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Jiao Z, Pan M, Yousaf K, Doveiko D, Maclean M, Griffin D, Chen Y, Li DDU. Smartphone-based optical sectioning (SOS) microscopy with a telecentric design for fluorescence imaging. J Microsc 2024; 296:10-23. [PMID: 38808665 DOI: 10.1111/jmi.13334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 04/15/2024] [Accepted: 05/17/2024] [Indexed: 05/30/2024]
Abstract
We propose a smartphone-based optical sectioning (SOS) microscope based on the HiLo technique, with a single smartphone replacing a high-cost illumination source and a camera sensor. We built our SOS with off-the-shelf optical, mechanical cage systems with 3D-printed adapters to seamlessly integrate the smartphone with the SOS main body. The liquid light guide can be integrated with the adapter, guiding the smartphone's LED light to the digital mirror device (DMD) with neglectable loss. We used an electrically tuneable lens (ETL) instead of a mechanical translation stage to realise low-cost axial scanning. The ETL was conjugated to the objective lens's back pupil plane (BPP) to construct a telecentric design by a 4f configuration to maintain the lateral magnification for different axial positions. SOS has a 571.5 µm telecentric scanning range and an 11.7 µm axial resolution. The broadband smartphone LED torch can effectively excite fluorescent polystyrene (PS) beads. We successfully used SOS for high-contrast fluorescent PS beads imaging with different wavelengths and optical sectioning imaging of multilayer fluorescent PS beads. To our knowledge, the proposed SOS is the first smartphone-based HiLo optical sectioning microscopy (£1965), which can save around £7035 compared with a traditional HiLo system (£9000). It is a powerful tool for biomedical research in resource-limited areas.
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Affiliation(s)
- Ziao Jiao
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
| | - Mingliang Pan
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
| | - Khadija Yousaf
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - Daniel Doveiko
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - Michelle Maclean
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Department of Electronic & Electrical Engineering, The Robertson Trust Laboratory for Electronic Sterilisation Technologies (ROLEST), University of Strathclyde, Glasgow, UK
| | - David Griffin
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
| | - Yu Chen
- Department of Physics, University of Strathclyde, Glasgow, Scotland, UK
| | - David Day Uei Li
- Department of Biomedical Engineering, University of Strathclyde, Glasgow, Scotland, UK
- Strathclyde Institute of Pharmacy and Biomedical Sciences, University of Strathclyde, Glasgow, Scotland, UK
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Sharma N, van Oijen AM, Spenkelink LM, Mueller SH. Insight into Single-Molecule Imaging Techniques for the Study of Prokaryotic Genome Maintenance. CHEMICAL & BIOMEDICAL IMAGING 2024; 2:595-614. [PMID: 39328428 PMCID: PMC11423410 DOI: 10.1021/cbmi.4c00037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Revised: 06/04/2024] [Accepted: 06/07/2024] [Indexed: 09/28/2024]
Abstract
Genome maintenance comprises a group of complex and interrelated processes crucial for preserving and safeguarding genetic information within all organisms. Key aspects of genome maintenance involve DNA replication, transcription, recombination, and repair. Improper regulation of these processes could cause genetic changes, potentially leading to antibiotic resistance in bacterial populations. Due to the complexity of these processes, ensemble averaging studies may not provide the level of detail required to capture the full spectrum of molecular behaviors and dynamics of each individual biomolecule. Therefore, researchers have increasingly turned to single-molecule approaches, as these techniques allow for the direct observation and manipulation of individual biomolecules, and offer a level of detail that is unattainable with traditional ensemble methods. In this review, we provide an overview of recent in vitro and in vivo single-molecule imaging approaches employed to study the complex processes involved in prokaryotic genome maintenance. We will first highlight the principles of imaging techniques such as total internal reflection fluorescence microscopy and atomic force microscopy, primarily used for in vitro studies, and highly inclined and laminated optical sheet and super-resolution microscopy, mainly employed in in vivo studies. We then demonstrate how applying these single-molecule techniques has enabled the direct visualization of biological processes such as replication, transcription, DNA repair, and recombination in real time. Finally, we will showcase the results obtained from super-resolution microscopy approaches, which have provided unprecedented insights into the spatial organization of different biomolecules within bacterial organisms.
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Affiliation(s)
- Nischal Sharma
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Antoine M van Oijen
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Lisanne M Spenkelink
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
| | - Stefan H Mueller
- Molecular Horizons and School of Chemistry and Molecular Bioscience, University of Wollongong, Wollongong, New South Wales 2522, Australia
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Hu Y, Liang D, Wang J, Xuan Y, Zhao F, Liu J, Li R. Background-free wide-field fluorescence imaging using edge detection combined with HiLo. JOURNAL OF BIOPHOTONICS 2022; 15:e202200031. [PMID: 35488180 DOI: 10.1002/jbio.202200031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 04/01/2022] [Accepted: 04/28/2022] [Indexed: 06/14/2023]
Abstract
Fluorescence microscopy has been widely used in the field of biological imaging, but the disturbance of background noise has always been an unavoidable phenomenon. To obtain a background free image, a virtual HiLo based on edge detection (V-HiLo-ED) method for background removing is proposed, which is different from the existing popular software algorithms that obtain the background-free image by subtracting the estimated background, but the background-free image is directly reconstructed by estimating the foreground. Compared with two other popular software-based methods, the wavelet-based background and noise subtraction algorithm (WBNS) and the rolling ball algorithm (RBA), the V-HiLo-ED owns a better quality on achieving background-free imaging. Compared with hardware-based method such as HiLo method, V-HiLo-ED exhibits almost the same performance but faster speed. In combination with light sheet microscopy, the V-HiLo-ED further improves the signal-to-noise ratio of images with thick light-sheet. These experiment results indicate that the V-HiLo-ED owns the potentiality in many other image applications such as endoscopy.
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Affiliation(s)
- Yuyao Hu
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Dong Liang
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- School of Physics Science and Engineering, Tongji University, Shanghai, China
| | - Jing Wang
- Institute of Photonic Chips, University of Shanghai for Science and Technology, Shanghai, China
- Centre for Artificial-Intelligence Nanophotonics, School of Optical-Electrical and Computer Engineering, University of Shanghai for Science and Technology, Shanghai, China
| | - Yaping Xuan
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Fu Zhao
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Jun Liu
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
| | - Ruxin Li
- State Key Laboratory of High Field Laser Physics and CAS Center for Excellence in Ultra-intense Laser Science, Shanghai Institute of Optics and Fine Mechanics, Chinese Academy of Sciences, Shanghai, China
- University Center of Materials Science and Optoelectronics Engineering, University of Chinese Academy of Sciences, Beijing, China
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Image improvement of temporal focusing multiphoton microscopy via superior spatial modulation excitation and Hilbert-Huang transform decomposition. Sci Rep 2022; 12:10079. [PMID: 35710746 PMCID: PMC9203560 DOI: 10.1038/s41598-022-14367-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/06/2022] [Indexed: 11/08/2022] Open
Abstract
Temporal focusing-based multiphoton excitation microscopy (TFMPEM) just provides the advantage of widefield optical sectioning ability with axial resolution of several micrometers. However, under the plane excitation, the photons emitted from the molecules in turbid tissues undergo scattering, resulting in complicated background noise and an impaired widefield image quality. Accordingly, this study constructs a general and comprehensive numerical model of TFMPEM utilizing Fourier optics and performs simulations to determine the superior spatial frequency and orientation of the structured pattern which maximize the axial excitation confinement. It is shown experimentally that the optimized pattern minimizes the intensity of the out-of-focus signal, and hence improves the quality of the image reconstructed using the Hilbert transform (HT). However, the square-like reflection components on digital micromirror device leads to pattern residuals in the demodulated image when applying high spatial frequency of structured pattern. Accordingly, the HT is replaced with Hilbert-Huang transform (HHT) in order to sift out the low-frequency background noise and pattern residuals in the demodulation process. The experimental results obtained using a kidney tissue sample show that the HHT yields a significant improvement in the TFMPEM image quality.
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Strain maps characterize the symmetry of convergence and extension patterns during zebrafish gastrulation. Sci Rep 2021; 11:19357. [PMID: 34588480 PMCID: PMC8481280 DOI: 10.1038/s41598-021-98233-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Accepted: 08/03/2021] [Indexed: 12/16/2022] Open
Abstract
During gastrulation of the zebrafish embryo, the cap of blastoderm cells organizes into the axial body plan of the embryo with left–right symmetry and head–tail, dorsal–ventral polarities. Our labs have been interested in the mechanics of early development and have investigated whether these large-scale cell movements can be described as tissue-level mechanical strain by a tectonics-based approach. The first step is to image the positions of all nuclei from mid-epiboly to early segmentation by digital sheet light microscopy, organize the surface of the embryo into multi-cell spherical domains, construct velocity fields from the movements of these domains and extract strain rate maps from the change in density of the domains. During gastrulation, tensile/expansive and compressive strains in the axial and equatorial directions are detected as anterior and posterior expansion along the anterior–posterior axis and medial–lateral compression across the dorsal–ventral axis and corresponds to the well characterized morphological movements of convergence and extension. Following gastrulation strain is represented by localized medial expansion at the onset of segmentation and anterior expansion at the onset of neurulation. In addition to linear strain, symmetric patterns of rotation/curl are first detected in the animal hemispheres at mid-epiboly and then the vegetal hemispheres by the end of gastrulation. In embryos treated with C59, a Wnt inhibitor that inhibits head and tail extension, the axial extension and vegetal curl are absent. By analysing the temporal sequence of large-scale movements, deformations across the embryo can be attributed to a combination of epiboly and dorsal convergence-extension.
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Chang CY, Lin CY, Hu YY, Tsai SF, Hsu FC, Chen SJ. Temporal focusing multiphoton microscopy with optimized parallel multiline scanning for fast biotissue imaging. JOURNAL OF BIOMEDICAL OPTICS 2021; 26:JBO-200171RR. [PMID: 33386708 PMCID: PMC7778456 DOI: 10.1117/1.jbo.26.1.016501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Accepted: 12/09/2020] [Indexed: 06/12/2023]
Abstract
SIGNIFICANCE Line scanning-based temporal focusing multiphoton microscopy (TFMPM) has superior axial excitation confinement (AEC) compared to conventional widefield TFMPM, but the frame rate is limited due to the limitation of the single line-to-line scanning mechanism. The development of the multiline scanning-based TFMPM requires only eight multiline patterns for full-field uniform multiphoton excitation and it still maintains superior AEC. AIM The optimized parallel multiline scanning TFMPM is developed, and the performance is verified with theoretical simulation. The system provides a sharp AEC equivalent to the line scanning-based TFMPM, but fewer scans are required. APPROACH A digital micromirror device is integrated in the TFMPM system and generates the multiline pattern for excitation. Based on the result of single-line pattern with sharp AEC, we can further model the multiline pattern to find the best structure that has the highest duty cycle together with the best AEC performance. RESULTS The AEC is experimentally improved to 1.7 μm from the 3.5 μm of conventional TFMPM. The adopted multiline pattern is akin to a pulse-width-modulation pattern with a spatial period of four times the diffraction-limited line width. In other words, ideally only four π / 2 spatial phase-shift scans are required to form a full two-dimensional image with superior AEC instead of image-size-dependent line-to-line scanning. CONCLUSIONS We have demonstrated the developed parallel multiline scanning-based TFMPM has the multiline pattern for sharp AEC and the least scans required for full-field uniform excitation. In the experimental results, the temporal focusing-based multiphoton images of disordered biotissue of mouse skin with improved axial resolution due to the near-theoretical limit AEC are shown to clearly reduce background scattering.
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Affiliation(s)
- Chia-Yuan Chang
- National Cheng Kung University, Department of Mechanical Engineering, Tainan, Taiwan
| | - Chun-Yun Lin
- National Chiao Tung University, College of Photonics, Tainan, Taiwan
| | - Yvonne Y. Hu
- National Cheng Kung University, Department of Photonics, Tainan, Taiwan
| | - Sheng-Feng Tsai
- National Cheng Kung University, Department of Cell Biology and Anatomy, Tainan, Taiwan
| | - Feng-Chun Hsu
- National Chiao Tung University, College of Photonics, Tainan, Taiwan
| | - Shean-Jen Chen
- National Chiao Tung University, College of Photonics, Tainan, Taiwan
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Deng M, Li S, Goy A, Kang I, Barbastathis G. Learning to synthesize: robust phase retrieval at low photon counts. LIGHT, SCIENCE & APPLICATIONS 2020; 9:36. [PMID: 32194950 PMCID: PMC7062747 DOI: 10.1038/s41377-020-0267-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Revised: 02/04/2020] [Accepted: 02/19/2020] [Indexed: 05/13/2023]
Abstract
The quality of inverse problem solutions obtained through deep learning is limited by the nature of the priors learned from examples presented during the training phase. Particularly in the case of quantitative phase retrieval, spatial frequencies that are underrepresented in the training database, most often at the high band, tend to be suppressed in the reconstruction. Ad hoc solutions have been proposed, such as pre-amplifying the high spatial frequencies in the examples; however, while that strategy improves the resolution, it also leads to high-frequency artefacts, as well as low-frequency distortions in the reconstructions. Here, we present a new approach that learns separately how to handle the two frequency bands, low and high, and learns how to synthesize these two bands into full-band reconstructions. We show that this "learning to synthesize" (LS) method yields phase reconstructions of high spatial resolution and without artefacts and that it is resilient to high-noise conditions, e.g., in the case of very low photon flux. In addition to the problem of quantitative phase retrieval, the LS method is applicable, in principle, to any inverse problem where the forward operator treats different frequency bands unevenly, i.e., is ill-posed.
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Affiliation(s)
- Mo Deng
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - Shuai Li
- Sensebrain Technology Limited LLC, 2550 N 1st Street, Suite 300, San Jose, CA 95131 USA
| | - Alexandre Goy
- Omnisens SA, Riond Bosson 3, 1110 Morges, VD Switzerland
| | - Iksung Kang
- Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
| | - George Barbastathis
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139 USA
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, Singapore, 117543 Singapore
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Hu B, Bolus D, Brown JQ. Improved contrast in inverted selective plane illumination microscopy of thick tissues using confocal detection and structured illumination. BIOMEDICAL OPTICS EXPRESS 2017; 8:5546-5559. [PMID: 29296487 PMCID: PMC5745102 DOI: 10.1364/boe.8.005546] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Revised: 10/26/2017] [Accepted: 11/09/2017] [Indexed: 05/08/2023]
Abstract
Inverted selective plane illumination microscopy (iSPIM) enables fast, large field-of-view, long term imaging with compatibility with conventional sample mounting. However, the imaging quality can be deteriorated in thick tissues due to sample scattering. Three strategies have been adopted in this paper to optimize the imaging performance of iSPIM on thick tissue imaging: electronic confocal slit detection (eCSD), structured illumination (SI) and the two combined. We compared the image contrast when using SPIM, confocal SPIM (using eCSD alone), SI SPIM (using SI alone) or confocal-SI SPIM (combining both methods) on images of gelatin phantom and highly-scattering fluorescently-stained human tissue. We demonstrate that all the three methods showed remarkable contrast enhancement on both samples compared to iSPIM alone, and SI SPIM and the combined confocal-SI mode outperformed confocal SPIM in contrast enhancement. Moreover, the use of SI at high pattern frequencies outperformed confocal SPIM in terms of optical sectioning capability. However, image signal-to-noise ratio (SNR) was decreased at high pattern frequencies when imaging scattering samples with SI SPIM. By combining eCSD with SI to reduce background signal and noise, the superior optical sectioning performance of SI could be achieved while also maintaining high image SNR.
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9
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Imag(in)ing growth and form. Mech Dev 2017; 145:13-21. [DOI: 10.1016/j.mod.2017.03.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2017] [Revised: 03/21/2017] [Accepted: 03/23/2017] [Indexed: 01/03/2023]
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10
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Duan Y, Chen N. Hybrid wide-field and scanning microscopy for high-speed 3D imaging. OPTICS LETTERS 2015; 40:5251-5254. [PMID: 26565847 DOI: 10.1364/ol.40.005251] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Wide-field optical microscopy is efficient and robust in biological imaging, but it lacks depth sectioning. In contrast, scanning microscopic techniques, such as confocal microscopy and multiphoton microscopy, have been successfully used for three-dimensional (3D) imaging with optical sectioning capability. However, these microscopic techniques are not very suitable for dynamic real-time imaging because they usually take a long time for temporal and spatial scanning. Here, a hybrid imaging technique combining wide-field microscopy and scanning microscopy is proposed to accelerate the image acquisition process while maintaining the 3D optical sectioning capability. The performance was demonstrated by proof-of-concept imaging experiments with fluorescent beads and zebrafish liver.
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Dufferwiel S, Schwarz S, Withers F, Trichet AAP, Li F, Sich M, Del Pozo-Zamudio O, Clark C, Nalitov A, Solnyshkov DD, Malpuech G, Novoselov KS, Smith JM, Skolnick MS, Krizhanovskii DN, Tartakovskii AI. Exciton-polaritons in van der Waals heterostructures embedded in tunable microcavities. Nat Commun 2015; 6:8579. [PMID: 26446783 PMCID: PMC4633950 DOI: 10.1038/ncomms9579] [Citation(s) in RCA: 148] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Accepted: 09/08/2015] [Indexed: 12/12/2022] Open
Abstract
Layered materials can be assembled vertically to fabricate a new class of van der Waals heterostructures a few atomic layers thick, compatible with a wide range of substrates and optoelectronic device geometries, enabling new strategies for control of light-matter coupling. Here, we incorporate molybdenum diselenide/hexagonal boron nitride (MoSe2/hBN) quantum wells in a tunable optical microcavity. Part-light-part-matter polariton eigenstates are observed as a result of the strong coupling between MoSe2 excitons and cavity photons, evidenced from a clear anticrossing between the neutral exciton and the cavity modes with a splitting of 20 meV for a single MoSe2 monolayer, enhanced to 29 meV in MoSe2/hBN/MoSe2 double-quantum wells. The splitting at resonance provides an estimate of the exciton radiative lifetime of 0.4 ps. Our results pave the way for room-temperature polaritonic devices based on multiple-quantum-well van der Waals heterostructures, where polariton condensation and electrical polariton injection through the incorporation of graphene contacts may be realized.
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Affiliation(s)
- S. Dufferwiel
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - S. Schwarz
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - F. Withers
- School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, UK
| | - A. A. P. Trichet
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - F. Li
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - M. Sich
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - O. Del Pozo-Zamudio
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - C. Clark
- Helia Photonics, Livingston EH54 7EJ, UK
| | - A. Nalitov
- Institut Pascal, Blaise Pascal University, 24 avenue des Landais, 63177 Aubiére, France
- Physics and Astronomy, University of Southampton, Highfield, Southampton, SO17 1BJ, UK
| | - D. D. Solnyshkov
- Institut Pascal, Blaise Pascal University, 24 avenue des Landais, 63177 Aubiére, France
| | - G. Malpuech
- Institut Pascal, Blaise Pascal University, 24 avenue des Landais, 63177 Aubiére, France
| | - K. S. Novoselov
- School of Physics and Astronomy, University of Manchester, Manchester M13 9PL, UK
| | - J. M. Smith
- Department of Materials, University of Oxford, Parks Road, Oxford OX1 3PH, UK
| | - M. S. Skolnick
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - D. N. Krizhanovskii
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
| | - A. I. Tartakovskii
- Department of Physics and Astronomy, University of Sheffield, Sheffield S3 7RH, UK
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Single molecule data under scrutiny: Comment on "Extracting physics of life at the molecular level: A review of single-molecule data analyses" by W. Colomb & S.K. Sarkar. Phys Life Rev 2015; 13:138-40. [PMID: 25843015 DOI: 10.1016/j.plrev.2015.03.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2015] [Accepted: 03/30/2015] [Indexed: 11/20/2022]
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13
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Chen HH, Singh VR, Luo Y. Speckle-based volume holographic microscopy for optically sectioned multi-plane fluorescent imaging. OPTICS EXPRESS 2015; 23:7075-7084. [PMID: 25837052 DOI: 10.1364/oe.23.007075] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Structured illumination microscopy has been widely used to reconstruct optically sectioned fluorescence images in wide-field fashion; however, it still requires axial scanning to obtain multiple depth information of a volumetric sample. In this paper, a new imaging scheme, called speckle-based volume holographic microscopy system, is presented. The proposed system incorporates volumetric speckle illumination and multiplexed volume holographic gratings to acquire multi-plane images with optical sectioning capability, without any axial scanning. We present the design, implementation, and experimental image data demonstrating the proposed system's ability to simultaneously obtain wide-field, optically sectioned, and multi-depth resolved images of fluorescently labeled microspheres and tissue structures.
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14
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Choi H, Wadduwage DN, Tu TY, Matsudaira P, So PTC. Three-dimensional image cytometer based on widefield structured light microscopy and high-speed remote depth scanning. Cytometry A 2014; 87:49-60. [PMID: 25352187 DOI: 10.1002/cyto.a.22584] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 10/05/2014] [Accepted: 10/07/2014] [Indexed: 12/18/2022]
Abstract
A high throughput 3D image cytometer have been developed that improves imaging speed by an order of magnitude over current technologies. This imaging speed improvement was realized by combining several key components. First, a depth-resolved image can be rapidly generated using a structured light reconstruction algorithm that requires only two wide field images, one with uniform illumination and the other with structured illumination. Second, depth scanning is implemented using the high speed remote depth scanning. Finally, the large field of view, high NA objective lens and the high pixelation, high frame rate sCMOS camera enable high resolution, high sensitivity imaging of a large cell population. This system can image at 800 cell/sec in 3D at submicron resolution corresponding to imaging 1 million cells in 20 min. The statistical accuracy of this instrument is verified by quantitatively measuring rare cell populations with ratio ranging from 1:1 to 1:10(5) . © 2014 International Society for Advancement of Cytometry.
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Affiliation(s)
- Heejin Choi
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139
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15
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Choi H, Wadduwage D, Matsudaira PT, So PT. Depth resolved hyperspectral imaging spectrometer based on structured light illumination and Fourier transform interferometry. BIOMEDICAL OPTICS EXPRESS 2014; 5:3494-507. [PMID: 25360367 PMCID: PMC4206319 DOI: 10.1364/boe.5.003494] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2014] [Accepted: 08/22/2014] [Indexed: 06/04/2023]
Abstract
A depth resolved hyperspectral imaging spectrometer can provide depth resolved imaging both in the spatial and the spectral domain. Images acquired through a standard imaging Fourier transform spectrometer do not have the depth-resolution. By post processing the spectral cubes (x, y, λ) obtained through a Sagnac interferometer under uniform illumination and structured illumination, spectrally resolved images with depth resolution can be recovered using structured light illumination algorithms such as the HiLo method. The proposed scheme is validated with in vitro specimens including fluorescent solution and fluorescent beads with known spectra. The system is further demonstrated in quantifying spectra from 3D resolved features in biological specimens. The system has demonstrated depth resolution of 1.8 μm and spectral resolution of 7 nm respectively.
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Affiliation(s)
- Heejin Choi
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Dushan Wadduwage
- BioSym, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore 138602, Singapore
| | - Paul T. Matsudaira
- Department of Biological Sciences, National University of Singapore, Singapore 138602, Singapore
| | - Peter T.C. So
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
- BioSym, Singapore-MIT Alliance for Research and Technology, Singapore 138602, Singapore
- Laser Biomedical Research Center, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
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Luo Y, Singh VR, Bhattacharya D, Yew EYS, Tsai JC, Yu SL, Chen HH, Wong JM, Matsudaira P, So PTC, Barbastathis G. Talbot holographic illumination nonscanning (THIN) fluorescence microscopy. LASER & PHOTONICS REVIEWS 2014; 8:L71-L75. [PMID: 25678936 PMCID: PMC4321697 DOI: 10.1002/lpor.201400053] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Optical sectioning techniques offer the ability to acquire three-dimensional information from various organ tissues by discriminating between the desired in-focus and out-of-focus (background) signals. Alternative techniques to confocal, such as active structured illumination, exist for fast optically sectioned images, but they require individual axial planes to be imaged consecutively. In this article, an imaging technique (THIN), by utilizing active Talbot illumination in 3D and multiplexed holographic Bragg filters for depth discrimination, is demonstrated for imaging in vivo 3D biopsy without mechanical or optical axial scanning.
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Affiliation(s)
- Yuan Luo
- Center for Optoelectronic Biomedicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan R.O.C
- Molecular Imaging Center, National Taiwan University, Taipei, 10055, Taiwan R.O.C
- Corresponding authors: ;
| | - Vijay Raj Singh
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, #10-01 CREATE Tower, 138602, Singapore
- Corresponding authors: ;
| | - Dipanjan Bhattacharya
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, #10-01 CREATE Tower, 138602, Singapore
- Centre for BioImaging Science (CBIS), Blk S1A, Level 2, National University of Singapore, 14 Science Drive 4, 117546, Singapore
- MechanoBiology Institute (MBI), National University of Singapore, 117411, Singapore
| | - Elijah Y. S. Yew
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, #10-01 CREATE Tower, 138602, Singapore
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - Jui-Chang Tsai
- Center for Optoelectronic Biomedicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan R.O.C
| | - Sung-Liang Yu
- Department of Clinical Laboratory Sciences and Medical Biotechnology, College of Medicine, National Taiwan University, Taipei, 10055, Taiwan R.O.C
| | - Hsi-Hsun Chen
- Center for Optoelectronic Biomedicine, College of Medicine, National Taiwan University, Taipei, 10051, Taiwan R.O.C
- Molecular Imaging Center, National Taiwan University, Taipei, 10055, Taiwan R.O.C
| | - Jau-Min Wong
- Department of Internal Medicine, National Taiwan University Hospital, Taipei, 10048, Taiwan, R.O.C
| | - Paul Matsudaira
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, #10-01 CREATE Tower, 138602, Singapore
- Centre for BioImaging Science (CBIS), Blk S1A, Level 2, National University of Singapore, 14 Science Drive 4, 117546, Singapore
- MechanoBiology Institute (MBI), National University of Singapore, 117411, Singapore
| | - Peter T. C. So
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, #10-01 CREATE Tower, 138602, Singapore
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
- Department of Biomedical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
| | - George Barbastathis
- Singapore-MIT Alliance for Research and Technology (SMART) Centre, 1 CREATE Way, #10-01 CREATE Tower, 138602, Singapore
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 02139, USA
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17
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Choi H, Yew EYS, Hallacoglu B, Fantini S, Sheppard CJR, So PTC. Improvement of axial resolution and contrast in temporally focused widefield two-photon microscopy with structured light illumination. BIOMEDICAL OPTICS EXPRESS 2013; 4:995-1005. [PMID: 23847726 PMCID: PMC3704103 DOI: 10.1364/boe.4.000995] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2013] [Revised: 05/17/2013] [Accepted: 05/29/2013] [Indexed: 05/18/2023]
Abstract
Although temporally focused wide-field two-photon microscopy (TFM) can perform depth resolved wide field imaging, it cannot avoid the image degradation due to scattering of excitation and emission photons when imaging in a turbid medium. Further, its axial resolution is inferior to standard point-scanning two-photon microscopy. We implemented a structured light illumination for TFM and have shown that it can effectively reject the out-of-focus scattered emission photons improving image contrast. Further, the depth resolution of the improved system is dictated by the spatial frequency of the structure light with the potential of attaining depth resolution better than point-scanning two-photon microscopy.
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Affiliation(s)
- Heejin Choi
- Department of Mechanical Engineering Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
| | - Elijah Y. S. Yew
- Singapore MIT Alliance for Research and Technology, Singapore 138602, Singapore
| | - Bertan Hallacoglu
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Sergio Fantini
- Department of Biomedical Engineering, Tufts University, Medford, Massachusetts 02155, USA
| | - Colin J. R. Sheppard
- Department of Nanophysics, Istituto Italiano di Tecnologia, Via Morego, 30, 1613 Genova, Italy
| | - Peter T. C. So
- Department of Mechanical Engineering Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA
- Singapore MIT Alliance for Research and Technology, Singapore 138602, Singapore
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