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Zeaiter L, Dabbous A, Baldini F, Pagano A, Bianchini P, Vergani L, Diaspro A. Unveiling nuclear chromatin distribution using IsoConcentraChromJ: A flourescence imaging plugin for IsoRegional and IsoVolumetric based ratios analysis. PLoS One 2024; 19:e0305809. [PMID: 38954704 PMCID: PMC11218964 DOI: 10.1371/journal.pone.0305809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 06/05/2024] [Indexed: 07/04/2024] Open
Abstract
Chromatin exhibits non-random distribution within the nucleus being arranged into discrete domains that are spatially organized throughout the nuclear space. Both the spatial distribution and structural rearrangement of chromatin domains in the nucleus depend on epigenetic modifications of DNA and/or histones and structural elements such as the nuclear envelope. These components collectively contribute to the organization and rearrangement of chromatin domains, thereby influencing genome architecture and functional regulation. This study develops an innovative, user-friendly, ImageJ-based plugin, called IsoConcentraChromJ, aimed quantitatively delineating the spatial distribution of chromatin regions in concentric patterns. The IsoConcentraChromJ can be applied to quantitative chromatin analysis in both two- and three-dimensional spaces. After DNA and histone staining with fluorescent probes, high-resolution images of nuclei have been obtained using advanced fluorescence microscopy approaches, including confocal and stimulated emission depletion (STED) microscopy. IsoConcentraChromJ workflow comprises the following sequential steps: nucleus segmentation, thresholding, masking, normalization, and trisection with specified ratios for either 2D or 3D acquisitions. The effectiveness of the IsoConcentraChromJ has been validated and demonstrated using experimental datasets consisting in nuclei images of pre-adipocytes and mature adipocytes, encompassing both 2D and 3D imaging. The outcomes allow to characterize the nuclear architecture by calculating the ratios between specific concentric nuclear areas/volumes of acetylated chromatin with respect to total acetylated chromatin and/or total DNA. The novel IsoConcentrapChromJ plugin could represent a valuable resource for researchers investigating the rearrangement of chromatin architecture driven by epigenetic mechanisms using nuclear images obtained by different fluorescence microscopy methods.
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Affiliation(s)
- Lama Zeaiter
- Department for the Earth, Environment and Life Sciences, University of Genoa, Genova, Italy
- Nanoscopy, Istituto Italiano Tecnologia, Genoa, Italy
| | - Ali Dabbous
- Department of Electrical, Electronic and Telecommunication Engineering, University of Genoa, Genova, Italy
| | | | - Aldo Pagano
- Department of Experimental Medicine, University of Genoa, Genova, Italy
- IRCCS Ospedale Policlinico San Martino, Genova, Italy
| | | | - Laura Vergani
- Department for the Earth, Environment and Life Sciences, University of Genoa, Genova, Italy
| | - Alberto Diaspro
- Nanoscopy, Istituto Italiano Tecnologia, Genoa, Italy
- Department of Physics, University of Genoa, Genova, Italy
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2
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Kockelkoren G, Lauritsen L, Shuttle CG, Kazepidou E, Vonkova I, Zhang Y, Breuer A, Kennard C, Brunetti RM, D'Este E, Weiner OD, Uline M, Stamou D. Molecular mechanism of GPCR spatial organization at the plasma membrane. Nat Chem Biol 2024; 20:142-150. [PMID: 37460675 PMCID: PMC10792125 DOI: 10.1038/s41589-023-01385-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 06/14/2023] [Indexed: 10/12/2023]
Abstract
G-protein-coupled receptors (GPCRs) mediate many critical physiological processes. Their spatial organization in plasma membrane (PM) domains is believed to encode signaling specificity and efficiency. However, the existence of domains and, crucially, the mechanism of formation of such putative domains remain elusive. Here, live-cell imaging (corrected for topography-induced imaging artifacts) conclusively established the existence of PM domains for GPCRs. Paradoxically, energetic coupling to extremely shallow PM curvature (<1 µm-1) emerged as the dominant, necessary and sufficient molecular mechanism of GPCR spatiotemporal organization. Experiments with different GPCRs, H-Ras, Piezo1 and epidermal growth factor receptor, suggest that the mechanism is general, yet protein specific, and can be regulated by ligands. These findings delineate a new spatiomechanical molecular mechanism that can transduce to domain-based signaling any mechanical or chemical stimulus that affects the morphology of the PM and suggest innovative therapeutic strategies targeting cellular shape.
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Affiliation(s)
- Gabriele Kockelkoren
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Line Lauritsen
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Christopher G Shuttle
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Eleftheria Kazepidou
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Ivana Vonkova
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Yunxiao Zhang
- Howard Hughes Medical Institute, Department of Neuroscience, Dorris Neuroscience Center, Scripps Research, La Jolla, CA, USA
| | - Artù Breuer
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark
| | - Celeste Kennard
- Department of Chemical Engineering, Biomedical Engineering Program, University of South Carolina, Columbia, SC, USA
| | - Rachel M Brunetti
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Center for Geometrically Engineered Cellular Membranes, University of California, San Francisco, CA, USA
| | - Elisa D'Este
- Max-Planck-Institute for Medical Research, Optical Microscopy Facility, Heidelberg, Germany
| | - Orion D Weiner
- Cardiovascular Research Institute, University of California, San Francisco, CA, USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, CA, USA
- Center for Geometrically Engineered Cellular Membranes, University of California, San Francisco, CA, USA
| | - Mark Uline
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Department of Chemical Engineering, Biomedical Engineering Program, University of South Carolina, Columbia, SC, USA.
| | - Dimitrios Stamou
- Center for Geometrically Engineered Cellular Membranes, Department of Chemistry, University of Copenhagen, Copenhagen, Denmark.
- Atomos Biotech, Copenhagen, Denmark.
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3
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Jeong S, Koh D, Gwak E, Srambickal CV, Seo D, Widengren J, Lee JC. Pushing the Resolution Limit of Stimulated Emission Depletion Optical Nanoscopy. Int J Mol Sci 2023; 25:26. [PMID: 38203197 PMCID: PMC10779414 DOI: 10.3390/ijms25010026] [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: 09/15/2023] [Revised: 12/08/2023] [Accepted: 12/13/2023] [Indexed: 01/12/2024] Open
Abstract
Optical nanoscopy, also known as super-resolution optical microscopy, has provided scientists with the means to surpass the diffraction limit of light microscopy and attain new insights into nanoscopic structures and processes that were previously inaccessible. In recent decades, numerous studies have endeavored to enhance super-resolution microscopy in terms of its spatial (lateral) resolution, axial resolution, and temporal resolution. In this review, we discuss recent efforts to push the resolution limit of stimulated emission depletion (STED) optical nanoscopy across multiple dimensions, including lateral resolution, axial resolution, temporal resolution, and labeling precision. We introduce promising techniques and methodologies building on the STED concept that have emerged in the field, such as MINSTED, isotropic STED, and event-triggered STED, and evaluate their respective strengths and limitations. Moreover, we discuss trade-off relationships that exist in far-field optical microscopy and how they come about in STED optical nanoscopy. By examining the latest developments addressing these aspects, we aim to provide an updated overview of the current state of STED nanoscopy and its potential for future research.
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Affiliation(s)
- Sejoo Jeong
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Dongbin Koh
- School of Undergraduate Studies, DGIST, Daegu 42988, Republic of Korea
| | - Eunha Gwak
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
| | - Chinmaya V. Srambickal
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Daeha Seo
- Department of Physics and Chemistry, DGIST, Daegu 42988, Republic of Korea
| | - Jerker Widengren
- Exp. Biomol. Physics, Dept. Applied Physics, KTH—Royal Institute of Technology, 106 91 Stockholm, Sweden
| | - Jong-Chan Lee
- Department of New Biology, DGIST, Daegu 42988, Republic of Korea
- New Biology Research Center, DGIST, Daegu 42988, Republic of Korea
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4
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Jeong S, Kim J, Koh D, Lee JC. Simultaneously enhancing the resolution and signal-to-background ratio in STED optical nanoscopy via differential depletion. OPTICS EXPRESS 2023; 31:37549-37563. [PMID: 38017882 DOI: 10.1364/oe.505430] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Accepted: 10/08/2023] [Indexed: 11/30/2023]
Abstract
STED (stimulated emission depletion) far-field optical nanoscopy achieves resolution beyond the diffraction limit by depleting fluorescence at the periphery of excitation with a donut-shaped depletion laser. What is traded off with the superior resolution of STED nanoscopy is the unwanted elevation of structured background noise which hampers the quality of STED images. Here, we alleviate the background noise problem by adopting the differential stimulated emission depletion (diffSTED) approach. In diffSTED nanoscopy, signals obtained with different depletion strengths are compared and properly subtracted to remove two major background noise sources in STED nanoscopy. We show via simulations that by using diffSTED nanoscopy, background noise is significantly decreased, and the image contrast is improved. In addition, we show by simulation and analytical calculation that diffSTED improves resolution simultaneously. We assess the effect of different parameters, such as the STED beam intensity, depletion intensity ratio of two STED beams, and the subtraction factor, on the signal-to-background ratio (SBR) and the resolution of diffSTED nanoscopy. We introduce a logical algorithm to determine the optimal subtraction factor and the depletion intensity ratio. DiffSTED nanoscopy is a versatile technique that can be readily applied to any STED system without requiring any hardware modifications. We predict the wide applicability of diffSTED for its enhanced resolution, improved SBR, and easiness of implementation.
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5
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Ishii H, Otomo K, Chang CP, Yamasaki M, Watanabe M, Yokoyama H, Nemoto T. All-synchronized picosecond pulses and time-gated detection improve the spatial resolution of two-photon STED microscopy in brain tissue imaging. PLoS One 2023; 18:e0290550. [PMID: 37616194 PMCID: PMC10449175 DOI: 10.1371/journal.pone.0290550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 08/09/2023] [Indexed: 08/26/2023] Open
Abstract
Super-resolution in two-photon excitation (2PE) microscopy offers new approaches for visualizing the deep inside the brain functions at the nanoscale. In this study, we developed a novel 2PE stimulated-emission-depletion (STED) microscope with all-synchronized picosecond pulse light sources and time-gated fluorescence detection, namely, all-pulsed 2PE-gSTED microscopy. The implementation of time-gating is critical to excluding undesirable signals derived from brain tissues. Even in a case using subnanosecond pulses for STED, the impact of time-gating was not negligible; the spatial resolution in the image of the brain tissue was improved by approximately 1.4 times compared with non time-gated image. This finding demonstrates that time-gating is more useful than previously thought for improving spatial resolution in brain tissue imaging. This microscopy will facilitate deeper super-resolution observation of the fine structure of neuronal dendritic spines and the intracellular dynamics in brain tissue.
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Affiliation(s)
- Hirokazu Ishii
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
| | - Kohei Otomo
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki, Japan
- Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Ching-Pu Chang
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki, Japan
- Faculty of Medicine, Hokkaido University, Sapporo, Japan
| | | | | | - Hiroyuki Yokoyama
- New Industry Creation Hatchery Center (NICHe), Tohoku University, Sendai, Japan
| | - Tomomi Nemoto
- Exploratory Research Center on Life and Living Systems (ExCELLS), National Institutes of Natural Sciences, Okazaki, Japan
- National Institute for Physiological Sciences (NIPS), National Institutes of Natural Sciences, Okazaki, Japan
- School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki, Japan
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6
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Barsanti L, Birindelli L, Sbrana F, Lombardi G, Gualtieri P. Advanced Microscopy Techniques for Molecular Biophysics. Int J Mol Sci 2023; 24:9973. [PMID: 37373120 DOI: 10.3390/ijms24129973] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 05/31/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
Though microscopy is most often intended as a technique for providing qualitative assessment of cellular and subcellular properties, when coupled with other instruments such as wavelength selectors, lasers, photoelectric devices and computers, it can perform a wide variety of quantitative measurements, which are demanding in establishing relationships between the properties and structures of biological material in all their spatial and temporal complexities. These combinations of instruments are a powerful approach to improve non-destructive investigations of cellular and subcellular properties (both physical and chemical) at a macromolecular scale resolution. Since many subcellular compartments in living cells are characterized by structurally organized molecules, this review deals with three advanced microscopy techniques well-suited for these kind of investigations, i.e., microspectrophotometry (MSP), super-resolution localization microscopy (SRLM) and holotomographic microscopy (HTM). These techniques can achieve an insight view into the role intracellular molecular organizations such as photoreceptive and photosynthetic structures and lipid bodies play in many cellular processes as well as their biophysical properties. Microspectrophotometry uses a set-up based on the combination of a wide-field microscope and a polychromator, which allows the measurement of spectroscopic features such as absorption spectra. Super resolution localization microscopy combines dedicated optics and sophisticated software algorithms to overcome the diffraction limit of light and allow the visualization of subcellular structures and dynamics in greater detail with respect to conventional optical microscopy. Holotomographic microscopy combines holography and tomography techniques into a single microscopy set-up, and allows 3D reconstruction by means of the phase separation of biomolecule condensates. This review is organized in sections, which for each technique describe some general aspects, a peculiar theoretical aspect, a specific experimental configuration and examples of applications (fish and algae photoreceptors, single labeled proteins and endocellular aggregates of lipids).
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Affiliation(s)
- Laura Barsanti
- Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa, Italy
| | | | | | - Giovanni Lombardi
- Istituto di Scienza e Tecnologia dell'Informazione, CNR, Via Moruzzi 1, 56124 Pisa, Italy
| | - Paolo Gualtieri
- Istituto di Biofisica, CNR, Via Moruzzi 1, 56124 Pisa, Italy
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7
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Chen YI, Chang YJ, Sun Y, Liao SC, Santacruz SR, Yeh HC. Spatial resolution enhancement in photon-starved STED imaging using deep learning-based fluorescence lifetime analysis. NANOSCALE 2023; 15:9449-9456. [PMID: 37159237 PMCID: PMC10460507 DOI: 10.1039/d3nr00305a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
As a super-resolution imaging method, stimulated emission depletion (STED) microscopy has unraveled fine intracellular structures and provided insights into nanoscale organizations in cells. Although image resolution can be further enhanced by continuously increasing the STED-beam power, the resulting photodamage and phototoxicity are major issues for real-world applications of STED microscopy. Here we demonstrate that, with 50% less STED-beam power, the STED image resolution can be improved up to 1.45-fold using the separation of photons by a lifetime tuning (SPLIT) scheme combined with a deep learning-based phasor analysis algorithm termed flimGANE (fluorescence lifetime imaging based on a generative adversarial network). This work offers a new approach for STED imaging in situations where only a limited photon budget is available.
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Affiliation(s)
- Yuan-I Chen
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
| | - Yin-Jui Chang
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
| | - Yuansheng Sun
- ISS, Inc., 1602 Newton Drive, Champaign, IL, 61822, USA
| | - Shih-Chu Liao
- ISS, Inc., 1602 Newton Drive, Champaign, IL, 61822, USA
| | - Samantha R Santacruz
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
- Electrical & Computer Engineering, University of Texas at Austin, Austin, TX, USA
- Institute for Neuroscience, University of Texas at Austin, Austin, TX, USA
| | - Hsin-Chih Yeh
- Biomedical Engineering, University of Texas at Austin, Austin, TX, USA.
- Texas Materials Institute, University of Texas at Austin, Austin, TX, USA
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8
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Westlund E, Bergenstråle A, Pokhrel A, Chan H, Skoglund U, Daley DO, Söderström B. Application of nanotags and nanobodies for live cell single-molecule imaging of the Z-ring in Escherichia coli. Curr Genet 2023; 69:153-163. [PMID: 37022498 PMCID: PMC10163087 DOI: 10.1007/s00294-023-01266-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/22/2023] [Accepted: 03/24/2023] [Indexed: 04/07/2023]
Abstract
Understanding where proteins are localized in a bacterial cell is essential for understanding their function and regulation. This is particularly important for proteins that are involved in cell division, which localize at the division septum and assemble into highly regulated complexes. Current knowledge of these complexes has been greatly facilitated by super-resolution imaging using fluorescent protein fusions. Herein, we demonstrate with FtsZ that single-molecule PALM images can be obtained in-vivo using a genetically fused nanotag (ALFA), and a corresponding nanobody fused to mEos3.2. The methodology presented is applicable to other bacterial proteins.
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Affiliation(s)
- Emma Westlund
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Axel Bergenstråle
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden
| | - Alaska Pokhrel
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia
| | - Helena Chan
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Ulf Skoglund
- Structural Cellular Biology Unit, Okinawa Institute of Science and Technology, Okinawa, 904-0495, Japan
| | - Daniel O Daley
- Department of Biochemistry and Biophysics, Stockholm University, 106 91, Stockholm, Sweden.
| | - Bill Söderström
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, NSW, 2007, Australia.
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9
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Han H, Wang L, Zhou H, Xing X, Guo Y, Zhu Y, Yan W, Qu J. Low-power compact continuous-wave stimulated emission depletion microscopy. JOURNAL OF BIOPHOTONICS 2023; 16:e202200233. [PMID: 36054472 DOI: 10.1002/jbio.202200233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 08/24/2022] [Accepted: 08/30/2022] [Indexed: 06/15/2023]
Abstract
Stimulated emission depletion (STED) microscopy can break the optical diffraction barrier and provide subdiffraction resolution. According to the STED superresolution imaging principle, the resolution of STED is positively related to the power of the depletion laser. However, high-laser power largely limits the study of living cells or living bodies. Moreover, the high complexity and high cost of conventional pulsed STED microscopy limit the application of this technique. Therefore, this paper describes a simple continuous-wave STED (CW-STED) system constructed on a 45 × 60 cm breadboard and combined with digitally enhanced (DE) technology; low-power superresolution imaging is realized, which has the advantages of reducing system complexity and cost. The low-system complexity, low cost, and low-power superresolution imaging features of CW-STED have great potential to advance the application of STED microscopy in biological research.
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Affiliation(s)
- HongYi Han
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Luwei Wang
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Hanqiu Zhou
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Xiuquan Xing
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yong Guo
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Yinru Zhu
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Wei Yan
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Junle Qu
- Shenzhen Key Laboratory of Photonics and Biophotonics, Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
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10
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Focus image scanning microscopy for sharp and gentle super-resolved microscopy. Nat Commun 2022; 13:7723. [PMID: 36513680 PMCID: PMC9747786 DOI: 10.1038/s41467-022-35333-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 11/28/2022] [Indexed: 12/15/2022] Open
Abstract
To date, the feasibility of super-resolution microscopy for imaging live and thick samples is still limited. Stimulated emission depletion (STED) microscopy requires high-intensity illumination to achieve sub-diffraction resolution, potentially introducing photodamage to live specimens. Moreover, the out-of-focus background may degrade the signal stemming from the focal plane. Here, we propose a new method to mitigate these limitations without drawbacks. First, we enhance a STED microscope with a detector array, enabling image scanning microscopy (ISM). Therefore, we implement STED-ISM, a method that exploits the working principle of ISM to reduce the depletion intensity and achieve a target resolution. Later, we develop Focus-ISM, a strategy to improve the optical sectioning and remove the background of any ISM-based imaging technique, with or without a STED beam. The proposed approach requires minimal architectural changes to a conventional microscope but provides substantial advantages for live and thick sample imaging.
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11
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Gonzalez Pisfil M, Nadelson I, Bergner B, Rottmeier S, Thomae AW, Dietzel S. Stimulated emission depletion microscopy with a single depletion laser using five fluorochromes and fluorescence lifetime phasor separation. Sci Rep 2022; 12:14027. [PMID: 35982114 PMCID: PMC9388687 DOI: 10.1038/s41598-022-17825-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 08/01/2022] [Indexed: 11/15/2022] Open
Abstract
Stimulated emission depletion (STED) microscopy achieves super-resolution by exciting a diffraction-limited volume and then suppressing fluorescence in its outer parts by depletion. Multiple depletion lasers may introduce misalignment and bleaching. Hence, a single depletion wavelength is preferable for multi-color analyses. However, this limits the number of usable spectral channels. Using cultured cells, common staining protocols, and commercially available fluorochromes and microscopes we exploit that the number of fluorochromes in STED or confocal microscopy can be increased by phasor based fluorescence lifetime separation of two dyes with similar emission spectra but different fluorescent lifetimes. In our multi-color FLIM-STED approach two fluorochromes in the near red (exc. 594 nm, em. 600–630) and two in the far red channel (633/641–680), supplemented by a single further redshifted fluorochrome (670/701–750) were all depleted with a single laser at 775 nm thus avoiding potential alignment issues. Generally, this approach doubles the number of fully distinguishable colors in laser scanning microscopy. We provide evidence that eight color FLIM-STED with a single depletion laser would be possible if suitable fluorochromes were identified and we confirm that a fluorochrome may have different lifetimes depending on the molecules to which it is coupled.
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Affiliation(s)
- Mariano Gonzalez Pisfil
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Iliya Nadelson
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Brigitte Bergner
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Sonja Rottmeier
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Andreas W Thomae
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany
| | - Steffen Dietzel
- Core Facility Bioimaging and Walter-Brendel-Centre of Experimental Medicine, Biomedical Center, Ludwig-Maximilians-Universität München, Großhaderner Straße 9, 82152, Planegg-Martinsried, Germany.
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12
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Shen X, Wang L, Li W, Wang H, Zhou H, Zhu Y, Yan W, Qu J. Ultralow Laser Power Three-Dimensional Superresolution Microscopy Based on Digitally Enhanced STED. BIOSENSORS 2022; 12:bios12070539. [PMID: 35884342 PMCID: PMC9351679 DOI: 10.3390/bios12070539] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 01/27/2023]
Abstract
The resolution of optical microscopes is limited by the optical diffraction limit; in particular, the axial resolution is much lower than the lateral resolution, which hinders the clear distinction of the three-dimensional (3D) structure of cells. Although stimulated emission depletion (STED) superresolution microscopy can break through the optical diffraction limit to achieve 3D superresolution imaging, traditional 3D STED requires high depletion laser power to acquire high-resolution images, which can cause irreversible light damage to biological samples and probes. Therefore, we developed an ultralow laser power 3D STED superresolution imaging method. On the basis of this method, we obtained lateral and axial resolutions of 71 nm and 144 nm, respectively, in fixed cells with 0.65 mW depletion laser power. This method will have broad application prospects in 3D superresolution imaging of living cells.
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13
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Lee M, Joo S. Effect of time‐gating on stimulated emission depletion microscopy using sub‐nanosecond pulses. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mina Lee
- Safety Measurement Institute Korea Research Institute of Standards and Science (KRISS) Daejeon South Korea
| | - Sihwa Joo
- Safety Measurement Institute Korea Research Institute of Standards and Science (KRISS) Daejeon South Korea
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14
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Mendoza-Coto A, Manzo Jaime D, Pérez Mellor AF, Coto Hernández I. Theoretical study of laser intensity noise effect on CW-STED microscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2022; 39:702-707. [PMID: 35471396 DOI: 10.1364/josaa.452035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 03/02/2022] [Indexed: 06/14/2023]
Abstract
Spatial resolution of stimulated emission depletion (STED) microscopy varies with sample labeling techniques and microscope components, e.g., lasers, lenses, and photodetectors. Fluctuations in the intensity of the depletion laser decrease achievable resolution in STED microscopy; the stronger the fluctuations, the higher the average intensity needed to achieve a given resolution. This phenomenon is encountered in every STED measurement. However, a theoretical framework that evaluates the effect of intensity fluctuations on spatial resolution is lacking. This paper presents an analytical formulation based on a stochastic model that characterizes the impact of the laser fluctuations and correlation time on the depletion efficiency in continuous-wave (CW) STED microscopy. We compared analytical results with simulations using a wide range of intensity noise conditions and found a high degree of agreement. The stochastic model used considers a colored noise distribution for the laser intensity fluctuations. Simple analytical expressions were obtained in the limit of small and large fluctuations' correlation time. These expressions fitted very well the available experimental data. Finally, this work offers a starting point to model other laser noise effects in various microscopy implementations.
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15
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Ma Y, Macmillan A, Yang Y, Gaus K. Lifetime based axial contrast enable simple 3D-STED imaging. Methods Appl Fluoresc 2022; 10. [PMID: 35290969 DOI: 10.1088/2050-6120/ac5e10] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 03/15/2022] [Indexed: 11/11/2022]
Abstract
Stimulated Emission Depletion (STED) microscopy increase spatial image resolution by laterally sharpening the illumination profile of the confocal microscope. However, it remains compromised in axial resolution. To improve axial STED resolution, constructive interference of the STED depletion beam must be formed surrounding the focal plane to turn off the fluorophores beyond the focal plane. For isotropic 3D-STED resolution, this axial STED interference pattern must be overlayed with the doughnut STED beam at nanometer accuracy. Such optical configurations can be challenging in alignment. In this current work, we introduced a straightforward lifetime based axial contrast in STED microscope by imaging the samples on an ITO coated glass coverslip. The STED laser generates surface plasmon resonance on the ITO surface that enhanced the metal induced energy transfer MIET effect on the ITO surface. The enhanced MIET effect established a lifetime gradient with ~20% dynamic range that extend for mor than 400 nm from the ITO surface. The axial contrast based on the lifetime gradient was directly used for 3D-STED imaging of tubulin fibers inside COS-7 cells, where the vertical displacement of single tubulin fiber was revealed. Lifetime gating could be applied to further improve lateral spatial resolution. Considering that most common implementation of STED microscopes uses pulsed lasers and timing electronics, there is no optical modification of the microscope is required in the current 3D-STED approach.
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Affiliation(s)
- Yuanqing Ma
- EMBL Australia Node in Single Molecule Science, University of New South Wales, Level 3, Lowy Research building, Sydney, New South Wales, 2052, AUSTRALIA
| | - Alex Macmillan
- University of New South Wales, Biomedical Imaging Facility, University of New South Wales, Sydney, New South Wales, 2052, AUSTRALIA
| | - Ying Yang
- University of New South Wales, School of Chemistry, Australian Centre for NanoMedicine, and ARC Centre of Excellence in Convergent Bio-Nano Science and Technology, Sydney, New South Wales, 2052, AUSTRALIA
| | - Katharina Gaus
- EMBL Australia Node in Single Molecule Science, The University of New South Wales, Level 3, Lowy Cancer Research Building, Sydney, NSW 2052, Sydney, New South Wales, 2052, AUSTRALIA
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16
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Delcanale P, Abbruzzetti S, Viappiani C. Photodynamic treatment of pathogens. LA RIVISTA DEL NUOVO CIMENTO 2022; 45:407-459. [PMCID: PMC8921710 DOI: 10.1007/s40766-022-00031-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 01/10/2022] [Indexed: 06/01/2023]
Abstract
The current viral pandemic has highlighted the compelling need for effective and versatile treatments, that can be quickly tuned to tackle new threats, and are robust against mutations. Development of such treatments is made even more urgent in view of the decreasing effectiveness of current antibiotics, that makes microbial infections the next emerging global threat. Photodynamic effect is one such method. It relies on physical processes proceeding from excited states of particular organic molecules, called photosensitizers, generated upon absorption of visible or near infrared light. The excited states of these molecules, tailored to undergo efficient intersystem crossing, interact with molecular oxygen and generate short lived reactive oxygen species (ROS), mostly singlet oxygen. These species are highly cytotoxic through non-specific oxidation reactions and constitute the basis of the treatment. In spite of the apparent simplicity of the principle, the method still has to face important challenges. For instance, the short lifetime of ROS means that the photosensitizer must reach the target within a few tens nanometers, which requires proper molecular engineering at the nanoscale level. Photoactive nanostructures thus engineered should ideally comprise a functionality that turns the system into a theranostic means, for instance, through introduction of fluorophores suitable for nanoscopy. We discuss the principles of the method and the current molecular strategies that have been and still are being explored in antimicrobial and antiviral photodynamic treatment.
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Affiliation(s)
- Pietro Delcanale
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Stefania Abbruzzetti
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
| | - Cristiano Viappiani
- Dipartimento di Scienze Matematiche, Fisiche e Informatiche, Università degli Studi di Parma, Parco Area delle Scienze 7A, 43124 Parma, Italy
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17
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Zhang J, Gao X, Wang L, Guo Y, Zhu Y, Yang Z, Yan W, Qu J. Low-Power Two-Color Stimulated Emission Depletion Microscopy for Live Cell Imaging. BIOSENSORS-BASEL 2021; 11:bios11090330. [PMID: 34562919 PMCID: PMC8468006 DOI: 10.3390/bios11090330] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 08/27/2021] [Accepted: 09/09/2021] [Indexed: 01/15/2023]
Abstract
Stimulated emission depletion (STED) microscopy is a typical laser-scanning super-resolution imaging technology, the emergence of which has opened a new research window for studying the dynamic processes of live biological samples on a nanometer scale. According to the characteristics of STED, a high depletion power is required to obtain a high resolution. However, a high laser power can induce severe phototoxicity and photobleaching, which limits the applications for live cell imaging, especially in two-color STED super-resolution imaging. Therefore, we developed a low-power two-color STED super-resolution microscope with a single supercontinuum white-light laser. Using this system, we achieved low-power two-color super-resolution imaging based on digital enhancement technology. Lateral resolutions of 109 and 78 nm were obtained for mitochondria and microtubules in live cells, respectively, with 0.8 mW depletion power. These results highlight the great potential of the novel digitally enhanced two-color STED microscopy for long-term dynamic imaging of live cells.
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Affiliation(s)
| | | | | | | | | | | | - Wei Yan
- Correspondence: (W.Y.); (J.Q.)
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18
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Wiktor J, Gynnå AH, Leroy P, Larsson J, Coceano G, Testa I, Elf J. RecA finds homologous DNA by reduced dimensionality search. Nature 2021; 597:426-429. [PMID: 34471288 PMCID: PMC8443446 DOI: 10.1038/s41586-021-03877-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Accepted: 08/04/2021] [Indexed: 11/21/2022]
Abstract
Homologous recombination is essential for the accurate repair of double-stranded DNA breaks (DSBs)1. Initially, the RecBCD complex2 resects the ends of the DSB into 3' single-stranded DNA on which a RecA filament assembles3. Next, the filament locates the homologous repair template on the sister chromosome4. Here we directly visualize the repair of DSBs in single cells, using high-throughput microfluidics and fluorescence microscopy. We find that, in Escherichia coli, repair of DSBs between segregated sister loci is completed in 15 ± 5 min (mean ± s.d.) with minimal fitness loss. We further show that the search takes less than 9 ± 3 min (mean ± s.d) and is mediated by a thin, highly dynamic RecA filament that stretches throughout the cell. We propose that the architecture of the RecA filament effectively reduces search dimensionality. This model predicts a search time that is consistent with our measurement and is corroborated by the observation that the search time does not depend on the length of the cell or the amount of DNA. Given the abundance of RecA homologues5, we believe this model to be widely conserved across living organisms.
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Affiliation(s)
- Jakub Wiktor
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Arvid H Gynnå
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Prune Leroy
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jimmy Larsson
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Giovanna Coceano
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Ilaria Testa
- Department of Applied Physics, Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Johan Elf
- Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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19
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Valli J, Sanderson J. Super-Resolution Fluorescence Microscopy Methods for Assessing Mouse Biology. Curr Protoc 2021; 1:e224. [PMID: 34436832 DOI: 10.1002/cpz1.224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Super-resolution (diffraction unlimited) microscopy was developed 15 years ago; the developers were awarded the Nobel Prize in Chemistry in recognition of their work in 2014. Super-resolution microscopy is increasingly being applied to diverse scientific fields, from single molecules to cell organelles, viruses, bacteria, plants, and animals, especially the mammalian model organism Mus musculus. In this review, we explain how super-resolution microscopy, along with fluorescence microscopy from which it grew, has aided the renaissance of the light microscope. We cover experiment planning and specimen preparation and explain structured illumination microscopy, super-resolution radial fluctuations, stimulated emission depletion microscopy, single-molecule localization microscopy, and super-resolution imaging by pixel reassignment. The final section of this review discusses the strengths and weaknesses of each super-resolution technique and how to choose the best approach for your research. © 2021 The Authors. Current Protocols published by Wiley Periodicals LLC.
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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
| | - Jeremy Sanderson
- MRC Harwell Institute, Mammalian Genetics Unit, Harwell Campus, Oxfordshire, United Kingdom
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20
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Siegmund R, Werner F, Jakobs S, Geisler C, Egner A. isoSTED microscopy with water-immersion lenses and background reduction. Biophys J 2021; 120:3303-3314. [PMID: 34246627 PMCID: PMC8392127 DOI: 10.1016/j.bpj.2021.05.031] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 04/26/2021] [Accepted: 05/18/2021] [Indexed: 01/17/2023] Open
Abstract
Fluorescence microscopy is an excellent tool to gain knowledge on cellular structures and biochemical processes. Stimulated emission depletion (STED) microscopy provides a resolution in the range of a few 10 nm at relatively fast data acquisition. As cellular structures can be oriented in any direction, it is of great benefit if the microscope exhibits an isotropic resolution. Here, we present an isoSTED microscope that utilizes water-immersion objective lenses and enables imaging of cellular structures with an isotropic resolution of better than 60 nm in living samples at room temperature and without CO2 supply or another pH control. This corresponds to a reduction of the focal volume by far more than two orders of magnitude as compared to confocal microscopy. The imaging speed is in the range of 0.8 s/μm3. Because fluorescence signal can only be detected from a diffraction-limited volume, a background signal is inevitably observed at resolutions well beyond the diffraction limit. Therefore, we additionally present a method that allows us to identify this unspecific background signal and to remove it from the image.
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Affiliation(s)
- René Siegmund
- Department of Optical Nanoscopy, Institute for Nanophotonics Göttingen, Göttingen, Germany
| | - Frank Werner
- Institute of Mathematics, University of Würzburg, Würzburg, Germany
| | - Stefan Jakobs
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany
| | - Claudia Geisler
- Department of Optical Nanoscopy, Institute for Nanophotonics Göttingen, Göttingen, Germany
| | - Alexander Egner
- Department of Optical Nanoscopy, Institute for Nanophotonics Göttingen, Göttingen, Germany; Cluster of Excellence "Multiscale Bioimaging: From Molecular Machines to Networks of Excitable Cells" (MBExC), University of Göttingen, Göttingen, Germany.
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21
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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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22
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Gonzalez Pisfil M, Rohilla S, König M, Krämer B, Patting M, Koberling F, Erdmann R. Triple-Color STED Nanoscopy: Sampling Absorption Spectra Differences for Efficient Linear Species Unmixing. J Phys Chem B 2021; 125:5694-5705. [PMID: 34048256 DOI: 10.1021/acs.jpcb.0c11390] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Stimulated emission depletion (STED) in confocal fluorescence microscopy enables a visualization of biological structures within cells far below the optical diffraction limit. To meet the demand in the field for simultaneous investigations of multiple species within a cell, a couple of different STED techniques have been proposed, each with their own challenges. By systemically exploiting spectral differences in the absorption of fluorescent labels, we present a novel, beneficial approach to multispecies STED nanoscopy. By using three excitation wavelengths in nanosecond pulsed interleaved excitation (PIE) mode, we probe quasi simultaneously multiple species with fluorescent labels having absorption maxima as close as 13 nm. The acquired image is decomposed into its single species contributions by application of a linear unmixing algorithm based on present reference patterns. For multispecies images containing single species regions, we introduce the image correlation map (ICM). Here, the single species regions easily can be identified in order to generate the necessary single species reference patterns. This avoids the otherwise cumbersome and artifact prone preparation and recording of additional reference samples. The power of the proposed imaging scheme persists in species separation quality at high speed shown for up to three species with established reference samples and dyes commonly used for cellular STED imaging.
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Affiliation(s)
- Mariano Gonzalez Pisfil
- PicoQuant Innovations GmbH, Rudower Chaussee 29, 12489 Berlin, Germany.,Department of Biology, Molecular Biophysics, IRI Life Sciences, Humboldt-Universität zu Berlin, Invalidenstrasse 42, 10115 Berlin, Germany
| | - Sumeet Rohilla
- PicoQuant Innovations GmbH, Rudower Chaussee 29, 12489 Berlin, Germany.,Department of Internal Medicine/Infectious Diseases and Respiratory Medicine, Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Charitéplatz 1, 10117 Berlin, Germany
| | - Marcelle König
- PicoQuant GmbH, Rudower Chaussee 29, 12489 Berlin, Germany
| | | | | | | | - Rainer Erdmann
- PicoQuant GmbH, Rudower Chaussee 29, 12489 Berlin, Germany
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23
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Zhu T, Yang G, Liu X, Xiang P, Yang Z, Zhang S, Chen J, Wang H, Campos de Souza S, Zhang Z, Zhang R, Tian Y, Wu J, Tian X. Live cell mitochondrial 3-dimensional dynamic ultrastructures under oxidative phosphorylation revealed by a Pyridine-BODIPY probe. Biosens Bioelectron 2021; 178:113036. [PMID: 33548656 DOI: 10.1016/j.bios.2021.113036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 01/15/2021] [Accepted: 01/22/2021] [Indexed: 02/05/2023]
Abstract
Recent advancements in super-resolution nanoscopy allowed the study of mitochondrial biology at nanoscale and boosted the understanding its correlated cellular processes those were previously poorly understood. Nevertheless, studying mitochondrial ultrastructure remains a challenge due to the lack of probes that could target specific mitochondrial substances (e.g. cristae or mtDNA) and survive under harsh super-resolution optical conditions. Herein, in this work, we have rationally constructed a pyridine-BODIPY (Py-BODIPY) derivative that could target mitochondrial membrane in living cells without interfering its physiological microenvironments. Furthermore, we found Py-BODIPY is a membrane potential independent probe, hence it is not limit to live-cell staining but also showed a strong internalization into pre-fixed and stimulus disrupted sample. Importantly, its cristae specificity and superb photostability allow the observation of mitochondrial dynamic nano-structures with an unprecedented resolution, allow demonstrating how mitochondrial 3D ultrastructure evolved under oxidative phosphorylation condition.
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Affiliation(s)
- Tong Zhu
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, 610041, China; School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Guanqing Yang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Xiaolu Liu
- School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Pan Xiang
- School of Life Science, Anhui University, Hefei, 230601, PR China
| | - Zhenghui Yang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China
| | - Sijing Zhang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Juan Chen
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Hong Wang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Senio Campos de Souza
- Department of Chemistry, University College London, London University College London, Gower Street, London, WC1E 6BT, UK
| | - Zhongping Zhang
- Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China; CAS Center for Excellence in Nanoscience, Institute of Intelligent Machines, Chinese Academy of Science, Hefei, China
| | - Ruilong Zhang
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Yupeng Tian
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Jieying Wu
- Department of Chemistry, Key Laboratory of Functional Inorganic Material Chemistry of Anhui Province, Anhui University, Hefei, 230601, PR China
| | - Xiaohe Tian
- Huaxi MR Research Center (HMRRC), Department of Radiology, Functional and Molecular Imaging Key Laboratory of Sichuan Province, West China Hospital of Sichuan University, Chengdu, 610041, China; School of Life Science, Anhui University, Hefei, 230601, PR China; Institutes of Physical Science and Information Technology, Anhui University, Hefei, 230601, PR China; Department of Chemistry, University College London, London University College London, Gower Street, London, WC1E 6BT, UK.
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24
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Xu Y, Xu R, Wang Z, Zhou Y, Shen Q, Ji W, Dang D, Meng L, Tang BZ. Recent advances in luminescent materials for super-resolution imaging via stimulated emission depletion nanoscopy. Chem Soc Rev 2021; 50:667-690. [DOI: 10.1039/d0cs00676a] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Recent progress on STED fluorophores for super-resolution imaging and also their characteristics are outlined here, thus providing some guidelines to select proper probes and even develop new materials for super-resolution imaging via STED nanoscopy.
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Affiliation(s)
- Yanzi Xu
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Ruohan Xu
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Zhi Wang
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Yu Zhou
- Instrumental Analysis Center
- Xi'an Jiao Tong University
- Xi'an
- P. R. China
| | - Qifei Shen
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Wenchen Ji
- Department of Orthopedics
- the First Affiliated Hospital of Xi’an Jiaotong University
- P. R. China
| | - Dongfeng Dang
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Lingjie Meng
- School of Chemistry
- Xi'an Key Laboratory of Sustainable Energy Material Chemistry
- MOE Key Laboratory for Non-equilibrium Synthesis and Modulation of Condensed Matter
- Xi'an Jiao Tong University
- Xi'an 710049
| | - Ben Zhong Tang
- Department of Chemistry
- The Hong Kong University of Science and Technology
- Clear Water Bay
- Kowloon
- P. R. China
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25
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Tian X, De Pace C, Ruiz-Perez L, Chen B, Su R, Zhang M, Zhang R, Zhang Q, Wang Q, Zhou H, Wu J, Zhang Z, Tian Y, Battaglia G. A Cyclometalated Iridium (III) Complex as a Microtubule Probe for Correlative Super-Resolution Fluorescence and Electron Microscopy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2020; 32:e2003901. [PMID: 32815192 DOI: 10.1002/adma.202003901] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Revised: 07/12/2020] [Indexed: 06/11/2023]
Abstract
The visualization of microtubules by combining optical and electron microscopy techniques provides valuable information to understand correlated intracellular activities. However, the lack of appropriate probes to bridge both microscopic resolutions restricts the areas and structures that can be comprehended within such highly assembled structures. Here, a versatile cyclometalated iridium (III) complex is designed that achieves synchronous fluorescence-electron microscopy correlation. The selective insertion of the probe into a microtubule triggers remarkable fluorescence enhancement and promising electron contrast. The long-life, highly photostable probe allows live-cell super-resolution imaging of tubulin localization and motion with a resolution of ≈30 nm. Furthermore, correlative light-electron microscopy and energy-filtered transmission electron microscopy reveal the well-associated optical and electron signal at a high specificity, with an interspace of ≈41 Å of microtubule monomer in cells.
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Affiliation(s)
- Xiaohe Tian
- School of Life Science, Anhui University, Hefei, 230000, P. R. China
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230000, P. R. China
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
| | - Cesare De Pace
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
- EPSRC/JEOL Centre for Liquid Phase Electron Microscopy, University College London, London, WC1H 0AJ, UK
| | - Lorena Ruiz-Perez
- Department of Chemistry, University College London, London, WC1H 0AJ, UK
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
- EPSRC/JEOL Centre for Liquid Phase Electron Microscopy, University College London, London, WC1H 0AJ, UK
| | - Bo Chen
- School of Materials Science and Engineering, Tongji University, Shanghai, 201804, China
| | - Rina Su
- School of Life Science, Anhui University, Hefei, 230000, P. R. China
| | - Mingzhu Zhang
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
| | - Ruilong Zhang
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
| | - Qiong Zhang
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
| | - Qin Wang
- Biotechnology Centre, Anhui Agriculture University, Hefei, 230036, China
| | - Hongping Zhou
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
| | - Jieying Wu
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
| | - Zhongping Zhang
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230000, P. R. China
- CAS Center for Excellence in Nanoscience, Institute of Intelligent Machines, Chinese Academy of Science, Hefei, 230031, China
| | - Yupeng Tian
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
| | - Giuseppe Battaglia
- Department of Chemistry, Anhui University, Hefei, 230000, P. R. China
- Institute of Physical Science and Information Technology, Anhui University, Hefei, 230000, P. R. China
- Institute for the Physics of Living Systems, University College London, London, WC1E 6BT, UK
- EPSRC/JEOL Centre for Liquid Phase Electron Microscopy, University College London, London, WC1H 0AJ, UK
- Institute for Bioengineering of Catalonia, The Barcelona Institute for Science and Technology (BIST), Barcelona, 08007, Spain
- Catalan Institution for Research and Advanced Studies, Barcelona, 08010, Spain
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Wang J, Zhang J, Wang L, Gao X, Shao Y, Liu L, Yang Z, Yan W, Qu J. Dual-color STED super-resolution microscope using a single laser source. JOURNAL OF BIOPHOTONICS 2020; 13:e202000057. [PMID: 32421923 DOI: 10.1002/jbio.202000057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Revised: 05/12/2020] [Accepted: 05/13/2020] [Indexed: 06/11/2023]
Abstract
STED (stimulated emission depletion) microscopy is one of the most promising super-resolution fluorescence microscopies,due to its fast imaging and ultra-high resolution. In this paper, we present a dual-color STED microscope with a single laser source. Polarization beam splitters are used to separate the output from a supercontinuum laser source into four laser beams, including two excitation beams (488, 635 nm) and two depletion beams (592, 775 nm). These four laser beams are then used to build a low cost dual-color STED system to achieve a spatial resolution of 75 nm in cell samples.
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Affiliation(s)
- Jialin Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Jia Zhang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Luwei Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Xinwei Gao
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yonghong Shao
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Liwei Liu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Zhigang Yang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Wei Yan
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, Guangdong, China
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27
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Coto Hernández I, Castello M, Tortarolo G, Jowett N, Diaspro A, Lanzanò L, Vicidomini G. Efficient two-photon excitation stimulated emission depletion nanoscope exploiting spatiotemporal information. NEUROPHOTONICS 2019; 6:045004. [PMID: 31720309 PMCID: PMC6830046 DOI: 10.1117/1.nph.6.4.045004] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 10/14/2019] [Indexed: 06/10/2023]
Abstract
Stimulated emission depletion (STED) microscopy is a powerful bioimaging technique that theoretically provides molecular spatial resolution while preserving the most important assets of fluorescence microscopy. When combined with two-photon excitation (2PE) microscopy (2PE-STED), subdiffraction resolution may be achieved for thick biological samples. The most straightforward implementation of 2PE-STED microscopy entails introduction of an STED beam operating in continuous wave (CW) into a conventional Ti:sapphire-based 2PE microscope (2PE CW-STED). In this implementation, resolution enhancement is typically achieved using time-gated detection schemes, often resulting in drastic signal-to-noise/-background ratio (SNR/SBR) reductions. Herein, we employ a pixel-by-pixel phasor approach to discard fluorescence photons lacking super-resolution information to enhance image SNR/SBR in 2PE CW-STED microscopy. We compare this separation of photons by lifetime tuning approach against other postprocessing algorithms and combine it with image deconvolution to further optimize image quality.
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Affiliation(s)
- Iván Coto Hernández
- Massachusetts Eye and Ear and Harvard Medical School, Surgical Photonics and Engineering Laboratory, Boston, United States
| | - Marco Castello
- Istituto Italiano di Tecnologia, Molecular Microscopy and Spectroscopy, Genoa, Italy
| | - Giorgio Tortarolo
- Istituto Italiano di Tecnologia, Molecular Microscopy and Spectroscopy, Genoa, Italy
| | - Nate Jowett
- Massachusetts Eye and Ear and Harvard Medical School, Surgical Photonics and Engineering Laboratory, Boston, United States
| | - Alberto Diaspro
- Istituto Italiano di Tecnologia, Nanoscopy and NIC@IIT, Genoa, Italy
- University of Genoa, Department of Physics, Genoa, Italy
| | - Luca Lanzanò
- Istituto Italiano di Tecnologia, Nanoscopy and NIC@IIT, Genoa, Italy
| | - Giuseppe Vicidomini
- Istituto Italiano di Tecnologia, Molecular Microscopy and Spectroscopy, Genoa, Italy
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28
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Lim G, Kim WC, Oh S, Lee H, Park NC. Enhanced lateral resolution in continuous wave stimulated emission depletion microscopy using tightly focused annular radially polarized excitation beam. JOURNAL OF BIOPHOTONICS 2019; 12:e201900060. [PMID: 31050861 DOI: 10.1002/jbio.201900060] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Revised: 04/29/2019] [Accepted: 05/02/2019] [Indexed: 06/09/2023]
Abstract
The lateral resolution of continuous wave (CW) stimulated emission depletion (STED) microscopy is enhanced about 12% by applying annular-shaped amplitude modulation to the radially polarized excitation beam. A focused annularly filtered radially polarized excitation beam provides a more condensed point spread function (PSF), which contributes to enhance effective STED resolution of CW STED microscopy. Theoretical analysis shows that the FWHM of the effective PSF on the detection plane is smaller than for conventional CW STED. Simulation shows the donut-shaped PSF of the depletion beam and confocal optics suppress undesired PSF sidelobes. Imaging experiments agree with the simulated resolution improvement.
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Affiliation(s)
- Geon Lim
- School of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea
| | - Wan-Chin Kim
- Department of Smart Manufacturing Applied Engineering, Hanbat National University, Daejeon, Republic of Korea
| | - Seunghee Oh
- School of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea
- Global Technology Center, Samsung Electronics, Suwon, Republic of Korea
| | - Hyungsuk Lee
- School of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea
| | - No-Cheol Park
- School of Mechanical Engineering, Yonsei University, Seoul, Republic of Korea
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29
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A photostable fluorescent marker for the superresolution live imaging of the dynamic structure of the mitochondrial cristae. Proc Natl Acad Sci U S A 2019; 116:15817-15822. [PMID: 31337683 DOI: 10.1073/pnas.1905924116] [Citation(s) in RCA: 112] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Stimulation emission depletion (STED) microscopy enables ultrastructural imaging of organelle dynamics with a high spatiotemporal resolution in living cells. For the visualization of the mitochondrial membrane dynamics in STED microscopy, rationally designed mitochondrial fluorescent markers with enhanced photostability are required. Herein, we report the development of a superphotostable fluorescent labeling reagent with long fluorescence lifetime, whose design is based on a structurally reinforced naphthophosphole fluorophore that is conjugated with an electron-donating diphenylamino group. The combination of long-lived fluorescence and superphotostable features of the fluorophore allowed us to selectively capture the ultrastructures of the mitochondrial cristae with a resolution of ∼60 nm when depleted at 660 nm. This chemical tool provides morphological information of the cristae, which has so far only been observed in fixed cells using electron microscopy. Moreover, this method gives information about the dynamic ultrastructures such as the intermembrane fusion in different mitochondria as well as the intercristae mergence in a single mitochondrion during the apoptosis-like mitochondrial swelling process.
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30
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Strategies to maximize performance in STimulated Emission Depletion (STED) nanoscopy of biological specimens. Methods 2019; 174:27-41. [PMID: 31344404 DOI: 10.1016/j.ymeth.2019.07.019] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 06/28/2019] [Accepted: 07/17/2019] [Indexed: 12/17/2022] Open
Abstract
Super-resolution fluorescence microscopy has become an important catalyst for discovery in the life sciences. In STimulated Emission Depletion (STED) microscopy, a pattern of light drives fluorophores from a signal-emitting on-state to a non-signalling off-state. Only emitters residing in a sub-diffraction volume around an intensity minimum are allowed to fluoresce, rendering them distinguishable from the nearby, but dark fluorophores. STED routinely achieves resolution in the few tens of nanometers range in biological samples and is suitable for live imaging. Here, we review the working principle of STED and provide general guidelines for successful STED imaging. The strive for ever higher resolution comes at the cost of increased light burden. We discuss techniques to reduce light exposure and mitigate its detrimental effects on the specimen. These include specialized illumination strategies as well as protecting fluorophores from photobleaching mediated by high-intensity STED light. This opens up the prospect of volumetric imaging in living cells and tissues with diffraction-unlimited resolution in all three spatial dimensions.
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31
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Abstract
STimulated emission depletion (STED) nanoscopy has been proposed to extend greatly our capability of using light to study a variety of biological problems with nanometer-scale resolution. However, in practice the unwanted background noise degrades the STED image quality and precludes quantitative analysis. Here, we discuss the underlying sources of the background noise in STED images, and review current approaches to alleviate this problem, such as time-gating, anti-Stokes excitation removal, and off-focus incomplete depletion suppression. Progress in correcting uncorrelated background photons in fluorescence correlation spectroscopy combined with STED (STED-FCS) will also be discussed.
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Affiliation(s)
- Ye Ma
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America
| | - Taekjip Ha
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, United States of America.,Departments of Biophysics and Biophysical Chemistry, Biophysics, Johns Hopkins University, Baltimore, MD, United States of America.,Howard Hughes Medical Institute, Baltimore, MD, United States of America.,Author to whom any correspondence should be addressed
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32
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Ishii H, Otomo K, Hung JH, Tsutsumi M, Yokoyama H, Nemoto T. Two-photon STED nanoscopy realizing 100-nm spatial resolution utilizing high-peak-power sub-nanosecond 655-nm pulses. BIOMEDICAL OPTICS EXPRESS 2019; 10:3104-3113. [PMID: 31467771 PMCID: PMC6706030 DOI: 10.1364/boe.10.003104] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Revised: 05/05/2019] [Accepted: 05/27/2019] [Indexed: 05/16/2023]
Abstract
We developed two-photon excitation stimulated emission depletion (STED) nanoscopy using high-peak-power sub-nanosecond 655-nm pulses. The STED pulse exhibited ideal optical properties and sufficient pulse energy to realize a 70-nm spatial resolution in the compact setup with electrically controllable components. For biological applications, we screened suitable fluorescent dyes or proteins and realized the sub-100 nm spatial resolution imaging of presynaptic protein clusters in fixed primary cultured neurons without severe photobleaching. We expect this method to enable visualization of ultrastructures and the cluster dynamics of biomolecules representing physiological functions in living cells and tissue.
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Affiliation(s)
- Hirokazu Ishii
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
| | - Kohei Otomo
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14 Nishi 9, Kita-ku, Sapporo 060-0814, Japan
| | - Jui-Hung Hung
- New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-10, Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Motosuke Tsutsumi
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
| | - Hiroyuki Yokoyama
- New Industry Creation Hatchery Center (NICHe), Tohoku University, 6-6-10, Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
- Graduate School of Engineering, Tohoku University, 6-6-05, Aoba, Aramaki, Aoba-ku, Sendai 980-8579, Japan
| | - Tomomi Nemoto
- Research Institute for Electronic Science, Hokkaido University, Kita 20 Nishi 10, Kita-ku, Sapporo 001-0020, Japan
- Graduate School of Information Science and Technology, Hokkaido University, Kita 14 Nishi 9, Kita-ku, Sapporo 060-0814, Japan
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33
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Combs CA, Sackett DL, Knutson JR. A simple empirical algorithm for optimising depletion power and resolution for dye and system specific STED imaging. J Microsc 2019; 274:168-176. [PMID: 31012103 DOI: 10.1111/jmi.12795] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Revised: 04/16/2019] [Accepted: 04/17/2019] [Indexed: 11/28/2022]
Abstract
Here we show an easy method for determining an effective dye saturation factor ('PSTED ') for STED (Stimulated Emission Depletion) microscopy. We define PSTED to be a combined microscope system plus dye factor (analogous to the traditional ground truth Is measurement, which is microscope independent) that is functionally defined as the power in the depletion beam that provides a resolution enhancement of 41% compared to confocal, according to the modified Abbe's formula for STED resolution enhancement. We show that the determination of PSTED provides insight not only into the suitability of a particular dye and the best imaging parameters to be used for an experiment, but also sets the critical value for correctly determining the point spread function (PSF) used in deconvolution of STED images. PSTED can be a function of many experimental variables, both microscope and sample related. Here we show the utility of doing PSTED determinations by (1) exploiting the simple relationship between width and a threshold-defined area provided by a Gaussian PSF, for either linear or spherical objects and (2) linearising the normally inverse hyperbolic function of resolution versus power that can determine PSTED . We show that this rearrangement allows us to determine PSTED using only a few measurements: either at a few relatively low depletion powers, on traditional bead size measurements or by finding the total area of a naturally occurring sub-limit sized biological feature (in this case, microtubules). We show the derivation of these equations and methods and the utility of its use by characterising several dyes and a local imaging parameter relevant to STED microscopy. This information is used to predict the enhancement of resolution of the point spread function necessary for post-processing deconvolution. LAY DESCRIPTION: Stimulated Emission Depletion (STED) microscopy is a fluorescence imaging superresolution technique that achieves tens of nanometres resolution. This is done by utilising a depletion laser to effectively quench (deplete) fluorescence in a donut shape overlapping the normally excited fluorescence spot. The size of the remaining (undepleted) central fluorescence spot is power dependent allowing 'tunable' resolution with the power of the STED depletion laser. This depletion power versus resolution relationship is dye and instrument dependent. We have developed a method for quickly measuring this relationship to optimise experiments based on individual dyes and microscope specific parameters. This allows for quickly optimising microscope settings and for correctly postprocessing images.
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Affiliation(s)
- Christian A Combs
- NHLBI Light Microscopy Facility, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Dan L Sackett
- NICHD Division of Basic and Translational Biophysics, National Institutes of Health, Bethesda, Maryland, U.S.A
| | - Jay R Knutson
- NHLBI Laboratory for Advanced Microscopy and Biophotonics, National Institutes of Health, Bethesda, Maryland, U.S.A
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34
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Tortarolo G, Sun Y, Teng KW, Ishitsuka Y, Lanzanó L, Selvin PR, Barbieri B, Diaspro A, Vicidomini G. Photon-separation to enhance the spatial resolution of pulsed STED microscopy. NANOSCALE 2019; 11:1754-1761. [PMID: 30624448 DOI: 10.1039/c8nr07485b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Stimulated emission depletion microscopy (STED) is one of the pivotal super-resolution techniques. It overcomes the spatial resolution limit imposed by the diffraction by using an additional laser beam, the STED beam, intensity of which is directly related to the achievable resolution. Despite reaching nanometer resolution, much effort in recent years has been devoted to reducing the STED beam intensity because it may lead to photo-damaging effects. Accessing the spatial information encoded in the temporal dynamics of the detected fluorescent photons has been proved to be a powerful strategy and has contributed to the separation by lifetime tuning (SPLIT) technique. The SPLIT method uses the phasor analysis to efficiently distinguish photons emitted from the center and the periphery of the excitation spot. It thus improves the resolution without increasing the STED beam intensity. This method was proposed for architectures based on the STED beam running in continuous waves (CW-STED microscopy). Here, we extend it to pulsed STED beam implementations (pSTED microscopy). We show, through simulated and experimental data, that the pSTED-SPLIT method reduces the detection volume of the pSTED microscope without significantly decreasing the signal-to-noise ratio of the final image, thus effectively improving the resolution without increasing the STED beam intensity.
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Affiliation(s)
- Giorgio Tortarolo
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Via Morego 30, 16163, Genoa, Italy.
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35
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Scipioni L, Lanzanó L, Diaspro A, Gratton E. Comprehensive correlation analysis for super-resolution dynamic fingerprinting of cellular compartments using the Zeiss Airyscan detector. Nat Commun 2018; 9:5120. [PMID: 30504919 PMCID: PMC6269422 DOI: 10.1038/s41467-018-07513-2] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Accepted: 10/29/2018] [Indexed: 11/08/2022] Open
Abstract
The availability of the Airyscan detector in the Zeiss LSM 880 has made possible the development of a new concept in fluctuation correlation spectroscopy using super-resolution. The Airyscan unit acquires data simultaneously on 32 detectors arranged in a hexagonal array. This detector opens up the possibility to use fluctuation methods based on time correlation at single points or at a number of points simultaneously, as well as methods based on spatial correlation in the area covered by the detector. Given the frame rate of this detector, millions of frames can be acquired in seconds, providing a robust statistical basis for fluctuation data. We apply the comprehensive analysis to the molecular fluctuations of free GFP diffusing in live cells at different subcellular compartments to show that at the nanoscale different cell environments can be distinguished by the comprehensive fluctuation analysis.
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Affiliation(s)
- L Scipioni
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, 92697, CA, USA
| | - L Lanzanó
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - A Diaspro
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
- Nikon Imaging Center, Istituto Italiano di Tecnologia, Genoa, 16163, Italy
| | - E Gratton
- Laboratory for Fluorescence Dynamics, Department of Biomedical Engineering, University of California, Irvine, 92697, CA, USA.
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36
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Barentine AE, Schroeder LK, Graff M, Baddeley D, Bewersdorf J. Simultaneously Measuring Image Features and Resolution in Live-Cell STED Images. Biophys J 2018; 115:951-956. [PMID: 30139523 PMCID: PMC6139878 DOI: 10.1016/j.bpj.2018.07.028] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 06/27/2018] [Accepted: 07/24/2018] [Indexed: 11/26/2022] Open
Abstract
Reliable interpretation and quantification of cellular features in fluorescence microscopy requires an accurate estimate of microscope resolution. This is typically obtained by measuring the image of a nonbiological proxy for a point-like object, such as a fluorescent bead. Although appropriate for confocal microscopy, bead-based measurements are problematic for stimulated emission depletion microscopy and similar techniques where the resolution depends critically on the choice of fluorophore and acquisition parameters. In this article, we demonstrate that for a known geometry (e.g., tubules), the resolution can be measured in situ by fitting a model that accounts for both the point spread function (PSF) and the fluorophore distribution. To address the problem of coupling between tubule diameter and PSF width, we developed a technique called nested-loop ensemble PSF fitting. This approach enables extraction of the size of cellular features and the PSF width in fixed-cell and live-cell images without relying on beads or precalibration. Nested-loop ensemble PSF fitting accurately recapitulates microtubule diameter from stimulated emission depletion images and can measure the diameter of endoplasmic reticulum tubules in live COS-7 cells. Our algorithm has been implemented as a plugin for the PYthon Microscopy Environment, a freely available and open-source software.
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Affiliation(s)
- Andrew E.S. Barentine
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut,Department of Biomedical Engineering, Yale University, New Haven, Connecticut
| | - Lena K. Schroeder
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
| | - Michael Graff
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut
| | - David Baddeley
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut; Auckland Bioengineering Institute, University of Auckland, Auckland, New Zealand.
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut; Department of Biomedical Engineering, Yale University, New Haven, Connecticut.
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37
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Wang L, Chen B, Yan W, Yang Z, Peng X, Lin D, Weng X, Ye T, Qu J. Resolution improvement in STED super-resolution microscopy at low power using a phasor plot approach. NANOSCALE 2018; 10:16252-16260. [PMID: 30124714 DOI: 10.1039/c8nr03584a] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Stimulated emission depletion (STED) microscopy is a powerful super-resolution microscopy technique that has achieved significant results in breaking the resolution limit and relevant applications. In principle, STED super resolution is obtained by stimulated emission partially inhibiting the spontaneous emission in the periphery of a diffraction-limited area. However, very high depletion laser power is generally necessary for the enhancement of imaging resolution, which is harmful to live biological specimens due to its high phototoxicity and photo-bleaching effects. Therefore, further improving the STED resolution at a lower depletion power level has recently attracted increasing interest from researchers in various fields. In this work, a phasor plot approach combined with fluorescence lifetime imaging microscopy (FLIM) is used to resolve the abovementioned problem based on a long- and short-lifetime criterion. Firstly, the time-resolved data obtained by STED-FLIM is converted to the frequency domain via a phasor approach. Next, partial data is extracted according to the information on the phase and amplitude for resolution improvement. Then, fluorescent microspheres (100 nm in diameter) are observed under different depletion powers, resulting in a series of improved resolution through phasor plots. Finally, this method is applied to image human Nup153 in fixed HeLa cells, providing a 86 nm higher resolution than that in traditional STED imaging at a depletion power of 20 mW.
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Affiliation(s)
- Luwei Wang
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen 518060, China.
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38
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Ye S, Yan W, Zhao M, Peng X, Song J, Qu J. Low-Saturation-Intensity, High-Photostability, and High-Resolution STED Nanoscopy Assisted by CsPbBr 3 Quantum Dots. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2018; 30:e1800167. [PMID: 29687514 DOI: 10.1002/adma.201800167] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2018] [Revised: 02/21/2018] [Indexed: 06/08/2023]
Abstract
Stimulated emission depletion (STED) nanoscopy is one of the most promising super-resolution imaging techniques for microstructure imaging. Commercial CdSe@ZnS quantum dots are used as STED probes and ≈50 nm lateral resolution is obtained. Compared with other quantum dots, perovskite CsPbBr3 nanoparticles (NPs) possess higher photoluminescence quantum yield and larger absorption cross-section, making them a more effective probe for STED nanoscopy. In this study, CsPbBr3 NPs are used as probes for STED nanoscopy imaging. The fluorescence intensity of the CsPbBr3 sample is hardly weakened at all after 200 min irradiation with a 39.8 mW depletion laser, indicating excellent photobleaching resistance of the CsPbBr3 NPs. The saturation intensity of the CsPbBr3 NPs is extremely low and estimated to be only 0.4 mW (0.126 MW cm-2 ). Finally, an ultrahigh lateral resolution of 20.6 nm is obtained for a single nanoparticle under 27.5 mW STED laser irradiation in CsPbBr3 -based STED nanoscopy imaging, which is a tenfold improvement compared with confocal microscopy. Because of its high fluorescence stability and ultrahigh resolution under lower depletion power, CsPbBr3 -assisted STED nanoscopy has great potential to investigate microstructures that require super-resolution and long-term imaging.
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Affiliation(s)
- Shuai Ye
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Wei Yan
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Mengjie Zhao
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Xiao Peng
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Jun Song
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
| | - Junle Qu
- Key Laboratory of Optoelectronic Devices and Systems of Ministry of Education and Guangdong Province, College of Optoelectronic Engineering, Shenzhen University, Shenzhen, 518060, P. R. China
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39
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Heine J, Wurm CA, Keller-Findeisen J, Schönle A, Harke B, Reuss M, Winter FR, Donnert G. Three dimensional live-cell STED microscopy at increased depth using a water immersion objective. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2018; 89:053701. [PMID: 29864829 DOI: 10.1063/1.5020249] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Modern fluorescence superresolution microscopes are capable of imaging living cells on the nanometer scale. One of those techniques is stimulated emission depletion (STED) which increases the microscope's resolution many times in the lateral and the axial directions. To achieve these high resolutions not only close to the coverslip but also at greater depths, the choice of objective becomes crucial. Oil immersion objectives have frequently been used for STED imaging since their high numerical aperture (NA) leads to high spatial resolutions. But during live-cell imaging, especially at great penetration depths, these objectives have a distinct disadvantage. The refractive index mismatch between the immersion oil and the usually aqueous embedding media of living specimens results in unwanted spherical aberrations. These aberrations distort the point spread functions (PSFs). Notably, during z- and 3D-STED imaging, the resolution increase along the optical axis is majorly hampered if at all possible. To overcome this limitation, we here use a water immersion objective in combination with a spatial light modulator for z-STED measurements of living samples at great depths. This compact design allows for switching between objectives without having to adapt the STED beam path and enables on the fly alterations of the STED PSF to correct for aberrations. Furthermore, we derive the influence of the NA on the axial STED resolution theoretically and experimentally. We show under live-cell imaging conditions that a water immersion objective leads to far superior results than an oil immersion objective at penetration depths of 5-180 μm.
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Affiliation(s)
- Jörn Heine
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Christian A Wurm
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Jan Keller-Findeisen
- Department of NanoBiophotonics, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Andreas Schönle
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Benjamin Harke
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Matthias Reuss
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Franziska R Winter
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Gerald Donnert
- Abberior Instruments GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
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40
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Lee WS, Lim G, Kim WC, Choi GJ, Yi HW, Park NC. Investigation on improvement of lateral resolution of continuous wave STED microscopy by standing wave illumination. OPTICS EXPRESS 2018; 26:9901-9919. [PMID: 29715937 DOI: 10.1364/oe.26.009901] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Accepted: 03/24/2018] [Indexed: 06/08/2023]
Abstract
In this paper, we report the enhancement of resolution of continuous wave (CW) stimulated emission depletion (STED) microscopy by a novel method of structured illumination of an excitation beam. Illumination by multiple excitation beams through the specific pupil apertures with high in-plane wave vectors leads to interference of diffracted light flux near the focal plane, resulting in the contraction of the point spread function (PSF) of the excitation. Light spot reduction by the suggested standing wave (SW) illumination method contributes to make up much lower depletion efficiency of the CW STED microscopy than that of the pulsed STED method. First, theoretical analysis showed that the full width at half maximum (FWHM) of the effective PSF on the detection plane is expected to be smaller than 25% of that of conventional CW STED. Second, through the simulation, it was elucidated that both the donut-shaped PSF of the depletion beam and the confocal optics suppress undesired contribution of sidelobes of the PSF by the SW illumination to the effective PSF of the STED system. Finally, through the imaging experiment on 40-nm fluorescent beads with the developed SW-CW STED microscopy system, we obtained the result which follows the overall tendency from the simulation in the aspects of resolution improvement and reduction of sidelobes. Based on the obtained result, we expect that the proposed method can become one of the strategies to enhance the resolution of the CW STED microscopy.
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41
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Li C, Liu S, Wang W, Liu W, Kuang C, Liu X. Recent research on stimulated emission depletion microscopy for reducing photobleaching. J Microsc 2018; 271:4-16. [PMID: 29600565 DOI: 10.1111/jmi.12698] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2017] [Revised: 02/23/2018] [Accepted: 02/28/2018] [Indexed: 12/11/2022]
Abstract
Stimulated emission depletion (STED) microscopy is a useful tool in investigation for super-resolution realm. By silencing the peripheral fluorophores of the excited spot, leaving only the very centre zone vigorous for fluorescence, the effective point spread function (PSF) could be immensely squeezed and subcellular structures, such as organelles, become discernable. Nevertheless, because of the low cross-section of stimulated emission and the short fluorescence lifetime, the depletion power density has to be extremely higher than the excitation power density and molecules are exposed in high risk of photobleaching. The existence of photobleaching greatly limits the research of STED in achieving higher resolution and more delicate imaging quality, as well as long-term and dynamic observation. Since the first experimental implementation of STED microscopy, researchers have lift out variety of methods and techniques to alleviate the problem. This paper would present some researches via conventional methods which have been explored and utilised relatively thoroughly, such as fast scanning, time-gating, two-photon excitation (TPE), triplet relaxation (T-Rex) and background suppression. Alternatively, several up-to-date techniques, especially adaptive illumination, would also be unveiled for discussion in this paper. The contrast and discussion of these modalities would play an important role in ameliorating the research of STED microscopy.
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Affiliation(s)
- C Li
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - S Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - W Wang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - W Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - C Kuang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - X Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
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42
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Combs CA, Shroff H. Fluorescence Microscopy: A Concise Guide to Current Imaging Methods. ACTA ACUST UNITED AC 2018; 79:2.1.1-2.1.25. [DOI: 10.1002/cpns.29] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Christian A. Combs
- NHLBI Light Microscopy Facility, National Institutes of Health Bethesda Maryland
| | - Hari Shroff
- NIBIB Section on High Resolution Optical Imaging, National Institutes of Health Bethesda Maryland
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43
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Vicidomini G, Bianchini P, Diaspro A. STED super-resolved microscopy. Nat Methods 2018; 15:173-182. [DOI: 10.1038/nmeth.4593] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2017] [Accepted: 08/23/2017] [Indexed: 12/18/2022]
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44
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Sarangi NK, Basu JK. Pathways for creation and annihilation of nanoscale biomembrane domains reveal alpha and beta-toxin nanopore formation processes. Phys Chem Chem Phys 2018; 20:29116-29130. [DOI: 10.1039/c8cp05729j] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Raft-like functional domains with putative sizes of 20–200 nm and which are evolving dynamically are believed to be the most crucial regions in cellular membranes which determine cell signaling and various functions of cells.
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Affiliation(s)
| | - Jaydeep Kumar Basu
- Department of Physics
- Indian Institute of Science
- Bangalore – 560 012
- India
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45
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Söderström B, Chan H, Shilling PJ, Skoglund U, Daley DO. Spatial separation of FtsZ and FtsN during cell division. Mol Microbiol 2017; 107:387-401. [DOI: 10.1111/mmi.13888] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Revised: 11/17/2017] [Accepted: 11/24/2017] [Indexed: 01/07/2023]
Affiliation(s)
- Bill Söderström
- Structural Cellular Biology Unit; Okinawa Institute of Science and Technology; Okinawa 904-0495 Japan
| | - Helena Chan
- Structural Cellular Biology Unit; Okinawa Institute of Science and Technology; Okinawa 904-0495 Japan
| | - Patrick J. Shilling
- Department of Biochemistry and Biophysics; Stockholm University; Stockholm 106 91 Sweden
| | - Ulf Skoglund
- Structural Cellular Biology Unit; Okinawa Institute of Science and Technology; Okinawa 904-0495 Japan
| | - Daniel O. Daley
- Department of Biochemistry and Biophysics; Stockholm University; Stockholm 106 91 Sweden
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46
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Diffraction-Unlimited Fluorescence Imaging with an EasySTED Retrofitted Confocal Microscope. Methods Mol Biol 2017. [PMID: 28924657 DOI: 10.1007/978-1-4939-7265-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
The easySTED technology provides the means to retrofit a confocal microscope to a diffraction-unlimited stimulated emission depletion (STED) microscope.Although commercial STED systems are available today, for many users of confocal laser scanning microscopes the option of retrofitting their confocal system to a STED system ready for diffraction-unlimited imaging may present an attractive option. The easySTED principle allowing for a joint beam path of excitation and depletion light promises some advantages concerning technical complexity and alignment effort for such an STED upgrade. In the one beam path design of easySTED the use of a common laser source, either a supercontinuum source or two separate lasers coupled into the same single-mode fiber, becomes feasible. The alignment of the focal light distribution of the STED beam relative to that of the excitation beam in all three spatial dimensions is therefore omitted respectively reduced to coupling the STED laser into the common single-mode fiber. Thus, only minor modifications need to be applied to the beam path in the confocal microscope to be upgraded. Those comprise adding polarization control elements and the easySTED waveplate, and adapting the beamsplitter to the excitation/STED wavelength combination.
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47
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Sarangi NK, Ayappa KG, Basu JK. Complex dynamics at the nanoscale in simple biomembranes. Sci Rep 2017; 7:11173. [PMID: 28894156 PMCID: PMC5593986 DOI: 10.1038/s41598-017-11068-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Accepted: 07/28/2017] [Indexed: 11/25/2022] Open
Abstract
Nature is known to engineer complex compositional and dynamical platforms in biological membranes. Understanding this complex landscape requires techniques to simultaneously detect membrane re-organization and dynamics at the nanoscale. Using super-resolution stimulated emission depletion (STED) microscopy coupled with fluorescence correlation spectroscopy (FCS), we reveal direct experimental evidence of dynamic heterogeneity at the nanoscale in binary phospholipid-cholesterol bilayers. Domain formation on the length scale of ~200–600 nm due to local cholesterol compositional heterogeneity is found to be more prominent at high cholesterol content giving rise to distinct intra-domain lipid dynamics. STED-FCS reveals unique dynamical crossover phenomena at length scales of ~100–150 nm within each of these macroscopic regions. The extent of dynamic heterogeneity due to intra-domain hindered lipid diffusion as reflected from the crossover length scale, is driven by cholesterol packing and organization, uniquely influenced by phospholipid type. These results on simple binary model bilayer systems provide novel insights into pathways leading to the emergence of complex nanodomain substructures with implications for a wide variety of membrane mediated cellular events.
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Affiliation(s)
- Nirod Kumar Sarangi
- Department of Physics, Indian Institute of Science, Bangalore, 560 012, India
| | - K G Ayappa
- Department of Chemical Engineering, Indian Institute of Science, Bangalore, 560 012, India. .,Center for Biosystems Science and Engineering, Indian Institute of Science, Bangalore, 560 012, India.
| | - Jaydeep Kumar Basu
- Department of Physics, Indian Institute of Science, Bangalore, 560 012, India.
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48
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Castello M, Tortarolo G, Coto Hernández I, Deguchi T, Diaspro A, Vicidomini G. Removal of anti-Stokes emission background in STED microscopy by FPGA-based synchronous detection. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2017; 88:053701. [PMID: 28571439 DOI: 10.1063/1.4983082] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
In stimulated emission depletion (STED) microscopy, the role of the STED beam is to de-excite, via stimulated emission, the fluorophores that have been previously excited by the excitation beam. This condition, together with specific beam intensity distributions, allows obtaining true sub-diffraction spatial resolution images. However, if the STED beam has a non-negligible probability to excite the fluorophores, a strong fluorescent background signal (anti-Stokes emission) reduces the effective resolution. For STED scanning microscopy, different synchronous detection methods have been proposed to remove this anti-Stokes emission background and recover the resolution. However, every method works only for a specific STED microscopy implementation. Here we present a user-friendly synchronous detection method compatible with any STED scanning microscope. It exploits a data acquisition (DAQ) card based on a field-programmable gate array (FPGA), which is progressively used in STED microscopy. In essence, the FPGA-based DAQ card synchronizes the fluorescent signal registration, the beam deflection, and the excitation beam interruption, providing a fully automatic pixel-by-pixel synchronous detection method. We validate the proposed method in both continuous wave and pulsed STED microscope systems.
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Affiliation(s)
- M Castello
- Molecular Microscopy and Spectroscopy, Nanophysics, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - G Tortarolo
- Molecular Microscopy and Spectroscopy, Nanophysics, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - I Coto Hernández
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - T Deguchi
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - A Diaspro
- Nanoscopy, Nanophysics, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
| | - G Vicidomini
- Molecular Microscopy and Spectroscopy, Nanophysics, Istituto Italiano di Tecnologia, Via Morego 30, 16163 Genoa, Italy
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49
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Gao P, Nienhaus GU. Precise background subtraction in stimulated emission double depletion nanoscopy. OPTICS LETTERS 2017; 42:831-834. [PMID: 28198876 DOI: 10.1364/ol.42.000831] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/09/2017] [Accepted: 01/26/2017] [Indexed: 06/06/2023]
Abstract
Low-resolution background in stimulated emission depletion (STED) nanoscopy can arise from incomplete depletion or re-excitation by the STED beam. We have recently introduced stimulated emission double depletion (STEDD), a technique to efficiently suppress this background. In STEDD, the conventional, doughnut-shaped STED pulse, which depletes excited fluorophores outside the center of the focal region, is followed by a second Gaussian STED pulse, which specifically depletes the central region. The background is removed by calculating a weighted difference of photon events collected before and after the second STED pulse. Here, we present a simple, yet powerful, method to determine the weight factor, which depends on the fluorescence decay, from a direct analysis of the acquired data. We vary the weight factor to identify its optimal value as the one for which the weight of high-frequency components in the spectrum of the acquired STEDD image is maximized. This strategy is also applicable to other differential approaches for background suppression in imaging.
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50
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Cortés E, Huidobro PA, Sinclair HG, Guldbrand S, Peveler WJ, Davies T, Parrinello S, Görlitz F, Dunsby C, Neil MAA, Sivan Y, Parkin IP, French PMW, Maier SA. Plasmonic Nanoprobes for Stimulated Emission Depletion Nanoscopy. ACS NANO 2016; 10:10454-10461. [PMID: 27794591 DOI: 10.1021/acsnano.6b06361] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Plasmonic nanoparticles influence the absorption and emission processes of nearby emitters due to local enhancements of the illuminating radiation and the photonic density of states. Here, we use the plasmon resonance of metal nanoparticles in order to enhance the stimulated depletion of excited molecules for super-resolved nanoscopy. We demonstrate stimulated emission depletion (STED) nanoscopy with gold nanorods with a long axis of only 26 nm and a width of 8 nm. These particles provide an enhancement of up to 50% of the resolution compared to fluorescent-only probes without plasmonic components irradiated with the same depletion power. The nanoparticle-assisted STED probes reported here represent a ∼2 × 103 reduction in probe volume compared to previously used nanoparticles. Finally, we demonstrate their application toward plasmon-assisted STED cellular imaging at low-depletion powers, and we also discuss their current limitations.
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Affiliation(s)
| | | | | | | | - William J Peveler
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
| | | | | | | | | | | | - Yonatan Sivan
- Unit of Electro-optics Engineering, Ben-Gurion University , Beer-Sheba 8410501, Israel
| | - Ivan P Parkin
- Department of Chemistry, University College London , 20 Gordon Street, London WC1H 0AJ, United Kingdom
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