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Gaire SK, Daneshkhah A, Flowerday E, Gong R, Frederick J, Backman V. Deep learning-based spectroscopic single-molecule localization microscopy. JOURNAL OF BIOMEDICAL OPTICS 2024; 29:066501. [PMID: 38799979 PMCID: PMC11122423 DOI: 10.1117/1.jbo.29.6.066501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 05/03/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024]
Abstract
Significance Spectroscopic single-molecule localization microscopy (sSMLM) takes advantage of nanoscopy and spectroscopy, enabling sub-10 nm resolution as well as simultaneous multicolor imaging of multi-labeled samples. Reconstruction of raw sSMLM data using deep learning is a promising approach for visualizing the subcellular structures at the nanoscale. Aim Develop a novel computational approach leveraging deep learning to reconstruct both label-free and fluorescence-labeled sSMLM imaging data. Approach We developed a two-network-model based deep learning algorithm, termed DsSMLM, to reconstruct sSMLM data. The effectiveness of DsSMLM was assessed by conducting imaging experiments on diverse samples, including label-free single-stranded DNA (ssDNA) fiber, fluorescence-labeled histone markers on COS-7 and U2OS cells, and simultaneous multicolor imaging of synthetic DNA origami nanoruler. Results For label-free imaging, a spatial resolution of 6.22 nm was achieved on ssDNA fiber; for fluorescence-labeled imaging, DsSMLM revealed the distribution of chromatin-rich and chromatin-poor regions defined by histone markers on the cell nucleus and also offered simultaneous multicolor imaging of nanoruler samples, distinguishing two dyes labeled in three emitting points with a separation distance of 40 nm. With DsSMLM, we observed enhanced spectral profiles with 8.8% higher localization detection for single-color imaging and up to 5.05% higher localization detection for simultaneous two-color imaging. Conclusions We demonstrate the feasibility of deep learning-based reconstruction for sSMLM imaging applicable to label-free and fluorescence-labeled sSMLM imaging data. We anticipate our technique will be a valuable tool for high-quality super-resolution imaging for a deeper understanding of DNA molecules' photophysics and will facilitate the investigation of multiple nanoscopic cellular structures and their interactions.
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Affiliation(s)
- Sunil Kumar Gaire
- North Carolina Agricultural and Technical State University, Department of Electrical and Computer Engineering, Greensboro, North Carolina, United States
| | - Ali Daneshkhah
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Ethan Flowerday
- University of Tulsa, Department of Computer Science and Cyber Security, Tulsa, Oklahoma, United States
| | - Ruyi Gong
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Jane Frederick
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
| | - Vadim Backman
- Northwestern University, Department of Biomedical Engineering, Evanston, Illinois, United States
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2
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Ossia Y, Levi A, Chefetz N, Peleg A, Remennik S, Vakahi A, Banin U. Seeing is believing: Correlating optoelectronic functionality with atomic scale imaging of single semiconductor nanocrystals. J Chem Phys 2024; 160:134201. [PMID: 38573848 DOI: 10.1063/5.0198140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 02/29/2024] [Indexed: 04/06/2024] Open
Abstract
A unique on-chip method for the direct correlation of optical properties, with atomic-scale chemical-structural characteristics for a single quantum dot (QD), is developed and utilized in various examples. This is based on performing single QD optical characterization on a modified glass substrate, followed by the extraction of the relevant region of interest by focused-ion-beam-scanning electron microscope processing into a lamella for high resolution scanning transmission electron microscopy (STEM) characterization with atomic scale resolution. The direct correlation of the optical response under an electric field with STEM analysis of the same particle allows addressing several single particle phenomena: first, the direct correlation of single QD photoluminescence (PL) polarization and its response to the external field with the QD crystal lattice alignment, so far inferred indirectly; second, the identification of unique yet rare few-QD assemblies, correlated directly with their special spectroscopic optical characteristics, serving as a guide for future designed assemblies; and third, the study on the effect of metal island growth on the PL behavior of hybrid semiconductor-metal nanoparticles, with relevance for their possible functionality in photocatalysis. This work, therefore, establishes the use of the direct on-chip optical-structural correlation method for numerous scenarios and timely questions in the field of QD research.
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Affiliation(s)
- Yonatan Ossia
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Adar Levi
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Nadav Chefetz
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Amir Peleg
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Sergei Remennik
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Atzmon Vakahi
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Uri Banin
- Institute of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
- The Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
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3
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Dunlap MK, Ryan DP, Goodwin PM, Sheehan CJ, Werner JH, Majumder S, Hollingsworth JA, Gelfand MP, Van Orden A. Nanoscale imaging of quantum dot dimers using time-resolved super-resolution microscopy combined with scanning electron microscopy. NANOTECHNOLOGY 2023; 34:275202. [PMID: 37011598 DOI: 10.1088/1361-6528/acc9c9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/03/2023] [Indexed: 06/19/2023]
Abstract
Time-resolved super-resolution microscopy was used in conjunction with scanning electron microscopy to image individual colloidal CdSe/CdS semiconductor quantum dots (QD) and QD dimers. The photoluminescence (PL) lifetimes, intensities, and structural parameters were acquired with nanometer scale spatial resolution and sub-nanosecond time resolution. The combination of these two techniques was more powerful than either alone, enabling us to resolve the PL properties of individual QDs within QD dimers as they blinked on and off, measure interparticle distances, and identify QDs that may be participating in energy transfer. The localization precision of our optical imaging technique was ∼3 nm, low enough that the emission from individual QDs within the dimers could be spatially resolved. While the majority of QDs within dimers acted as independent emitters, at least one pair of QDs in our study exhibited lifetime and intensity behaviors consistent with resonance energy transfer from a shorter lifetime and lower intensity donor QD to a longer lifetime and higher intensity acceptor QD. For this case, we demonstrate how the combined super-resolution optical imaging and scanning electron microscopy data can be used to characterize the energy transfer rate.
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Affiliation(s)
- Megan K Dunlap
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, United States of America
| | - Duncan P Ryan
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Peter M Goodwin
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Chris J Sheehan
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - James H Werner
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Somak Majumder
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Jennifer A Hollingsworth
- Center for Integrated Nanotechnologies, Los Alamos National Laboratory, Los Alamos, NM 87545, United States of America
| | - Martin P Gelfand
- Department of Physics, Colorado State University, Fort Collins, CO 80523-1872, United States of America
| | - Alan Van Orden
- Department of Chemistry, Colorado State University, Fort Collins, CO 80523, United States of America
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Sartor A, Dahlberg PD, Perez D, Moerner WE. Characterization of mApple as a Red Fluorescent Protein for Cryogenic Single-Molecule Imaging with Turn-Off and Turn-On Active Control Mechanisms. J Phys Chem B 2023; 127:2690-2700. [PMID: 36943356 PMCID: PMC10069424 DOI: 10.1021/acs.jpcb.2c08995] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 03/01/2023] [Indexed: 03/23/2023]
Abstract
Single-molecule superresolution microscopy is a powerful tool for the study of biological structures on size scales smaller than the optical diffraction limit. Imaging samples at cryogenic temperatures (77 K) reduces the quantum yield of photobleaching for many fluorescent labels, yielding localization precisions below 10 nm. Cryogenic imaging further enables correlation with cryogenic electron tomography. A key limitation in applying methods such as PALM and STORM to samples maintained at 77 K is the limited number of fluorophores known to undergo efficient turn-on and turn-off mechanisms necessary to control the sparsity of active emitters. We find that mApple, a red-emitting fluorescent protein, undergoes a novel turn-off mechanism in response to simultaneous illumination with two colors of light. This turn-off mechanism enables localization of many individual molecules in initially bright samples, but the final density of localizable emitters is limited by relatively inefficient turn-on (photoactivation). Bulk excitation and emission spectroscopy shows that mApple has access to two distinct emissive states as well as dark states accessible optically or through changes in pH. The bright and stable emission of mApple enables widefield collection of single-molecule emission spectra, which highlight the complex nature and environmental sensitivity of states observed in red fluorescent proteins.
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Affiliation(s)
- Annina
M. Sartor
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - Peter D. Dahlberg
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
- Division
of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, California 94025, United States
| | - Davis Perez
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department
of Chemistry, Stanford University, Stanford, California 94305, United States
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Dahlberg PD, Perez D, Hecksel CW, Chiu W, Moerner WE. Metallic support films reduce optical heating in cryogenic correlative light and electron tomography. J Struct Biol 2022; 214:107901. [PMID: 36191745 PMCID: PMC9729463 DOI: 10.1016/j.jsb.2022.107901] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 08/28/2022] [Accepted: 09/26/2022] [Indexed: 12/30/2022]
Abstract
Super-resolved cryogenic correlative light and electron tomography is an emerging method that provides both the single-molecule sensitivity and specificity of fluorescence imaging, and the molecular scale resolution and detailed cellular context of tomography, all in vitrified cells preserved in their native hydrated state. Technical hurdles that limit these correlative experiments need to be overcome for the full potential of this approach to be realized. Chief among these is sample heating due to optical excitation which leads to devitrification, a phase transition from amorphous to crystalline ice. Here we show that much of this heating is due to the material properties of the support film of the electron microscopy grid, specifically the absorptivity and thermal conductivity. We demonstrate through experiment and simulation that the properties of the standard holey carbon electron microscopy grid lead to substantial heating under optical excitation. In order to avoid devitrification, optical excitation intensities must be kept orders of magnitude lower than the intensities commonly employed in room temperature super-resolution experiments. We further show that the use of metallic films, either holey gold grids, or custom made holey silver grids, alleviate much of this heating. For example, the holey silver grids permit 20× the optical intensities used on the standard holey carbon grids. Super-resolution correlative experiments conducted on holey silver grids under these increased optical excitation intensities have a corresponding increase in the rate of single-molecule fluorescence localizations. This results in an increased density of localizations and improved correlative imaging without deleterious effects from sample heating.
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Affiliation(s)
- Peter D Dahlberg
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
| | - Davis Perez
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
| | - Corey W Hecksel
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Wah Chiu
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA; Department of Bioengineering, Stanford University, Stanford, CA 94305, USA
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, CA 94305, USA
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6
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Perez D, Dahlberg PD, Wang J, Sartor AM, Borden JS, Shapiro L, Moerner WE. Identification and demonstration of roGFP2 as an environmental sensor for cryogenic correlative light and electron microscopy. J Struct Biol 2022; 214:107881. [PMID: 35811036 PMCID: PMC9452478 DOI: 10.1016/j.jsb.2022.107881] [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: 02/22/2022] [Revised: 06/29/2022] [Accepted: 07/04/2022] [Indexed: 10/17/2022]
Abstract
Cryogenic correlative light and electron microscopy (cryo-CLEM) seeks to leverage orthogonal information present in two powerful imaging modalities. While recent advances in cryogenic electron microscopy (cryo-EM) allow for the visualization and identification of structures within cells at the nanometer scale, information regarding the cellular environment, such as pH, membrane potential, ionic strength, etc., which influences the observed structures remains absent. Fluorescence microscopy can potentially be used to reveal this information when specific labels, known as fluorescent biosensors, are used, but there has been minimal use of such biosensors in cryo-CLEM to date. Here we demonstrate the applicability of one such biosensor, the fluorescent protein roGFP2, for cryo-CLEM experiments. At room temperature, the ratio of roGFP2 emission brightness when excited at 425 nm or 488 nm is known to report on the local redox potential. When samples containing roGFP2 are rapidly cooled to 77 K in a manner compatible with cryo-EM, the ratio of excitation peaks remains a faithful indicator of the redox potential at the time of freezing. Using purified protein in different oxidizing/reducing environments, we generate a calibration curve which can be used to analyze in situ measurements. As a proof-of-principle demonstration, we investigate the oxidation/reduction state within vitrified Caulobacter crescentus cells. The polar organizing protein Z (PopZ) localizes to the polar regions of C. crescentus where it is known to form a distinct microdomain. By expressing an inducible roGFP2-PopZ fusion we visualize individual microdomains in the context of their redox environment.
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Affiliation(s)
- Davis Perez
- Department of Chemistry, Stanford University, United States
| | - Peter D Dahlberg
- Division of CryoEM and Bioimaging, Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, United States
| | - Jiarui Wang
- Department of Chemistry, Stanford University, United States; Department of Developmental Biology, Stanford University, United States
| | | | - Julia S Borden
- Department of Molecular and Cell Biology, University of California, Berkeley, United States
| | - Lucy Shapiro
- Department of Developmental Biology, Stanford University, United States
| | - W E Moerner
- Department of Chemistry, Stanford University, United States
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7
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Dahlberg PD, Moerner WE. Cryogenic Super-Resolution Fluorescence and Electron Microscopy Correlated at the Nanoscale. Annu Rev Phys Chem 2021; 72:253-278. [PMID: 33441030 PMCID: PMC8877847 DOI: 10.1146/annurev-physchem-090319-051546] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/28/2023]
Abstract
We review the emerging method of super-resolved cryogenic correlative light and electron microscopy (srCryoCLEM). Super-resolution (SR) fluorescence microscopy and cryogenic electron tomography (CET) are both powerful techniques for observing subcellular organization, but each approach has unique limitations. The combination of the two brings the single-molecule sensitivity and specificity of SR to the detailed cellular context and molecular scale resolution of CET. The resulting correlative data is more informative than the sum of its parts. The correlative images can be used to pinpoint the positions of fluorescently labeled proteins in the high-resolution context of CET with nanometer-scale precision and/or to identify proteins in electron-dense structures. The execution of srCryoCLEM is challenging and the approach is best described as a method that is still in its infancy with numerous technical challenges. In this review, we describe state-of-the-art srCryoCLEM experiments, discuss the most pressing challenges, and give a brief outlook on future applications.
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Affiliation(s)
- Peter D Dahlberg
- Department of Chemistry, Stanford University, Stanford, California 94305, USA;
| | - W E Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, USA;
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8
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Wu GH, Mitchell PG, Galaz-Montoya JG, Hecksel CW, Sontag EM, Gangadharan V, Marshman J, Mankus D, Bisher ME, Lytton-Jean AKR, Frydman J, Czymmek K, Chiu W. Multi-scale 3D Cryo-Correlative Microscopy for Vitrified Cells. Structure 2020; 28:1231-1237.e3. [PMID: 32814034 PMCID: PMC7642057 DOI: 10.1016/j.str.2020.07.017] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Revised: 07/10/2020] [Accepted: 07/29/2020] [Indexed: 10/23/2022]
Abstract
Three-dimensional (3D) visualization of vitrified cells can uncover structures of subcellular complexes without chemical fixation or staining. Here, we present a pipeline integrating three imaging modalities to visualize the same specimen at cryogenic temperature at different scales: cryo-fluorescence confocal microscopy, volume cryo-focused ion beam scanning electron microscopy, and transmission cryo-electron tomography. Our proof-of-concept benchmark revealed the 3D distribution of organelles and subcellular structures in whole heat-shocked yeast cells, including the ultrastructure of protein inclusions that recruit fluorescently-labeled chaperone Hsp104. Since our workflow efficiently integrates imaging at three different scales and can be applied to other types of cells, it could be used for large-scale phenotypic studies of frozen-hydrated specimens in a variety of healthy and diseased conditions with and without treatments.
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Affiliation(s)
- Gong-Her Wu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Patrick G Mitchell
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Jesus G Galaz-Montoya
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Corey W Hecksel
- Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA
| | - Emily M Sontag
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | | | - Jeffrey Marshman
- Zeiss Research Microscopy Solutions, White Plains, NY 10601, USA
| | - David Mankus
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Margaret E Bisher
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Abigail K R Lytton-Jean
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Judith Frydman
- Department of Biology, James H. Clark Center, Stanford University, Stanford, CA 94305, USA
| | - Kirk Czymmek
- Advanced Bioimaging Laboratory, Donald Danforth Plant Science Center, Saint Louis, MO 63132, USA
| | - Wah Chiu
- Department of Bioengineering, James H. Clark Center, Stanford University, Stanford, CA 94305, USA; Division of CryoEM and Bioimaging, SSRL, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA.
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Möckl L, Moerner WE. Super-resolution Microscopy with Single Molecules in Biology and Beyond-Essentials, Current Trends, and Future Challenges. J Am Chem Soc 2020; 142:17828-17844. [PMID: 33034452 PMCID: PMC7582613 DOI: 10.1021/jacs.0c08178] [Citation(s) in RCA: 82] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Indexed: 12/31/2022]
Abstract
Single-molecule super-resolution microscopy has developed from a specialized technique into one of the most versatile and powerful imaging methods of the nanoscale over the past two decades. In this perspective, we provide a brief overview of the historical development of the field, the fundamental concepts, the methodology required to obtain maximum quantitative information, and the current state of the art. Then, we will discuss emerging perspectives and areas where innovation and further improvement are needed. Despite the tremendous progress, the full potential of single-molecule super-resolution microscopy is yet to be realized, which will be enabled by the research ahead of us.
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Affiliation(s)
- Leonhard Möckl
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
| | - W. E. Moerner
- Department of Chemistry, Stanford University, Stanford, California 94305, United States
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