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Lai JZ, Lin CY, Chen SJ, Cheng YM, Abe M, Lin TC, Chien FC. Temporal-Focusing Multiphoton Excitation Single-Molecule Localization Microscopy Using Spontaneously Blinking Fluorophores. Angew Chem Int Ed Engl 2024; 63:e202404942. [PMID: 38641901 DOI: 10.1002/anie.202404942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/16/2024] [Accepted: 04/16/2024] [Indexed: 04/21/2024]
Abstract
Single-molecule localization microscopy (SMLM) based on temporal-focusing multiphoton excitation (TFMPE) and single-wavelength excitation is used to visualize the three-dimensional (3D) distribution of spontaneously blinking fluorophore-labeled subcellular structures in a thick specimen with a nanoscale-level spatial resolution. To eliminate the photobleaching effect of unlocalized molecules in out-of-focus regions for improving the utilization rate of the photon budget in 3D SMLM imaging, SMLM with single-wavelength TFMPE achieves wide-field and axially confined two-photon excitation (TPE) of spontaneously blinking fluorophores. TPE spectral measurement of blinking fluorophores is then conducted through TFMPE imaging at a tunable excitation wavelength, yielding the optimal TPE wavelength for increasing the number of detected photons from a single blinking event during SMLM. Subsequently, the TPE fluorescence of blinking fluorophores is recorded to obtain a two-dimensional TFMPE-SMLM image of the microtubules in cancer cells with a localization precision of 18±6 nm and an overall imaging resolution of approximately 51 nm, which is estimated based on the contribution of Nyquist resolution and localization precision. Combined with astigmatic imaging, the system is capable of 3D TFMPE-SMLM imaging of brain tissue section of a 5XFAD transgenic mouse with the pathological features of Alzheimer's disease, revealing the distribution of neurotoxic amyloid-beta peptide deposits.
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Affiliation(s)
- Jian-Zong Lai
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, No.301, Sec.2, Gaofa 3rd Rd., Guiren Dist., Tainan City, 71150, Taiwan
| | - Yu-Min Cheng
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Manabu Abe
- Department of Chemistry, Graduate School of Advanced Science and Engineering, Hiroshima University, 1-3-1 Kagamiyama, Higashi-Hiroshima City, Hiroshima, 739-8526, Japan
| | - Tzu-Chau Lin
- Department of Chemistry, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, No. 300, Zhongda Rd., Zhongli Dist., Taoyuan City, 32001, Taiwan
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2
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Szczypkowski P, Pawlowska M, Lapkiewicz R. 3D super-resolution optical fluctuation imaging with temporal focusing two-photon excitation. BIOMEDICAL OPTICS EXPRESS 2024; 15:4381-4389. [PMID: 39022538 PMCID: PMC11249675 DOI: 10.1364/boe.523430] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 06/07/2024] [Accepted: 06/07/2024] [Indexed: 07/20/2024]
Abstract
3D super-resolution fluorescence microscopy typically requires sophisticated setups, sample preparation, or long measurements. A notable exception, SOFI, only requires recording a sequence of frames and no hardware modifications whatsoever but being a wide-field method, it faces problems in thick, dense samples. We combine SOFI with temporal focusing two-photon excitation - the wide-field method that is capable of exciting a thin slice in 3D volume. Temporal focusing is simple to implement whenever the excitation path of the microscope can be accessed. The implementation of SOFI is straightforward. By merging these two methods, we obtain super-resolved 3D images of neurons stained with quantum dots. Our approach offers reduced bleaching of out-of-focus fluorescent probes and an improved signal-to-background ratio that can be used when robust resolution improvement is required in thick, dense samples.
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Affiliation(s)
- Pawel Szczypkowski
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
| | - Monika Pawlowska
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
- Nencki Institute of Experimental Biology PAS, Pasteura 3, Warsaw 02-093, Poland
| | - Radek Lapkiewicz
- Institute of Experimental Physics, Faculty of Physics, University of Warsaw, Pasteura 5, Warsaw 02-093, Poland
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3
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Hsu FC, Lin CY, Hu YY, Hwu YK, Chiang AS, Chen SJ. Light-field microscopy with temporal focusing multiphoton illumination for scanless volumetric bioimaging. BIOMEDICAL OPTICS EXPRESS 2022; 13:6610-6620. [PMID: 36589593 PMCID: PMC9774856 DOI: 10.1364/boe.473807] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Revised: 10/14/2022] [Accepted: 11/13/2022] [Indexed: 06/17/2023]
Abstract
A temporal focusing multiphoton illumination (TFMI) method is proposed for achieving selective volume illumination (SVI) (i.e., illuminating only the volume of interest) in light-field microscopy (LFM). The proposed method minimizes the background noise of the LFM images and enhances the contrast, and thus improves the imaging quality. Three-dimensional (3D) volumetric imaging is achieved by reconstructing the LFM images using a phase-space deconvolution algorithm. The experimental results obtained using 100-nm fluorescent beads show that the proposed TFMI-LFM system achieves lateral and axial resolutions of 1.2 µm and 1.1 µm, respectively, at the focal plane. Furthermore, the TFMI-LFM system enables 3D images of the single lobe of the drosophila mushroom body with GFP biomarker (OK-107) to be reconstructed in a one-snapshot record.
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Affiliation(s)
- Feng-Chun Hsu
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 112, Taiwan
| | - Chun-Yu Lin
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 112, Taiwan
| | - Yvonne Yuling Hu
- Department of Photonics, National Cheng Kung University, Tainan 701, Taiwan
| | - Yeu-kuang Hwu
- Institute of Physics, Academia Sinica, Taipei 115, Taiwan
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu 300, Taiwan
| | - Shean-Jen Chen
- College of Photonics, National Yang Ming Chiao Tung University, Tainan 112, Taiwan
- Taiwan Instrument Research Institute, National Applied Research Laboratories, Hsinchu 300, Taiwan
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Valli J, Garcia-Burgos A, Rooney LM, Vale de Melo E Oliveira B, Duncan RR, Rickman C. Seeing beyond the limit: A guide to choosing the right super-resolution microscopy technique. J Biol Chem 2021; 297:100791. [PMID: 34015334 PMCID: PMC8246591 DOI: 10.1016/j.jbc.2021.100791] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/14/2021] [Accepted: 05/14/2021] [Indexed: 02/06/2023] Open
Abstract
Super-resolution microscopy has become an increasingly popular and robust tool across the life sciences to study minute cellular structures and processes. However, with the increasing number of available super-resolution techniques has come an increased complexity and burden of choice in planning imaging experiments. Choosing the right super-resolution technique to answer a given biological question is vital for understanding and interpreting biological relevance. This is an often-neglected and complex task that should take into account well-defined criteria (e.g., sample type, structure size, imaging requirements). Trade-offs in different imaging capabilities are inevitable; thus, many researchers still find it challenging to select the most suitable technique that will best answer their biological question. This review aims to provide an overview and clarify the concepts underlying the most commonly available super-resolution techniques as well as guide researchers through all aspects that should be considered before opting for a given technique.
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Affiliation(s)
- Jessica Valli
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
| | - Adrian Garcia-Burgos
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Liam M Rooney
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Beatriz Vale de Melo E Oliveira
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Rory R Duncan
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom
| | - Colin Rickman
- Edinburgh Super Resolution Imaging Consortium (ESRIC), Institute of Biological Chemistry, Biophysics and Bioengineering, Heriot-Watt University, Edinburgh, United Kingdom.
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Paasila PJ, Fok SYY, Flores‐Rodriguez N, Sajjan S, Svahn AJ, Dennis CV, Holsinger RMD, Kril JJ, Becker TS, Banati RB, Sutherland GT, Graeber MB. Ground state depletion microscopy as a tool for studying microglia-synapse interactions. J Neurosci Res 2021; 99:1515-1532. [PMID: 33682204 PMCID: PMC8251743 DOI: 10.1002/jnr.24819] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 02/02/2021] [Accepted: 02/06/2021] [Indexed: 01/09/2023]
Abstract
Ground state depletion followed by individual molecule return microscopy (GSDIM) has been used in the past to study the nanoscale distribution of protein co-localization in living cells. We now demonstrate the successful application of GSDIM to archival human brain tissue sections including from Alzheimer's disease cases as well as experimental tissue samples from mouse and zebrafish larvae. Presynaptic terminals and microglia and their cell processes were visualized at a resolution beyond diffraction-limited light microscopy, allowing clearer insights into their interactions in situ. The procedure described here offers time and cost savings compared to electron microscopy and opens the spectrum of molecular imaging using antibodies and super-resolution microscopy to the analysis of routine formalin-fixed paraffin sections of archival human brain. The investigation of microglia-synapse interactions in dementia will be of special interest in this context.
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Affiliation(s)
- Patrick Jarmo Paasila
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - Sandra Y. Y. Fok
- Biomedical Imaging FacilityMark Wainwright Analytical CentreUniversity of New South Wales SydneyKensingtonNSWAustralia
| | - Neftali Flores‐Rodriguez
- Charles Perkins CentreSydney Microscopy and MicroanalysisThe University of SydneyCamperdownNSWAustralia
| | - Sujata Sajjan
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Adam J. Svahn
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Claude V. Dennis
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - R. M. Damian Holsinger
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Jillian J. Kril
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - Thomas S. Becker
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
| | - Richard B. Banati
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
- Life SciencesAustralian Nuclear Science and Technology OrganisationKirraweeNSWAustralia
| | - Greg T. Sutherland
- Faculty of Medicine and HealthCharles Perkins Centre and School of Medical SciencesThe University of SydneyCamperdownNSWAustralia
| | - Manuel B. Graeber
- Faculty of Medicine and HealthBrain and Mind CentreThe University of SydneyCamperdownNSWAustralia
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6
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Li W, Pan W, Huang M, Yang Z, He Y, Zhang W, Zhang J, Gu Z, Zhang D, Yan W, Qu J. Disulfide-Reduction-Triggered Spontaneous Photoblinking Cy5 Probe for Nanoscopic Imaging of Mitochondrial Dynamics in Live Cells. Anal Chem 2021; 93:2596-2602. [PMID: 33464055 DOI: 10.1021/acs.analchem.0c04658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Mitochondria are highly dynamic organelles with interconnected tubule structures that are sensitive to environmental stress and light illumination. Super-resolution optical imaging of mitochondrial dynamics is of significance for understanding such biological events. Direct stochastic optical reconstruction microscopy has the advantages of a high spatial resolution, low phototoxicity in live-cell imaging, and the capacity to incorporate smart fluorescent probes. However, dSTORM imaging in live cells is challenging because of the requirement for an imaging buffer and a low temporal resolution. In this work, we achieved dSTORM imaging of mitochondrial dynamics in live cells with a disulfide-substituted Cy5 probe without using any toxic imaging buffer. Under the illumination of very low laser power, the probe exhibited spontaneous photoblinking triggered by disulfide-bond reduction in mitochondria of live cells. The obtained thiol attacked nearby carbon to form a six-membered ring and the reversible opening/closing of the ring produced spontaneous photoblinking behavior. With this new STORM strategy, we achieved observation of mitochondrial dynamics for more than 3 min, which provides a promising tool for further studies of mitochondria with an ultrafine structure.
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Affiliation(s)
- Wen Li
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wenhui Pan
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Meina Huang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhigang Yang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Ying He
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Jianguo Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Zhenyu Gu
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Dan Zhang
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Wei Yan
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
| | - Junle Qu
- Center for Biomedical Photonics & Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China
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7
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8
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Stegner D, Heinze KG. Intravital imaging of megakaryocytes. Platelets 2020; 31:599-609. [PMID: 32153253 DOI: 10.1080/09537104.2020.1738366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
The dynamics of platelet formation could only be investigated since the development of two-photon microscopy in combination with suitable fluorescent labeling strategies. In this review paper, we give an overview of recent advances in fluorescence imaging of the bone marrow that have contributed to our understanding of platelet biogenesis during the last decade. We make a brief survey through the perspectives and limitations of today's intravital imaging, but also discuss complementary methods that may help to piece together the puzzle of megakaryopoiesis and platelet formation.
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Affiliation(s)
- David Stegner
- Institute of Experimental Biomedicine, University Hospital Würzburg , Würzburg, Germany
| | - Katrin G Heinze
- Rudolf Virchow Center for Experimental Biomedicine, University of Würzburg , Würzburg, Germany
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9
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Liu S, Huh H, Lee SH, Huang F. Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens. Annu Rev Biomed Eng 2020; 22:155-184. [PMID: 32243765 PMCID: PMC7430714 DOI: 10.1146/annurev-bioeng-060418-052203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.
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Affiliation(s)
- Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Hyun Huh
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sang-Hyuk Lee
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA;
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, USA
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10
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Ma H, Liu Y. Super-resolution localization microscopy: Toward high throughput, high quality, and low cost. APL PHOTONICS 2020; 5:060902. [PMID: 34350342 PMCID: PMC8330581 DOI: 10.1063/5.0011731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
After nearly 15 years since its initial debut, super-resolution localization microscopy that surpasses the diffraction-limited resolution barrier of optical microscopy has rapidly gotten out of the ivory tower and entered a new phase to address various challenging biomedical questions. Recent advances in this technology greatly increased the imaging throughput, improved the imaging quality, simplified the sample preparation, and reduced the system cost, making this technology suitable for routine biomedical research. We will provide our perspective on the recent technical advances and their implications in serving the community of biomedical research.
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Affiliation(s)
- Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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11
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Papagiakoumou E, Ronzitti E, Emiliani V. Scanless two-photon excitation with temporal focusing. Nat Methods 2020; 17:571-581. [PMID: 32284609 DOI: 10.1038/s41592-020-0795-y] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 02/28/2020] [Indexed: 11/09/2022]
Abstract
Temporal focusing, with its ability to focus light in time, enables scanless illumination of large surface areas at the sample with micrometer axial confinement and robust propagation through scattering tissue. In conventional two-photon microscopy, widely used for the investigation of intact tissue in live animals, images are formed by point scanning of a spatially focused pulsed laser beam, resulting in limited temporal resolution of the excitation. Replacing point scanning with temporally focused widefield illumination removes this limitation and represents an important milestone in two-photon microscopy. Temporal focusing uses a diffusive or dispersive optical element placed in a plane conjugate to the objective focal plane to generate position-dependent temporal pulse broadening that enables axially confined multiphoton absorption, without the need for tight spatial focusing. Many techniques have benefitted from temporal focusing, including scanless imaging, super-resolution imaging, photolithography, uncaging of caged neurotransmitters and control of neuronal activity via optogenetics.
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Affiliation(s)
- Eirini Papagiakoumou
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France
| | - Emiliano Ronzitti
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France
| | - Valentina Emiliani
- Wavefront-Engineering Microscopy Group, Photonics Department, Institut de la Vision, Sorbonne University, Inserm S968, CNRS UMR7210, Fondation Voir et Entendre, Paris, France.
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12
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Rapid single-wavelength lightsheet localization microscopy for clarified tissue. Nat Commun 2019; 10:4762. [PMID: 31628310 PMCID: PMC6800451 DOI: 10.1038/s41467-019-12715-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 09/27/2019] [Indexed: 02/02/2023] Open
Abstract
Optical super-resolution microscopy allows nanoscale imaging of protein molecules in intact biological tissues. However, it is still challenging to perform large volume super-resolution imaging for entire animal organs. Here we develop a single-wavelength Bessel lightsheet method, optimized for refractive-index matching with clarified specimens to overcome the aberrations encountered in imaging thick tissues. Using spontaneous blinking fluorophores to label proteins of interest, we resolve the morphology of most, if not all, dopaminergic neurons in the whole adult brain (3.64 × 107 µm3) of Drosophila melanogaster at the nanometer scale with high imaging speed (436 µm3 per second) for localization. Quantitative single-molecule localization reveals the subcellular distribution of a monoamine transporter protein in the axons of a single, identified serotonergic Dorsal Paired Medial (DPM) neuron. Large datasets are obtained from imaging one brain per day to provide a robust statistical analysis of these imaging data.
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13
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Hesse L, Bunk K, Leupold J, Speck T, Masselter T. Structural and functional imaging of large and opaque plant specimens. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:3659-3678. [PMID: 31188449 DOI: 10.1093/jxb/erz186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 04/08/2019] [Indexed: 05/20/2023]
Abstract
Three- and four-dimensional imaging techniques are a prerequisite for spatially resolving the form-structure-function relationships in plants. However, choosing the right imaging method is a difficult and time-consuming process as the imaging principles, advantages and limitations, as well as the appropriate fields of application first need to be compared. The present study aims to provide an overview of three imaging methods that allow for imaging opaque, large and thick (>5 mm, up to several centimeters), hierarchically organized plant samples that can have complex geometries. We compare light microscopy of serial thin sections followed by 3D reconstruction (LMTS3D) as an optical imaging technique, micro-computed tomography (µ-CT) based on ionizing radiation, and magnetic resonance imaging (MRI) which uses the natural magnetic properties of a sample for image acquisition. We discuss the most important imaging principles, advantages, and limitations, and suggest fields of application for each imaging technique (LMTS, µ-CT, and MRI) with regard to static (at a given time; 3D) and dynamic (at different time points; quasi 4D) structural and functional plant imaging.
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Affiliation(s)
- Linnea Hesse
- Plant Biomechanics Group and Botanic Garden, University of Freiburg, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Freiburg, Germany
| | - Katharina Bunk
- Plant Biomechanics Group and Botanic Garden, University of Freiburg, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Freiburg, Germany
| | - Jochen Leupold
- Department of Radiology, Medical Physics, Medical Center University of Freiburg, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Speck
- Plant Biomechanics Group and Botanic Garden, University of Freiburg, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Freiburg, Germany
- Cluster of Excellence livMatS @ FIT - Freiburg Center for Interactive Materials and Bioinspired Technologies, University of Freiburg, Germany
| | - Tom Masselter
- Plant Biomechanics Group and Botanic Garden, University of Freiburg, Freiburg, Germany
- Freiburg Center for Interactive Materials and Bioinspired Technologies (FIT), Freiburg, Germany
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14
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15
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Jradi FM, Lavis LD. Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy. ACS Chem Biol 2019; 14:1077-1090. [PMID: 30997987 DOI: 10.1021/acschembio.9b00197] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing "super-resolution" fluorescence microscopy below the diffraction limit of light. The past decade has seen an explosion in not only optical hardware for SMLM but also the development or repurposing of fluorescent proteins and small-molecule fluorescent probes for this technique. In this review, written by chemists for chemists, we detail the history of single-molecule localization microscopy and collate the collection of probes with demonstrated utility in SMLM. We hope it will serve as a primer for probe choice in localization microscopy as well as an inspiration for the development of new fluorophores that enable imaging of biological samples with exquisite detail.
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Affiliation(s)
- Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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16
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Lu CH, Tang WC, Liu YT, Chang SW, Wu FCM, Chen CY, Tsai YC, Yang SM, Kuo CW, Okada Y, Hwu YK, Chen P, Chen BC. Lightsheet localization microscopy enables fast, large-scale, and three-dimensional super-resolution imaging. Commun Biol 2019; 2:177. [PMID: 31098410 PMCID: PMC6509110 DOI: 10.1038/s42003-019-0403-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2018] [Accepted: 03/26/2019] [Indexed: 01/08/2023] Open
Abstract
Recent advances in super-resolution microscopy allow the localization of single molecules within individual cells but not within multiple whole cells due to weak signals from single molecules and slow acquisition process for point accumulation to reconstruct super-resolution images. Here, we report a fast, large-scale, and three-dimensional super-resolution fluorescence microscope based on single-wavelength Bessel lightsheet to selectively illuminate spontaneous blinking fluorophores tagged to the proteins of interest in space. Critical parameters such as labeling density, excitation power, and exposure time were systematically optimized resulting in a maximum imaging speed of 2.7 × 104 µm3 s-1. Fourier ring correlation analysis revealed a reconstructed image with a lateral resolution of ~75 nm through the accumulation of 250 image volumes on immobilized samples within 15 min. Hence, the designed system could open new insights into the discovery of complex biological structures and live 3D localization imaging.
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Affiliation(s)
- Chieh-Han Lu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Wei-Chun Tang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yen-Ting Liu
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Shu-Wei Chang
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | | | - Chin-Yi Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yun-Chi Tsai
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Shun-Min Yang
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan
| | - Chiung-Wen Kuo
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Yasushi Okada
- Laboratory for Cell Polarity Regulation, Center for Biosystems Dynamics Research, RIKEN, Suita, Osaka, 565-0874 Japan
- Department of Physics, Universal Biology Institute and International Research Center for Neurointelligence, The University of Tokyo, Tokyo, 113-0033 Japan
| | - Yeu-Kuang Hwu
- Institute of Physics, Academia Sinica, Taipei, 11529 Taiwan
| | - Peilin Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
| | - Bi-Chang Chen
- Research Center for Applied Sciences, Academia Sinica, Taipei, 11529 Taiwan
- Brain Research Center, National Tsing Hua University, Hsinchu, 30013 Taiwan
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17
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Lin HY, Chu LA, Yang H, Hsu KJ, Lin YY, Lin KH, Chu SW, Chiang AS. Imaging through the Whole Brain of Drosophila at λ/20 Super-resolution. iScience 2019; 14:164-170. [PMID: 30978667 PMCID: PMC6460254 DOI: 10.1016/j.isci.2019.03.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/27/2019] [Accepted: 03/19/2019] [Indexed: 11/26/2022] Open
Abstract
Recently, many super-resolution technologies have been demonstrated, significantly affecting biological studies by observation of cellular structures down to nanometer precision. However, current super-resolution techniques mostly rely on wavefront engineering or wide-field imaging of signal blinking or fluctuation, and thus imaging depths are limited due to tissue scattering or aberration. Here we present a technique that is capable of imaging through an intact Drosophila brain with 20-nm lateral resolution at ∼200 μm depth. The spatial resolution is provided by molecular localization of a photoconvertible fluorescent protein Kaede, whose red form is found to exhibit blinking state. The deep-tissue observation is enabled by optical sectioning of spinning disk microscopy, as well as reduced scattering from optical clearing. Together these techniques are readily available for many biologists, providing three-dimensional resolution of densely entangled dendritic fibers in a complete Drosophila brain. The method paves the way toward whole-brain neural network studies and is applicable to other high-resolution bioimaging.
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Affiliation(s)
- Han-Yuan Lin
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan
| | - Li-An Chu
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Hsuan Yang
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan
| | - Kuo-Jen Hsu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan; Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yen-Yin Lin
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Keng-Hui Lin
- Institute of Physics, Academia Sinica, Taipei 11529, Taiwan.
| | - Shi-Wei Chu
- Department of Physics, National Taiwan University, Taipei 10617, Taiwan; Molecular Imaging Center, National Taiwan University, Taipei 10617, Taiwan.
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of Physics, Academia Sinica, Taipei 11529, Taiwan; Institute of Systems Neuroscience, National Tsing Hua University, Hsinchu 30013, Taiwan; Institute of Molecular and Genomic Medicine, National Health Research Institutes, Zhunan, Miaoli 35053, Taiwan; Kavli Institute for Brain and Mind, University of California, San Diego, La Jolla, CA 92093-0526, USA.
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18
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Sie YD, Chang CY, Lin CY, Chang NS, Campagnola PJ, Chen SJ. Fast and improved bioimaging via temporal focusing multiphoton excitation microscopy with binary digital-micromirror-device holography. JOURNAL OF BIOMEDICAL OPTICS 2018; 23:1-8. [PMID: 30444085 DOI: 10.1117/1.jbo.23.11.116502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Accepted: 10/25/2018] [Indexed: 06/09/2023]
Abstract
Conventional temporal focusing-based multiphoton excitation microscopy (TFMPEM) can offer widefield optical sectioning with an axial excitation confinement of a few microns. To improve the axial confinement of TFMPEM, a binary computer-generated Fourier hologram (CGFH) via a digital-micromirror-device (DMD) was implemented to intrinsically improve the axial confinement by filling the back-focal aperture of the objective lens. Experimental results show that the excitation focal volume can be condensed and the axial confinement improved about 24% according to the DMD holography. In addition, pseudouniform MPE can be achieved using two complementary CGFHs with rapid pulse-width modulation switching via the DMD. Furthermore, bioimaging of CV-1 in origin with SV40 genes-7 cells demonstrates that the TFMPEM with binary DMD holography can improve image quality by enhancing axial excitation confinement and rejecting out-of-focus excitation.
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Affiliation(s)
- Yong Da Sie
- National Cheng Kung University, Department of Engineering Science, Tainan, Taiwan
| | - Chia-Yuan Chang
- National Cheng Kung University, Advanced Optoelectronic Technology Center, Tainan, Taiwan
| | - Chun-Yu Lin
- National Cheng Kung University, Advanced Optoelectronic Technology Center, Tainan, Taiwan
| | - Nan-Shan Chang
- National Cheng Kung University, Institute of Molecular Medicine, Tainan, Taiwan
- SUNY Upstate Medical University, Neuroscience and Physiology, Syracuse, New York, United States
| | - Paul J Campagnola
- University of Wisconsin-Madison, Department of Biomedical Engineering, Madison, Wisconsin, United States
| | - Shean-Jen Chen
- National Chiao Tung University, College of Photonics, Tainan, Taiwan
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19
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Hainsworth AH, Lee S, Foot P, Patel A, Poon WW, Knight AE. Super-resolution imaging of subcortical white matter using stochastic optical reconstruction microscopy (STORM) and super-resolution optical fluctuation imaging (SOFI). Neuropathol Appl Neurobiol 2018; 44:417-426. [PMID: 28696566 PMCID: PMC5835206 DOI: 10.1111/nan.12426] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Revised: 07/06/2017] [Accepted: 07/11/2017] [Indexed: 01/25/2023]
Abstract
AIMS The spatial resolution of light microscopy is limited by the wavelength of visible light (the 'diffraction limit', approximately 250 nm). Resolution of sub-cellular structures, smaller than this limit, is possible with super resolution methods such as stochastic optical reconstruction microscopy (STORM) and super-resolution optical fluctuation imaging (SOFI). We aimed to resolve subcellular structures (axons, myelin sheaths and astrocytic processes) within intact white matter, using STORM and SOFI. METHODS Standard cryostat-cut sections of subcortical white matter from donated human brain tissue and from adult rat and mouse brain were labelled, using standard immunohistochemical markers (neurofilament-H, myelin-associated glycoprotein, glial fibrillary acidic protein, GFAP). Image sequences were processed for STORM (effective pixel size 8-32 nm) and for SOFI (effective pixel size 80 nm). RESULTS In human, rat and mouse, subcortical white matter high-quality images for axonal neurofilaments, myelin sheaths and filamentous astrocytic processes were obtained. In quantitative measurements, STORM consistently underestimated width of axons and astrocyte processes (compared with electron microscopy measurements). SOFI provided more accurate width measurements, though with somewhat lower spatial resolution than STORM. CONCLUSIONS Super resolution imaging of intact cryo-cut human brain tissue is feasible. For quantitation, STORM can under-estimate diameters of thin fluorescent objects. SOFI is more robust. The greatest limitation for super-resolution imaging in brain sections is imposed by sample preparation. We anticipate that improved strategies to reduce autofluorescence and to enhance fluorophore performance will enable rapid expansion of this approach.
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Affiliation(s)
- A H Hainsworth
- Molecular and Clinical Sciences Research Institute, St Georges University of London, London, UK
- Neurology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - S Lee
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - P Foot
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - A Patel
- Cellular Pathology, St George's University Hospitals NHS Foundation Trust, London, UK
| | - W W Poon
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, CA, USA
| | - A E Knight
- National Physical Laboratory, Teddington, UK
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20
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Toda K, Isobe K, Namiki K, Kawano H, Miyawaki A, Midorikawa K. Interferometric temporal focusing microscopy using three-photon excitation fluorescence. BIOMEDICAL OPTICS EXPRESS 2018; 9:1510-1519. [PMID: 29675298 PMCID: PMC5905902 DOI: 10.1364/boe.9.001510] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/06/2018] [Accepted: 02/14/2018] [Indexed: 06/08/2023]
Abstract
Super-resolution microscopy has become a powerful tool for biological research. However, its spatial resolution and imaging depth are limited, largely due to background light. Interferometric temporal focusing (ITF) microscopy, which combines structured illumination microscopy and three-photon excitation fluorescence microscopy, can overcome these limitations. Here, we demonstrate ITF microscopy using three-photon excitation fluorescence, which has a spatial resolution of 106 nm at an imaging depth of 100 µm with an excitation wavelength of 1060 nm.
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Affiliation(s)
- Keisuke Toda
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
| | - Keisuke Isobe
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama, 332-0012, Japan
| | - Kana Namiki
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Hiroyuki Kawano
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Atsushi Miyawaki
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Laboratory for Cell Function Dynamics, RIKEN Brain Science Institute, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumi Midorikawa
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-Okubo, Sakura, Saitama 338-8570, Japan
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21
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Giliberti V, Badioli M, Nucara A, Calvani P, Ritter E, Puskar L, Aziz EF, Hegemann P, Schade U, Ortolani M, Baldassarre L. Heterogeneity of the Transmembrane Protein Conformation in Purple Membranes Identified by Infrared Nanospectroscopy. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2017; 13:1701181. [PMID: 28960799 DOI: 10.1002/smll.201701181] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 08/02/2017] [Indexed: 06/07/2023]
Abstract
Cell membranes are intrinsically heterogeneous, as the local protein and lipid distribution is critical to physiological processes. Even in template systems embedding a single protein type, like purple membranes, there can be a different local response to external stimuli or environmental factors, resulting in heterogeneous conformational changes. Despite the dramatic advances of microspectroscopy techniques, the identification of the conformation heterogeneity is still a challenging task. Tip-enhanced infrared nanospectroscopy is here used to identify conformational changes connected to the hydration state of the transmembrane proteins contained in a 50 nm diameter cell membrane area, without the need for fluorescent labels. In dried purple membrane monolayers, areas with fully hydrated proteins are found among large numbers of molecules with randomly distributed hydration states. Infrared nanospectroscopy results are compared to the spectra obtained with diffraction-limited infrared techniques based on the use of synchrotron radiation, in which the diffraction limit still prevents the observation of nanoscale heterogeneity.
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Affiliation(s)
- Valeria Giliberti
- Istituto Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161, Roma, Italy
| | - Michela Badioli
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Alessandro Nucara
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Paolo Calvani
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Eglof Ritter
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstraße 42, D-10115, Berlin, Germany
| | - Ljiljana Puskar
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Emad Flear Aziz
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Peter Hegemann
- Humboldt-Universität zu Berlin, Institut für Biologie, Invalidenstraße 42, D-10115, Berlin, Germany
| | - Ulrich Schade
- Helmholtz-Zentrum Berlin für Materialien und Energie GmbH, Albert-Einstein-Str. 15, 12489, Berlin, Germany
| | - Michele Ortolani
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
| | - Leonetta Baldassarre
- Istituto Italiano di Tecnologia, Center for Life NanoScience, Viale Regina Elena 291, I-00161, Roma, Italy
- Dipartimento di Fisica, Sapienza Università di Roma, Piazzale Aldo Moro 2, I-00185, Roma, Italy
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22
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von Diezmann A, Shechtman Y, Moerner WE. Three-Dimensional Localization of Single Molecules for Super-Resolution Imaging and Single-Particle Tracking. Chem Rev 2017; 117:7244-7275. [PMID: 28151646 PMCID: PMC5471132 DOI: 10.1021/acs.chemrev.6b00629] [Citation(s) in RCA: 255] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Single-molecule super-resolution fluorescence microscopy and single-particle tracking are two imaging modalities that illuminate the properties of cells and materials on spatial scales down to tens of nanometers or with dynamical information about nanoscale particle motion in the millisecond range, respectively. These methods generally use wide-field microscopes and two-dimensional camera detectors to localize molecules to much higher precision than the diffraction limit. Given the limited total photons available from each single-molecule label, both modalities require careful mathematical analysis and image processing. Much more information can be obtained about the system under study by extending to three-dimensional (3D) single-molecule localization: without this capability, visualization of structures or motions extending in the axial direction can easily be missed or confused, compromising scientific understanding. A variety of methods for obtaining both 3D super-resolution images and 3D tracking information have been devised, each with their own strengths and weaknesses. These include imaging of multiple focal planes, point-spread-function engineering, and interferometric detection. These methods may be compared based on their ability to provide accurate and precise position information on single-molecule emitters with limited photons. To successfully apply and further develop these methods, it is essential to consider many practical concerns, including the effects of optical aberrations, field dependence in the imaging system, fluorophore labeling density, and registration between different color channels. Selected examples of 3D super-resolution imaging and tracking are described for illustration from a variety of biological contexts and with a variety of methods, demonstrating the power of 3D localization for understanding complex systems.
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Affiliation(s)
| | - Yoav Shechtman
- Department of Chemistry, Stanford University, Stanford, CA 94305
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305
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23
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Compans B, Choquet D, Hosy E. Review on the role of AMPA receptor nano-organization and dynamic in the properties of synaptic transmission. NEUROPHOTONICS 2016; 3:041811. [PMID: 27981061 PMCID: PMC5109202 DOI: 10.1117/1.nph.3.4.041811] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 10/19/2016] [Indexed: 06/06/2023]
Abstract
Receptor trafficking and its regulation have appeared in the last two decades to be a major controller of basal synaptic transmission and its activity-dependent plasticity. More recently, considerable advances in super-resolution microscopy have begun deciphering the subdiffraction organization of synaptic elements and their functional roles. In particular, the dynamic nanoscale organization of neurotransmitter receptors in the postsynaptic membrane has recently been suggested to play a major role in various aspects of synapstic function. We here review the recent advances in our understanding of alpha-amino-3-hydroxy-5-méthyl-4-isoxazolepropionic acid subtype glutamate receptors subsynaptic organization and their role in short- and long-term synaptic plasticity.
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Affiliation(s)
- Benjamin Compans
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
| | - Daniel Choquet
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
- University of Bordeaux, Bordeaux Imaging Center, UMS 3420 CNRS, US4 INSERM, France
| | - Eric Hosy
- University of Bordeaux, Interdisciplinary Institute for Neuroscience, UMR 5297, Bordeaux F-33000, France
- Interdisciplinary Institute for Neuroscience, CNRS, UMR 5297, Bordeaux F-33000, France
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24
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Ding Y, Li C. Dual-color multiple-particle tracking at 50-nm localization and over 100-µm range in 3D with temporal focusing two-photon microscopy. BIOMEDICAL OPTICS EXPRESS 2016; 7:4187-4197. [PMID: 27867724 PMCID: PMC5102526 DOI: 10.1364/boe.7.004187] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 09/09/2016] [Accepted: 09/14/2016] [Indexed: 05/12/2023]
Abstract
Nanoscale particle tracking in three dimensions is crucial to directly observe dynamics of molecules and nanoparticles in living cells. Here we present a three-dimensional particle tracking method based on temporally focused two-photon excitation. Multiple particles are imaged at 30 frames/s in volume up to 180 × 180 × 100 µm3. The spatial localization precision can reach 50 nm. We demonstrate its capability of tracking fast swimming microbes at speed of ~200 µm/s. Two-photon dual-color tracking is achieved by simultaneously exciting two kinds of fluorescent beads at 800 nm to demonstrate its potential in molecular interaction studies. Our method provides a simple wide-field fluorescence imaging approach for deep multiple-particle tracking.
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Affiliation(s)
- Yu Ding
- Department of Physics, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
| | - Chunqiang Li
- Department of Physics, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
- Border Biomedical Research Center, The University of Texas at El Paso, 500 W University Avenue, El Paso, TX 79968, USA
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25
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Teshima T, Onoe H, Tottori S, Aonuma H, Mizutani T, Kamiya K, Ishihara H, Kanuka H, Takeuchi S. High-Resolution Vertical Observation of Intracellular Structure Using Magnetically Responsive Microplates. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:3366-3373. [PMID: 27185344 DOI: 10.1002/smll.201600339] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2016] [Revised: 02/09/2016] [Indexed: 06/05/2023]
Abstract
A vertical confocal observation system capable of high-resolution observation of intracellular structure is demonstrated. The system consists of magnet-active microplates to rotate, incline, and translate single adherent cells in the applied magnetic field. Appended to conventional confocal microscopes, this system enables high-resolution cross-sectional imaging with single-molecule sensitivity in single scanning.
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Affiliation(s)
- Tetsuhiko Teshima
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hiroaki Onoe
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Soichiro Tottori
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hiroka Aonuma
- Department of Tropical Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Takeomi Mizutani
- Graduate School of Science, Hokkaido University, Kita 10 Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-0810, Japan
| | - Koki Kamiya
- Kanagawa Academy of Science and Technology, 3-2-1 Sakado, Takatsu-ku, Kawasaki, Kanagawa, 213-0012, Japan
| | - Hirotaka Ishihara
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
| | - Hirotaka Kanuka
- Department of Tropical Medicine, The Jikei University School of Medicine, 3-25-8 Nishi-Shinbashi, Minato-ku, Tokyo, 105-8461, Japan
| | - Shoji Takeuchi
- Institute of Industrial Science, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8505, Japan
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26
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Hernandez O, Papagiakoumou E, Tanese D, Fidelin K, Wyart C, Emiliani V. Three-dimensional spatiotemporal focusing of holographic patterns. Nat Commun 2016; 7:11928. [PMID: 27306044 PMCID: PMC4912686 DOI: 10.1038/ncomms11928] [Citation(s) in RCA: 73] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Accepted: 05/12/2016] [Indexed: 12/11/2022] Open
Abstract
Two-photon excitation with temporally focused pulses can be combined with phase-modulation approaches, such as computer-generated holography and generalized phase contrast, to efficiently distribute light into two-dimensional, axially confined, user-defined shapes. Adding lens-phase modulations to 2D-phase holograms enables remote axial pattern displacement as well as simultaneous pattern generation in multiple distinct planes. However, the axial confinement linearly degrades with lateral shape area in previous reports where axially shifted holographic shapes were not temporally focused. Here we report an optical system using two spatial light modulators to independently control transverse- and axial-target light distribution. This approach enables simultaneous axial translation of single or multiple spatiotemporally focused patterns across the sample volume while achieving the axial confinement of temporal focusing. We use the system's capability to photoconvert tens of Kaede-expressing neurons with single-cell resolution in live zebrafish larvae. Three-dimensional computer-generated holography cannot be implemented with temporal focusing. Here, Hernandez et al. use two spatial light modulators to control transverse- and axial-target light distribution, generating spatiotemporally focused patterns with uniform light distribution throughout the entire volume.
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Affiliation(s)
- Oscar Hernandez
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, CNRS UMR 8250, Paris Descartes University, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Eirini Papagiakoumou
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, CNRS UMR 8250, Paris Descartes University, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France.,Institut national de la santé et de la recherche médicale (Inserm), France
| | - Dimitrii Tanese
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, CNRS UMR 8250, Paris Descartes University, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
| | - Kevin Fidelin
- Institut du Cerveau et de la Moelle Épinière, UPMC, Inserm UMR S975, CNRS UMR 7225, Campus Hospitalier Pitié Salpêtrière, 47 building de l'Hôpital, 75013 Paris, France
| | - Claire Wyart
- Institut du Cerveau et de la Moelle Épinière, UPMC, Inserm UMR S975, CNRS UMR 7225, Campus Hospitalier Pitié Salpêtrière, 47 building de l'Hôpital, 75013 Paris, France
| | - Valentina Emiliani
- Wavefront-Engineering Microscopy Group, Neurophotonics Laboratory, CNRS UMR 8250, Paris Descartes University, UFR Biomédicale, 45 rue des Saints-Pères, 75270 Paris Cedex 06, France
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27
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Sergé A. The Molecular Architecture of Cell Adhesion: Dynamic Remodeling Revealed by Videonanoscopy. Front Cell Dev Biol 2016; 4:36. [PMID: 27200348 PMCID: PMC4854873 DOI: 10.3389/fcell.2016.00036] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 04/18/2016] [Indexed: 12/20/2022] Open
Abstract
The plasma membrane delimits the cell, which is the basic unit of living organisms, and is also a privileged site for cell communication with the environment. Cell adhesion can occur through cell-cell and cell-matrix contacts. Adhesion proteins such as integrins and cadherins also constitute receptors for inside-out and outside-in signaling within proteolipidic platforms. Adhesion molecule targeting and stabilization relies on specific features such as preferential segregation by the sub-membrane cytoskeleton meshwork and within membrane proteolipidic microdomains. This review presents an overview of the recent insights brought by the latest developments in microscopy, to unravel the molecular remodeling occurring at cell contacts. The dynamic aspect of cell adhesion was recently highlighted by super-resolution videomicroscopy, also named videonanoscopy. By circumventing the diffraction limit of light, nanoscopy has allowed the monitoring of molecular localization and behavior at the single-molecule level, on fixed and living cells. Accessing molecular-resolution details such as quantitatively monitoring components entering and leaving cell contacts by lateral diffusion and reversible association has revealed an unexpected plasticity. Adhesion structures can be highly specialized, such as focal adhesion in motile cells, as well as immune and neuronal synapses. Spatiotemporal reorganization of adhesion molecules, receptors, and adaptors directly relates to structure/function modulation. Assembly of these supramolecular complexes is continuously balanced by dynamic events, remodeling adhesions on various timescales, notably by molecular conformation switches, lateral diffusion within the membrane and endo/exocytosis. Pathological alterations in cell adhesion are involved in cancer evolution, through cancer stem cell interaction with stromal niches, growth, extravasation, and metastasis.
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Affiliation(s)
- Arnauld Sergé
- Centre de Cancérologie de Marseille, Équipe "Interactions Leuco/Stromales", Institut Paoli-Calmettes, Institut National de la Santé et de la Recherche Médicale U1068, Centre National de la Recherche Scientifique UMR7258, Aix-Marseille Université UM105 Marseille, France
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Axial superresolution via multiangle TIRF microscopy with sequential imaging and photobleaching. Proc Natl Acad Sci U S A 2016; 113:4368-73. [PMID: 27044072 DOI: 10.1073/pnas.1516715113] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report superresolution optical sectioning using a multiangle total internal reflection fluorescence (TIRF) microscope. TIRF images were constructed from several layers within a normal TIRF excitation zone by sequentially imaging and photobleaching the fluorescent molecules. The depth of the evanescent wave at different layers was altered by tuning the excitation light incident angle. The angle was tuned from the highest (the smallest TIRF depth) toward the critical angle (the largest TIRF depth) to preferentially photobleach fluorescence from the lower layers and allow straightforward observation of deeper structures without masking by the brighter signals closer to the coverglass. Reconstruction of the TIRF images enabled 3D imaging of biological samples with 20-nm axial resolution. Two-color imaging of epidermal growth factor (EGF) ligand and clathrin revealed the dynamics of EGF-activated clathrin-mediated endocytosis during internalization. Furthermore, Bayesian analysis of images collected during the photobleaching step of each plane enabled lateral superresolution (<100 nm) within each of the sections.
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29
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Two-photon excited photoconversion of cyanine-based dyes. Sci Rep 2016; 6:23866. [PMID: 27029524 PMCID: PMC4814926 DOI: 10.1038/srep23866] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 03/15/2016] [Indexed: 12/02/2022] Open
Abstract
The advent of phototransformable fluorescent proteins has led to significant advances in optical imaging, including the unambiguous tracking of cells over large spatiotemporal scales. However, these proteins typically require activating light in the UV-blue spectrum, which limits their in vivo applicability due to poor light penetration and associated phototoxicity on cells and tissue. We report that cyanine-based, organic dyes can be efficiently photoconverted by nonlinear excitation at the near infrared (NIR) window. Photoconversion likely involves singlet-oxygen mediated photochemical cleavage, yielding blue-shifted fluorescent products. Using SYTO62, a biocompatible and cell-permeable dye, we demonstrate photoconversion in a variety of cell lines, including depth-resolved labeling of cells in 3D culture. Two-photon photoconversion of cyanine-based dyes offer several advantages over existing photoconvertible proteins, including use of minimally toxic NIR light, labeling without need for genetic intervention, rapid kinetics, remote subsurface targeting, and long persistence of photoconverted signal. These findings are expected to be useful for applications involving rapid labeling of cells deep in tissue.
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30
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High-density three-dimensional localization microscopy across large volumes. Nat Methods 2016; 13:359-65. [PMID: 26950745 PMCID: PMC4889433 DOI: 10.1038/nmeth.3797] [Citation(s) in RCA: 185] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2015] [Accepted: 01/28/2016] [Indexed: 12/18/2022]
Abstract
Extending three-dimensional (3D) single molecule localization microscopy away from the coverslip and into thicker specimens will greatly broaden its biological utility. However, localizing molecules in 3D with high precision in such samples, while simultaneously achieving the extreme labeling densities required for high resolution of densely crowded structures is challenging due to the limitations both of conventional imaging modalities and of conventional labeling techniques. Here, we combine lattice light sheet microscopy with newly developed, freely diffusing, cell permeable chemical probes with targeted affinity towards either DNA, intracellular membranes, or the plasma membrane. We use this combination to perform high localization precision, ultra-high labeling density, multicolor localization microscopy in samples up to 20 microns thick, including dividing cells and the neuromast organ of a zebrafish embryo. We also demonstrate super-resolution correlative imaging with protein specific photoactivable fluorophores, providing a mutually compatible, single platform alternative to correlative light-electron microscopy over large volumes.
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31
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Spesyvtsev R, Rendall HA, Dholakia K. Wide-field three-dimensional optical imaging using temporal focusing for holographically trapped microparticles. OPTICS LETTERS 2015; 40:4847-50. [PMID: 26512465 DOI: 10.1364/ol.40.004847] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
A contemporary challenge across the natural sciences is the simultaneous optical imaging or stimulation of small numbers of cells or colloidal particles organized into arbitrary geometries. We demonstrate the use of temporal focusing with holographic optical tweezers in order to achieve depth-resolved two-photon imaging of trapped objects arranged in arbitrary three-dimensional (3D) geometries using a single objective. Trapping allows for the independent position control of multiple objects by holographic beam shaping. Temporal focusing of ultrashort pulses provides the wide-field two-photon depth-selective activation of fluorescent samples. We demonstrate the wide-field depth-resolved illumination of both trapped fluorescent beads and trapped HL60 cells in suspension with full 3D positioning control. These approaches are compatible with implementation through scattering media and can be beneficial for emergent studies in colloidal science and particularly optogenetics, offering targeted photoactivation over a wide area with micrometer-precision depth control.
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32
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Dong B, Yang X, Zhu S, Bassham DC, Fang N. Stochastic Optical Reconstruction Microscopy Imaging of Microtubule Arrays in Intact Arabidopsis thaliana Seedling Roots. Sci Rep 2015; 5:15694. [PMID: 26503365 PMCID: PMC4621606 DOI: 10.1038/srep15694] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 09/30/2015] [Indexed: 12/19/2022] Open
Abstract
Super-resolution fluorescence microscopy has generated tremendous success in revealing detailed subcellular structures in animal cells. However, its application to plant cell biology remains extremely limited due to numerous technical challenges, including the generally high fluorescence background of plant cells and the presence of the cell wall. In the current study, stochastic optical reconstruction microscopy (STORM) imaging of intact Arabidopsis thaliana seedling roots with a spatial resolution of 20-40 nm was demonstrated. Using the super-resolution images, the spatial organization of cortical microtubules in different parts of a whole Arabidopsis root tip was analyzed quantitatively, and the results show the dramatic differences in the density and spatial organization of cortical microtubules in cells of different differentiation stages or types. The method developed can be applied to plant cell biological processes, including imaging of additional elements of the cytoskeleton, organelle substructure, and membrane domains.
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Affiliation(s)
- Bin Dong
- Ames Laboratory, US Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Xiaochen Yang
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
| | - Shaobin Zhu
- Ames Laboratory, US Department of Energy and Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Diane C. Bassham
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011
- Plant Sciences Institute, Iowa State University, Ames, Iowa 50011
| | - Ning Fang
- Department of Chemistry, Georgia State University, P.O. Box 3965, Atlanta, Georgia 30302
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33
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Song Q, Nakamura A, Hirosawa K, Isobe K, Midorikawa K, Kannari F. Two-dimensional spatiotemporal focusing of femtosecond pulses and its applications in microscopy. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2015; 86:083701. [PMID: 26329197 DOI: 10.1063/1.4927532] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We demonstrate and theoretically analyze the two-dimensional spatiotemporal focusing of femtosecond pulses by utilizing a two-dimensional spectral disperser. Compared with spatiotemporal focusing with a diffraction grating, it can achieve widefield illumination with better sectioning ability for a multiphoton excitation process. By utilizing paraxial approximation, our analytical method improves the axial confinement ability and identifies that the free spectra range (FSR) of the two-dimensional spectral disperser affects the out-of-focus multiphoton excitation intensity due to the temporal self-imaging effect. Based on our numerical simulation, a FSR of 50 GHz is necessary to reduce the out-of-focus two-photon excitation by 2 orders of magnitude compared with that in a grating-based spatiotemporal focusing scheme for a 90-fs excitation laser pulse. We build a two-dimensional spatiotemporal focusing microscope using a virtually imaged phased array and achieve an axial resolution of 1.3 μm, which outperforms the resolution of conventional spatiotemporal focusing using a grating by a factor of 1.7, and demonstrate better image contrast inside a tissue-like phantom.
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Affiliation(s)
- Qiyuan Song
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Aoi Nakamura
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Kenichi Hirosawa
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
| | - Keisuke Isobe
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Katsumi Midorikawa
- RIKEN Center for Advanced Photonics, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Fumihiko Kannari
- Department of Electronics and Electrical Engineering, Keio University, 3-14-1 Hiyoshi, Kohoku-ku, Yokohama 223-8522, Japan
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34
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Cattoni DI, Valeri A, Le Gall A, Nollmann M. A matter of scale: how emerging technologies are redefining our view of chromosome architecture. Trends Genet 2015; 31:454-64. [PMID: 26113398 DOI: 10.1016/j.tig.2015.05.011] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/21/2015] [Accepted: 05/22/2015] [Indexed: 11/25/2022]
Abstract
The 3D folding of the genome and its relation to fundamental processes such as gene regulation, replication, and segregation remains one of the most puzzling and exciting questions in genetics. In this review, we describe how the use of new technologies is starting to revolutionize the field of chromosome organization, and to shed light on the mechanisms of transcription, replication, and repair. In particular, we concentrate on recent studies using genome-wide methods, single-molecule technologies, and super-resolution microscopy (SRM). We summarize some of the main concerns when employing these techniques, and discuss potential new and exciting perspectives that illuminate the connection between 3D genomic organization and gene regulation.
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Affiliation(s)
- Diego I Cattoni
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Alessandro Valeri
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Antoine Le Gall
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France
| | - Marcelo Nollmann
- Centre de Biochimie Structurale, CNRS UMR5048, INSERM U1054, Université de Montpellier, 29 rue de Navacelles, 34090 Montpellier, France.
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35
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Baránek M, Bouchal P, Šiler M, Bouchal Z. Aberration resistant axial localization using a self-imaging of vortices. OPTICS EXPRESS 2015; 23:15316-15331. [PMID: 26193512 DOI: 10.1364/oe.23.015316] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The vortex self-imaging (SI) implemented in optical imaging systems and its usage for a robust axial localization of point-like objects are presented. The vortex SI is used to generate a double-helix point spread function (DH PSF) maintaining its shape and size unchanged in a large working area. The robustness of the axial localization is demonstrated by a resistance against the spherical aberration. Using a thorough analysis, the experiments are optimized to achieve the highest localization sensitivity and to find a trade-off between the aberration stability of the DH PSF, the length of the localization range and the energy efficiency. The benefits of the method are achieved by applying the SI of nondiffracting vortices prepared by a spatial light modulator (SLM). The feasibility of the proposed technique is demonstrated by a defocusing induced rotation of the fixed and moving 1μm polystyrene beads, carried out in the transmitted light illumination.
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36
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Hajj B, El Beheiry M, Izeddin I, Darzacq X, Dahan M. Accessing the third dimension in localization-based super-resolution microscopy. Phys Chem Chem Phys 2015; 16:16340-8. [PMID: 24901106 DOI: 10.1039/c4cp01380h] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Only a few years after its inception, localization-based super-resolution microscopy has become widely employed in biological studies. Yet, it is primarily used in two-dimensional imaging and accessing the organization of cellular structures at the nanoscale in three dimensions (3D) still poses important challenges. Here, we review optical and computational techniques that enable the 3D localization of individual emitters and the reconstruction of 3D super-resolution images. These techniques are grouped into three main categories: PSF engineering, multiple plane imaging and interferometric approaches. We provide an overview of their technical implementation as well as commentary on their applicability. Finally, we discuss future trends in 3D localization-based super-resolution microscopy.
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Affiliation(s)
- Bassam Hajj
- Laboratoire Physico-Chimie Curie, Institut Curie, CNRS UMR 168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris, France.
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37
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Abstract
Axial localization of multiphoton excitation to a single plane is achieved by temporal focusing of an ultrafast pulsed excitation. We take advantage of geometrical dispersion in an extremely simple experimental setup, where an ultrashort pulse is temporally stretched and hence its peak intensity is lowered outside the focal plane of the microscope. Using this strategy, out-of-focus multiphoton excitation is dramatically reduced, and the achieved axial resolution is comparable to line-scanning multiphoton microscopy for wide-field excitation and to point-scanning multiphoton microscopy for line excitation. In this introduction, we provide a detailed description of the considerations in choosing the experimental parameters, as well as the alignment of a temporal focusing add-on to a multiphoton microscope. We also review current advances and applications for this technique.
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38
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Lin CY, Li PK, Cheng LC, Li YC, Chang CY, Chiang AS, Dong CY, Chen SJ. High-throughput multiphoton-induced three-dimensional ablation and imaging for biotissues. BIOMEDICAL OPTICS EXPRESS 2015; 6:491-9. [PMID: 25780739 PMCID: PMC4354595 DOI: 10.1364/boe.6.000491] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2014] [Revised: 12/22/2014] [Accepted: 12/22/2014] [Indexed: 05/23/2023]
Abstract
In this study, a temporal focusing-based high-throughput multiphoton-induced ablation system with axially-resolved widefield multiphoton excitation has been successfully applied to rapidly disrupt biotissues. Experimental results demonstrate that this technique features high efficiency for achieving large-area laser ablation without causing serious photothermal damage in non-ablated regions. Furthermore, the rate of tissue processing can reach around 1.6 × 10(6) μm(3)/s in chicken tendon. Moreover, the temporal focusing-based multiphoton system can be efficiently utilized in optical imaging through iterating high-throughput multiphoton-induced ablation machining followed by widefield optical sectioning; hence, it has the potential to obtain molecular images for a whole bio-specimen.
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Affiliation(s)
- Chun-Yu Lin
- Department of Engineering Science, National Cheng Kung University, Tainan 701,
Taiwan
| | - Pei-Kao Li
- Department of Engineering Science, National Cheng Kung University, Tainan 701,
Taiwan
| | - Li-Chung Cheng
- Department of Photonics, National Cheng Kung University, Tainan 701,
Taiwan
| | - Yi-Cheng Li
- Department of Photonics, National Cheng Kung University, Tainan 701,
Taiwan
| | - Chia-Yuan Chang
- Department of Photonics, National Cheng Kung University, Tainan 701,
Taiwan
| | - Ann-Shyn Chiang
- Brain Research Center, National Tsing Hua University, Hsinchu 300,
Taiwan
- Institute of Biotechnology and Department of Life Science, National Tsing Hua University, Hsinchu 300,
Taiwan
| | - Chen Yuan Dong
- Department of Physics, National Taiwan University, Taipei 106,
Taiwan
| | - Shean-Jen Chen
- Department of Engineering Science, National Cheng Kung University, Tainan 701,
Taiwan
- Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701,
Taiwan
- Advanced Optoelectronic Technology Center, National Cheng Kung University, Tainan 701,
Taiwan
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39
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Whole-cell, multicolor superresolution imaging using volumetric multifocus microscopy. Proc Natl Acad Sci U S A 2014; 111:17480-5. [PMID: 25422417 DOI: 10.1073/pnas.1412396111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Single molecule-based superresolution imaging has become an essential tool in modern cell biology. Because of the limited depth of field of optical imaging systems, one of the major challenges in superresolution imaging resides in capturing the 3D nanoscale morphology of the whole cell. Despite many previous attempts to extend the application of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) techniques into three dimensions, effective localization depths do not typically exceed 1.2 µm. Thus, 3D imaging of whole cells (or even large organelles) still demands sequential acquisition at different axial positions and, therefore, suffers from the combined effects of out-of-focus molecule activation (increased background) and bleaching (loss of detections). Here, we present the use of multifocus microscopy for volumetric multicolor superresolution imaging. By simultaneously imaging nine different focal planes, the multifocus microscope instantaneously captures the distribution of single molecules (either fluorescent proteins or synthetic dyes) throughout an ∼ 4-µm-deep volume, with lateral and axial localization precisions of ∼ 20 and 50 nm, respectively. The capabilities of multifocus microscopy to rapidly image the 3D organization of intracellular structures are illustrated by superresolution imaging of the mammalian mitochondrial network and yeast microtubules during cell division.
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40
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So PTC, Yew EYS, Rowlands C. High-throughput nonlinear optical microscopy. Biophys J 2014; 105:2641-54. [PMID: 24359736 DOI: 10.1016/j.bpj.2013.08.051] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2013] [Revised: 08/19/2013] [Accepted: 08/22/2013] [Indexed: 01/06/2023] Open
Abstract
High-resolution microscopy methods based on different nonlinear optical (NLO) contrast mechanisms are finding numerous applications in biology and medicine. While the basic implementations of these microscopy methods are relatively mature, an important direction of continuing technological innovation lies in improving the throughput of these systems. Throughput improvement is expected to be important for studying fast kinetic processes, for enabling clinical diagnosis and treatment, and for extending the field of image informatics. This review will provide an overview of the fundamental limitations on NLO microscopy throughput. We will further cover several important classes of high-throughput NLO microscope designs with discussions on their strengths and weaknesses and their key biomedical applications. Finally, this review will close with a perspective of potential future technological improvements in this field.
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Affiliation(s)
- Peter T C So
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts; Laser Biomedical Research Center, Massachusetts Institute of Technology, Cambridge, Massachusetts; BioSyM Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore.
| | - Elijah Y S Yew
- BioSyM Interdisciplinary Research Group, Singapore-MIT Alliance for Research and Technology, Singapore, Singapore
| | - Christopher Rowlands
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts; Laser Biomedical Research Center, Massachusetts Institute of Technology, Cambridge, Massachusetts
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41
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Li YC, Yeh TF, Huang HC, Chang HY, Lin CY, Cheng LC, Chang CY, Teng H, Chen SJ. Graphene oxide-based micropatterns via high-throughput multiphoton-induced reduction and ablation. OPTICS EXPRESS 2014; 22:19726-34. [PMID: 25321055 DOI: 10.1364/oe.22.019726] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
In this study, a developed temporal focusing-based femtosecond laser system provides high-throughput multiphoton-induced reduction and ablation of graphene oxide (GO) films. Integrated with a digital micromirror device to locally control the laser pulse numbers, GO-based micropatterns can be quickly achieved instantly. Furthermore, the degree of reduction and ablation can be precisely adjusted via controlling the laser wavelength, power, and pulse number. Compared to point-by-point scanning laser direct writing, this approach offers a high-throughput and multiple-function approach to accomplish a large area of micro-scale patterns on GO films. The high-throughput micropatterning of GO via the temporal focusing-based femtosecond laser system fulfills the requirement of mass production for GO-based applications in microelectronic devices.
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42
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Cheng LC, Lien CH, Da Sie Y, Hu YY, Lin CY, Chien FC, Xu C, Dong CY, Chen SJ. Nonlinear structured-illumination enhanced temporal focusing multiphoton excitation microscopy with a digital micromirror device. BIOMEDICAL OPTICS EXPRESS 2014; 5:2526-36. [PMID: 25136483 PMCID: PMC4132986 DOI: 10.1364/boe.5.002526] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/18/2014] [Accepted: 07/03/2014] [Indexed: 05/18/2023]
Abstract
In this study, the light diffraction of temporal focusing multiphoton excitation microscopy (TFMPEM) and the excitation patterning of nonlinear structured-illumination microscopy (NSIM) can be simultaneously and accurately implemented via a single high-resolution digital micromirror device. The lateral and axial spatial resolutions of the TFMPEM are remarkably improved through the second-order NSIM and projected structured light, respectively. The experimental results demonstrate that the lateral and axial resolutions are enhanced from 397 nm to 168 nm (2.4-fold) and from 2.33 μm to 1.22 μm (1.9-fold), respectively, in full width at the half maximum. Furthermore, a three-dimensionally rendered image of a cytoskeleton cell featuring ~25 nm microtubules is improved, with other microtubules at a distance near the lateral resolution of 168 nm also able to be distinguished.
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Affiliation(s)
- Li-Chung Cheng
- Department of Photonics, National Cheng Kung University, Tainan 701, Taiwan
| | - Chi-Hsiang Lien
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Yong Da Sie
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Yvonne Yuling Hu
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Chun-Yu Lin
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
| | - Fan-Ching Chien
- Department of Optics and Photonics, National Central University, Jhongli 320, Taiwan
| | - Chris Xu
- School of Applied and Engineering Physics, Cornell University, Ithaca, NY 14853, USA
| | - Chen Yuan Dong
- Department of Physics, National Taiwan University, Taipei 106, Taiwan
| | - Shean-Jen Chen
- Department of Engineering Science, National Cheng Kung University, Tainan 701, Taiwan
- Advanced Optoelectronic Technology Center, National Cheng Kung University, Tainan 701, Taiwan
- Center for Micro/Nano Science and Technology, National Cheng Kung University, Tainan 701, Taiwan
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43
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Hybrid multiphoton volumetric functional imaging of large-scale bioengineered neuronal networks. Nat Commun 2014; 5:3997. [PMID: 24898000 PMCID: PMC4113029 DOI: 10.1038/ncomms4997] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2013] [Accepted: 04/29/2014] [Indexed: 01/07/2023] Open
Abstract
Planar neural networks and interfaces serve as versatile in vitro models of central nervous system physiology, but adaptations of related methods to three dimensions (3D) have met with limited success. Here, we demonstrate for the first time volumetric functional imaging in a bio-engineered neural tissue growing in a transparent hydrogel with cortical cellular and synaptic densities, by introducing complementary new developments in nonlinear microscopy and neural tissue engineering. Our system uses a novel hybrid multiphoton microscope design combining a 3D scanning-line temporal-focusing subsystem and a conventional laser-scanning multiphoton microscope to provide functional and structural volumetric imaging capabilities: dense microscopic 3D sampling at tens of volumes/sec of structures with mm-scale dimensions containing a network of over 1000 developing cells with complex spontaneous activity patterns. These developments open new opportunities for large-scale neuronal interfacing and for applications of 3D engineered networks ranging from basic neuroscience to the screening of neuroactive substances.
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44
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Yih JN, Hu YY, Sie YD, Cheng LC, Lien CH, Chen SJ. Temporal focusing-based multiphoton excitation microscopy via digital micromirror device. OPTICS LETTERS 2014; 39:3134-3137. [PMID: 24875995 DOI: 10.1364/ol.39.003134] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
This Letter presents an enhanced temporal focusing-based multiphoton excitation (MPE) microscope in which the conventional diffraction grating is replaced by a digital micromirror device (DMD). Experimental results from imaging a thin fluorescence film show that the 4.0 μm axial resolution of the microscope is comparable with that of a setup incorporating a 600 lines/mm grating; hence, the optical sectioning ability of the proposed setup is demonstrated. Similar to a grating, the DMD diffracts illuminating light frequencies for temporal focusing; additionally, it generates arbitrary patterns. Since the DMD is placed on the image-conjugate plane of the objective lens' focal plane, the MPE pattern can be projected on the focal plane precisely.
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45
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Allen JR, Ross ST, Davidson MW. Sample preparation for single molecule localization microscopy. Phys Chem Chem Phys 2014; 15:18771-83. [PMID: 24084850 DOI: 10.1039/c3cp53719f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Single molecule localization-based optical nanoscopy was introduced in 2006, surpassing traditional diffraction-limited resolutions by an order of magnitude. Seven years later, this superresolution technique is continuing to follow a trend of increasing popularity and pervasiveness, with the proof-of-concept work long finished and commercial implementations now available. However one important aspect that tends to become lost in translation is the importance of proper sample preparation, with very few resources addressing the considerations that must be made when preparing samples for imaging with single molecule level sensitivity. Presented here is a an in-depth analysis of all aspects of sample preparation for single molecule superresolution, including both live and fixed cell preparation, choice of fluorophore, fixation and staining techniques, and imaging buffer considerations.
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Affiliation(s)
- John R Allen
- National High Magnetic Field Laboratory and Department of Biological Science, The Florida State University, 1800 East Paul Dirac Drive, Tallahassee, 32304, Florida, USA.
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Hartwich TMP, Subach FV, Cooley L, Verkhusha VV, Bewersdorf J. Determination of two-photon photoactivation rates of fluorescent proteins. Phys Chem Chem Phys 2014; 15:14868-72. [PMID: 23852136 DOI: 10.1039/c3cp51035b] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
The application of two-photon activation of photoactivatable fluorescent proteins is limited by a lack of information about two-photon activation rates. Here we present rates for the commonly used photoactivatable proteins PAmCherry, PAmKate and PA-GFP at different wavelengths using a novel method that allows us to determine the two-photon activation rates directly, independent of any reference data, with microscopic sample volumes. We show that PAmCherry features the highest rates of the tested proteins at 700 nm activation wavelength followed by PAmKate. Towards longer wavelengths, two-photon activation rates decrease for all three proteins. For PAmCherry, our data contradicts an activation model relying solely on two-photon activation and suggests additional activation pathways requiring at least two absorption steps. Our method is readily expandable to other photoactivatable fluorescent molecules. The presented results allow optimization of experimental conditions in spectroscopic and imaging techniques such as super-resolution fluorescence microscopy.
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Affiliation(s)
- Tobias M P Hartwich
- Department of Cell Biology, Yale School of Medicine, New Haven, CT 06520, USA
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Sun B, Salter PS, Booth MJ. Effects of aberrations in spatiotemporal focusing of ultrashort laser pulses. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2014; 31:765-72. [PMID: 24695138 DOI: 10.1364/josaa.31.000765] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Spatiotemporal focusing, or simultaneous spatial and temporal focusing (SSTF), has already been adopted for various applications in microscopy, photoactivation for biological studies, and laser fabrication. We investigate the effects of aberrations on focus formation in SSTF, in particular, the effects of phase aberrations related to low-order Zernike modes and a refractive index mismatch between the immersion medium and sample. By considering a line focus, we are able to draw direct comparison between the performance of SSTF and conventional spatial focusing (SF). Wide-field SSTF is also investigated and is found to be much more robust to aberrations than either line SSTF or SF. These results show the sensitivity of certain focusing methods to specific aberrations, and can inform on the necessity and benefit of aberration correction.
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Leshem B, Hernandez O, Papagiakoumou E, Emiliani V, Oron D. When can temporally focused excitation be axially shifted by dispersion? OPTICS EXPRESS 2014; 22:7087-7098. [PMID: 24664057 DOI: 10.1364/oe.22.007087] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
Temporal focusing (TF) allows for axially confined wide-field multi-photon excitation at the temporal focal plane. For temporally focused Gaussian beams, it was shown both theoretically and experimentally that the temporal focus plane can be shifted by applying a quadratic spectral phase to the incident beam. However, the case for more complex wave-fronts is quite different. Here we study the temporal focus plane shift (TFS) for a broader class of excitation profiles, with particular emphasis on the case of temporally focused computer generated holography (CGH) which allows for generation of arbitrary, yet speckled, 2D patterns. We present an analytical, numerical and experimental study of this phenomenon. The TFS is found to depend mainly on the autocorrelation of the CGH pattern in the direction of the beam dispersion after the grating in the TF setup. This provides a pathway for 3D control of multi-photon excitation patterns.
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49
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Fluorescence microscopy gets faster and clearer: roles of photochemistry and selective illumination. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2014; 87:21-32. [PMID: 24600334 PMCID: PMC3941456] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Significant advances in fluorescence microscopy tend be a balance between two competing qualities wherein improvements in resolution and low light detection are typically accompanied by losses in acquisition rate and signal-to-noise, respectively. These trade-offs are becoming less of a barrier to biomedical research as recent advances in optoelectronic microscopy and developments in fluorophore chemistry have enabled scientists to see beyond the diffraction barrier, image deeper into live specimens, and acquire images at unprecedented speed. Selective plane illumination microscopy has provided significant gains in the spatial and temporal acquisition of fluorescence specimens several mm in thickness. With commercial systems now available, this method promises to expand on recent advances in 2-photon deep-tissue imaging with improved speed and reduced photobleaching compared to laser scanning confocal microscopy. Superresolution microscopes are also available in several modalities and can be coupled with selective plane illumination techniques. The combination of methods to increase resolution, acquisition speed, and depth of collection are now being married to common microscope systems, enabling scientists to make significant advances in live cell and in situ imaging in real time. We show that light sheet microscopy provides significant advantages for imaging live zebrafish embryos compared to laser scanning confocal microscopy.
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Hedde PN, Nienhaus GU. Super-resolution localization microscopy with photoactivatable fluorescent marker proteins. PROTOPLASMA 2014; 251:349-62. [PMID: 24162869 DOI: 10.1007/s00709-013-0566-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2013] [Accepted: 10/08/2013] [Indexed: 05/02/2023]
Abstract
Fluorescent proteins (FPs) have become popular imaging tools because of their high specificity, minimal invasive labeling and allowing visualization of proteins and structures inside living organisms. FPs are genetically encoded and expressed in living cells, therefore, labeling involves minimal effort in comparison to approaches involving synthetic dyes. Photoactivatable FPs (paFPs) comprise a subclass of FPs that can change their absorption/emission properties such as brightness and color upon irradiation. This methodology has found a broad range of applications in the life sciences, especially in localization-based super-resolution microscopy of cells, tissues and even entire organisms. In this review, we discuss recent developments and applications of paFPs in super-resolution localization imaging.
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Affiliation(s)
- Per Niklas Hedde
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), 76128, Karlsruhe, Germany
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