatically rotated to obtain views from different perspective angles under which distances of corresponding pairs of objects were determined. From these angle dependent distance values, the real 3D distance was calculated with a precision in the ten nanometer range (corresponding here to an optical resolution of 10-30 nm) using standard microscopic equipment. As a proof of concept, the spindle apparatus of a mature mouse oocyte was imaged during metaphase II meiotic arrest under different perspectives. Only very few images registered under different rotation angles are sufficient for full 3D reconstruction. The results indicate the principal advantage of the micro axial tomography approach for many microscopic setups therein and also those of improved resolutions as obtained by high precision localization determination.
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Affiliation(s)
- Florian Staier
- Kirchhoff Institute for Physics, University of Heidelberg, Im Neuenheimer Feld 227, 69120 Heidelberg, Germany
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27
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Rieckher M, Birk UJ, Meyer H, Ripoll J, Tavernarakis N. Microscopic optical projection tomography in vivo. PLoS One 2011; 6:e18963. [PMID: 21559481 PMCID: PMC3084718 DOI: 10.1371/journal.pone.0018963] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2010] [Accepted: 03/14/2011] [Indexed: 11/18/2022] Open
Abstract
We describe a versatile optical projection tomography system for rapid three-dimensional imaging of microscopic specimens in vivo. Our tomographic setup eliminates the in xy and z strongly asymmetric resolution, resulting from optical sectioning in conventional confocal microscopy. It allows for robust, high resolution fluorescence as well as absorption imaging of live transparent invertebrate animals such as C. elegans. This system offers considerable advantages over currently available methods when imaging dynamic developmental processes and animal ageing; it permits monitoring of spatio-temporal gene expression and anatomical alterations with single-cell resolution, it utilizes both fluorescence and absorption as a source of contrast, and is easily adaptable for a range of small model organisms.
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Affiliation(s)
- Matthias Rieckher
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Udo Jochen Birk
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Heiko Meyer
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, Crete, Greece
| | - Jorge Ripoll
- Institute of Electronic Structure and Laser, Foundation for Research and Technology-Hellas, Crete, Greece
- * E-mail: (JR); (NT)
| | - Nektarios Tavernarakis
- Institute of Molecular Biology and Biotechnology, Foundation for Research and Technology-Hellas, Crete, Greece
- * E-mail: (JR); (NT)
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28
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McGinty J, Taylor HB, Chen L, Bugeon L, Lamb JR, Dallman MJ, French PMW. In vivo fluorescence lifetime optical projection tomography. BIOMEDICAL OPTICS EXPRESS 2011; 2:1340-50. [PMID: 21559145 PMCID: PMC3087590 DOI: 10.1364/boe.2.001340] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2011] [Revised: 04/21/2011] [Accepted: 04/21/2011] [Indexed: 05/21/2023]
Abstract
We demonstrate the application of fluorescence lifetime optical projection tomography (FLIM-OPT) to in vivo imaging of lysC:GFP transgenic zebrafish embryos (Danio rerio). This method has been applied to unambiguously distinguish between the fluorescent protein (GFP) signal in myeloid cells from background autofluorescence based on the fluorescence lifetime. The combination of FLIM, an inherently ratiometric method, in conjunction with OPT results in a quantitative 3-D tomographic technique that could be used as a robust method for in vivo biological and pharmaceutical research, for example as a readout of Förster resonance energy transfer based interactions.
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Affiliation(s)
- James McGinty
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ, UK
| | - Harriet B. Taylor
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Lingling Chen
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ, UK
| | - Laurence Bugeon
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Jonathan R. Lamb
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Margaret J. Dallman
- Division of Cell and Molecular Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
- Centre for Integrative Systems Biology, Department of Life Sciences, Imperial College London, SW7 2AZ, UK
| | - Paul M. W. French
- Photonics Group, Department of Physics, Imperial College London, SW7 2AZ, UK
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29
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Birk UJ, Darrell A, Konstantinides N, Sarasa-Renedo A, Ripoll J. Improved reconstructions and generalized filtered back projection for optical projection tomography. APPLIED OPTICS 2011; 50:392-398. [PMID: 21283227 DOI: 10.1364/ao.50.000392] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
Optical projection tomography (OPT) is a noninvasive imaging technique that enables imaging of small specimens (<1 cm), such as organs or animals in early developmental stages. In this paper, we present a set of computational methods that can be applied to the acquired data sets in order to correct for (a) unknown background or illumination intensity distributions over the field of view, (b) intensity spikes in single CCD pixels (so-called "hot pixels"), and (c) refractive index mismatch between the media in which the specimens are embedded and the environment. We have tested these correction methods using a variety of samples and present results obtained from Parhyale hawaiensis embedded in glycerol and in sea water. Successful reconstructions of fluorescence and absorption OPT images have been obtained for weakly scattering specimens embedded in media with nonmatched refractive index, thus advancing OPT toward routine in vivo imaging.
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Affiliation(s)
- Udo Jochen Birk
- Institute of Electronic Structure & Laser, Foundation for Research and Technology-Hellas, FORTH, Heraklion, Greece. ‐heidelberg.de
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