1
|
Batey JE, Kim GW, Yang M, Heffer DC, Pott ED, Giang H, Dong B. High throughput spectrally resolved super-resolution fluorescence microscopy with improved photon usage. Analyst 2024; 149:2801-2805. [PMID: 38682955 DOI: 10.1039/d4an00343h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2024]
Abstract
Single-molecule localization microscopy (SMLM), a type of super-resolution fluorescence microscopy, has become a strong technique in the toolbox of chemists, biologists, physicists, and engineers in recent years for its unique ability to resolve characteristic features at the nanoscopic level. It drastically improves the resolution of optical microscopes beyond the diffraction limit, with which previously unresolvable structures can now be studied. Spectrally resolved super-resolution fluorescence microscopy via multiplexing of different fluorophores is one of the greatest advancements among SMLM techniques. However, current spectrally resolved SMLM (SR-SMLM) methodologies present low spatial resolution due to loss of photons, low throughput due to spectral interferences, or require complex optical systems. Here, we overcome these drawbacks by developing a SR-SMLM methodology using a color glass filter. It enables high throughput and improved photon usage for hyperspectral imaging at the nanoscopic level. Our methodology can readily distinguish fluorophores of close spectral emission and achieves sub-10 nm localization and sub-5 nm spectral precisions.
Collapse
Affiliation(s)
- James Ethan Batey
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Geun Wan Kim
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Meek Yang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Darby Claire Heffer
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Elric Dion Pott
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Hannah Giang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| | - Bin Dong
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA.
| |
Collapse
|
2
|
Seabury AG, Khodabocus AJ, Kogan IM, Hoy GR, DeSalvo GA, Wustholz KL. Blinking characteristics of organic fluorophores for blink-based multiplexing. Commun Chem 2024; 7:18. [PMID: 38280979 PMCID: PMC10821931 DOI: 10.1038/s42004-024-01106-5] [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: 09/20/2023] [Accepted: 01/12/2024] [Indexed: 01/29/2024] Open
Abstract
Single-molecule fluorescence experiments have transformed our understanding of complex materials and biological systems. Whether single molecules are used to report on their nano-environment or provide for localization, understanding their blinking dynamics (i.e., stochastic fluctuations in emission intensity under continuous illumination) is paramount. We recently demonstrated another use for blinking dynamics called blink-based multiplexing (BBM), where individual emitters are classified using a single excitation laser based on blinking dynamics, rather than color. This study elucidates the structure-activity relationships governing BBM performance in a series of model rhodamine, BODIPY, and anthraquinone fluorophores that undergo different photo-physical and-chemical processes during blinking. Change point detection and multinomial logistic regression analyses show that BBM can leverage spectral fluctuations, electron and proton transfer kinetics, as well as photostability for molecular classification-even within the context of a shared blinking mechanism. In doing so, we demonstrate two- and three-color BBM with ≥ 93% accuracy using spectrally-overlapped fluorophores.
Collapse
Affiliation(s)
| | | | | | - Grayson R Hoy
- Chemistry Department, William & Mary, Williamsburg, VA, USA
| | | | | |
Collapse
|
3
|
Liu Y, Shahid MA, Mao H, Chen J, Waddington M, Song KH, Zhang Y. Switchable and Functional Fluorophores for Multidimensional Single-Molecule Localization Microscopy. CHEMICAL & BIOMEDICAL IMAGING 2023; 1:403-413. [PMID: 37655169 PMCID: PMC10466381 DOI: 10.1021/cbmi.3c00045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/05/2023] [Accepted: 06/08/2023] [Indexed: 09/02/2023]
Abstract
Multidimensional single-molecule localization microscopy (mSMLM) represents a paradigm shift in the realm of super-resolution microscopy techniques. It affords the simultaneous detection of single-molecule spatial locations at the nanoscale and functional information by interrogating the emission properties of switchable fluorophores. The latter is finely tuned to report its local environment through carefully manipulated laser illumination and single-molecule detection strategies. This Perspective highlights recent strides in mSMLM with a focus on fluorophore designs and their integration into mSMLM imaging systems. Particular interests are the accomplishments in simultaneous multiplexed super-resolution imaging, nanoscale polarity and hydrophobicity mapping, and single-molecule orientational imaging. Challenges and prospects in mSMLM are also discussed, which include the development of more vibrant and functional fluorescent probes, the optimization of optical implementation to judiciously utilize the photon budget, and the advancement of imaging analysis and machine learning techniques.
Collapse
Affiliation(s)
- Yunshu Liu
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Md Abul Shahid
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Hongjing Mao
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Jiahui Chen
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Michael Waddington
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| | - Ki-Hee Song
- Quantum
Optics Research Division, Korea Atomic Energy
Research Institute, Yuseong-gu, Daejeon 34057, Republic of Korea
| | - Yang Zhang
- Molecular
Analytics and Photonics (MAP) Laboratory, Department of Textile Engineering,
Chemistry and Science, North Carolina State
University, Raleigh, North Carolina 27606, United States
| |
Collapse
|
4
|
Manko H, Mély Y, Godet J. Advancing Spectrally-Resolved Single Molecule Localization Microscopy with Deep Learning. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2300728. [PMID: 37093225 DOI: 10.1002/smll.202300728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 03/21/2023] [Indexed: 05/03/2023]
Abstract
Spectrally-resolved single molecule localization microscopy (srSMLM) is a recent technique enriching single molecule localization microscopy with the simultaneous recording of spectra of the single emitters. srSMLM resolution is limited by the number of photons collected per emitters. Sharing a photon budget to record the localization and the spectroscopic information results in a loss of spatial and spectral resolution-or forces the sacrifice of one at the expense of the other. Here, srUnet-a deep-learning Unet-based image processing routine trained to increase the spectral and spatial signals to compensate for the resolution loss inherent in additionally recording the spectral component is reported. Both localization and spectral precision are improved by srUnet-particularly for the low-emitting species. srUnet increases the fraction of localization whose signal can be both spatially and spectrally characterized. It preserves spectral shifts and the linearity of the dispersion of light. It strongly facilitates wavelength assignment in multicolor experiments. srUnet is a simple post-processing add-on boosting srSMLM performance close to conventional SMLM with the potential to turn srSMLM into the new standard for multicolor single molecule imaging.
Collapse
Affiliation(s)
- Hanna Manko
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, ITI InnoVec, Université de Strasbourg, Illkirch, 67401, France
| | - Yves Mély
- Laboratoire de BioImagerie et Pathologies, UMR CNRS 7021, Université de Strasbourg, Illkirch, 67401, France
| | - Julien Godet
- Groupe Méthodes Recherche Clinique, Hôpitaux Universitaires de Strasbourg, Strasbourg, 67091, France
- Laboratoire iCube, UMR CNRS 7357, Equipe IMAGeS, Université de Strasbourg, Illkirch, 67400, France
| |
Collapse
|
5
|
Brenner B, Sun C, Raymo FM, Zhang HF. Spectroscopic single-molecule localization microscopy: applications and prospective. NANO CONVERGENCE 2023; 10:14. [PMID: 36943541 PMCID: PMC10030755 DOI: 10.1186/s40580-023-00363-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/10/2023] [Accepted: 03/05/2023] [Indexed: 05/25/2023]
Abstract
Single-molecule localization microscopy (SMLM) breaks the optical diffraction limit by numerically localizing sparse fluorescence emitters to achieve super-resolution imaging. Spectroscopic SMLM or sSMLM further allows simultaneous spectroscopy and super-resolution imaging of fluorescence molecules. Hence, sSMLM can extract spectral features with single-molecule sensitivity, higher precision, and higher multiplexity than traditional multicolor microscopy modalities. These new capabilities enabled advanced multiplexed and functional cellular imaging applications. While sSMLM suffers from reduced spatial precision compared to conventional SMLM due to splitting photons to form spatial and spectral images, several methods have been reported to mitigate these weaknesses through innovative optical design and image processing techniques. This review summarizes the recent progress in sSMLM, its applications, and our perspective on future work.
Collapse
Affiliation(s)
- Benjamin Brenner
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL, 60208, USA
| | - Françisco M Raymo
- Department of Chemistry, University of Miami, Coral Gables, FL, 33146, USA
| | - Hao F Zhang
- Department of Biomedical Engineering, Northwestern University, Evanston, IL, 60208, USA.
| |
Collapse
|
6
|
Jeong D, Kim D. Super‐resolution fluorescence microscopy‐based single‐molecule spectroscopy. B KOREAN CHEM SOC 2022. [DOI: 10.1002/bkcs.12471] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Dokyung Jeong
- Department of Chemistry Hanyang University Seoul Republic of Korea
| | - Doory Kim
- Department of Chemistry Hanyang University Seoul Republic of Korea
- Research Institute for Convergence of Basic Science, Institute of Nano Science and Technology, and Research Institute for Natural Sciences Hanyang University Seoul Republic of Korea
| |
Collapse
|
7
|
Xiang L, Chen K, Xu K. Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy. ACS NANO 2021; 15:12483-12496. [PMID: 34304562 PMCID: PMC8789943 DOI: 10.1021/acsnano.1c04708] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The rise of single-molecule localization microscopy (SMLM) and related super-resolution methods over the past 15 years has revolutionized how we study biological and materials systems. In this Perspective, we reflect on the underlying philosophy of how diffraction-unlimited pictures containing rich spatial and functional information may gradually emerge through the local accumulation of single-molecule measurements. Starting with the basic concepts, we analyze the uniqueness of and opportunities in building up the final picture one molecule at a time. After brief introductions to the more established multicolor and three-dimensional measurements, we highlight emerging efforts to extend SMLM to new dimensions and functionalities as fluorescence polarization, emission spectra, and molecular motions, and discuss rising opportunities and future directions. With single molecules as our quanta, the bottom-up accumulation approach provides a powerful conduit for multidimensional microscopy at the nanoscale.
Collapse
|
8
|
Jeffet J, Ionescu A, Michaeli Y, Torchinsky D, Perlson E, Craggs TD, Ebenstein Y. Multimodal single-molecule microscopy with continuously controlled spectral resolution. BIOPHYSICAL REPORTS 2021; 1:100013. [PMID: 36425313 PMCID: PMC9680784 DOI: 10.1016/j.bpr.2021.100013] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Accepted: 08/03/2021] [Indexed: 02/08/2023]
Abstract
Color is a fundamental contrast mechanism in fluorescence microscopy, providing the basis for numerous imaging and spectroscopy techniques. Building on spectral imaging schemes that encode color into a fixed spatial intensity distribution, here, we introduce continuously controlled spectral-resolution (CoCoS) microscopy, which allows the spectral resolution of the system to be adjusted in real-time. By optimizing the spectral resolution for each experiment, we achieve maximal sensitivity and throughput, allowing for single-frame acquisition of multiple color channels with single-molecule sensitivity and 140-fold larger fields of view compared with previous super-resolution spectral imaging techniques. Here, we demonstrate the utility of CoCoS in three experimental formats, single-molecule spectroscopy, single-molecule Förster resonance energy transfer, and multicolor single-particle tracking in live neurons, using a range of samples and 12 distinct fluorescent markers. A simple add-on allows CoCoS to be integrated into existing fluorescence microscopes, rendering spectral imaging accessible to the wider scientific community.
Collapse
Affiliation(s)
- Jonathan Jeffet
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel,Center for Light Matter Interaction, Tel Aviv University, Tel Aviv, Israel
| | - Ariel Ionescu
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Yael Michaeli
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel
| | - Dmitry Torchinsky
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel,Center for Light Matter Interaction, Tel Aviv University, Tel Aviv, Israel
| | - Eran Perlson
- Department of Physiology and Pharmacology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel,Sagol School of Neuroscience, Tel Aviv University, Tel Aviv, Israel
| | - Timothy D. Craggs
- Sheffield Institute for Nucleic Acids, Department of Chemistry, University of Sheffield, Sheffield, United Kingdom
| | - Yuval Ebenstein
- Raymond and Beverly Sackler Faculty of Exact Sciences, Tel Aviv University, Tel Aviv, Israel,Center for Nanoscience and Nanotechnology, Tel Aviv University, Tel Aviv, Israel,Center for Light Matter Interaction, Tel Aviv University, Tel Aviv, Israel,Corresponding author
| |
Collapse
|
9
|
Zhang Y, Zhang Y, Song KH, Lin W, Sun C, Schatz GC, Zhang HF. Investigating Single-Molecule Fluorescence Spectral Heterogeneity of Rhodamines Using High-Throughput Single-Molecule Spectroscopy. J Phys Chem Lett 2021; 12:3914-3921. [PMID: 33861598 PMCID: PMC8607629 DOI: 10.1021/acs.jpclett.1c00192] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
We experimentally investigated several intramolecular coordinate and environmental changes as potential causes of single-molecule fluorescence spectral heterogeneities (smFSH). We developed a high-throughput single-molecule spectroscopy method to analyze more than 5000 single-molecule emission spectra from each of 9 commonly used fluorophores with different structural rigidities and deposited on substrates with different polarities. We observed an unexpectedly high smFSH from structurally rigid Rhodamine B compared with a structurally flexible Cyanine dye-Alexa Fluor 647. Based on experimentally measured smFSH, we ruled out the system's noise uncertainty, single-molecule spectral diffusion, and environmental polarity as the primary causes of the high smFSH. We found that the rotational flexibility of N,N-dialkylated groups contributed to the smFSH. With the high smFSH observed in structurally more rigid model fluorophores, we speculated that other intramolecular coordinate and environmental changes might also contribute to the high smFSH in Rhodamines.
Collapse
Affiliation(s)
- Yang Zhang
- Departments of Biomedical Engineering, Northwestern University, Evanston, IL60208, United States
- Corresponding Author:
| | - Yu Zhang
- Department of Chemistry, Northwestern University, Evanston, IL60208, United States
| | - Ki-Hee Song
- Departments of Biomedical Engineering, Northwestern University, Evanston, IL60208, United States
| | - Wei Lin
- Department of Chemistry, Northwestern University, Evanston, IL60208, United States
| | - Cheng Sun
- Department of Mechanical Engineering, Northwestern University, Evanston, IL60208, United States
| | - George C. Schatz
- Department of Chemistry, Northwestern University, Evanston, IL60208, United States
| | - Hao F. Zhang
- Departments of Biomedical Engineering, Northwestern University, Evanston, IL60208, United States
| |
Collapse
|