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Friedl K, Mau A, Boroni-Rueda F, Caorsi V, Bourg N, Lévêque-Fort S, Leterrier C. Assessing crosstalk in simultaneous multicolor single-molecule localization microscopy. CELL REPORTS METHODS 2023; 3:100571. [PMID: 37751691 PMCID: PMC10545913 DOI: 10.1016/j.crmeth.2023.100571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 07/03/2023] [Accepted: 08/04/2023] [Indexed: 09/28/2023]
Abstract
Single-molecule localization microscopy (SMLM) can reach sub-50 nm resolution using techniques such as stochastic optical reconstruction microscopy (STORM) or DNA-point accumulation for imaging in nanoscale topography (PAINT). Here we implement two approaches for faster multicolor SMLM by splitting the emitted fluorescence toward two cameras: simultaneous two-color DNA-PAINT (S2C-DNA-PAINT) that images spectrally separated red and far-red imager strands on each camera, and spectral demixing dSTORM (SD-dSTORM) where spectrally close far-red fluorophores appear on both cameras before being identified by demixing. Using S2C-DNA-PAINT as a reference for low crosstalk, we evaluate SD-dSTORM crosstalk using three types of samples: DNA origami nanorulers of different sizes, single-target labeled cells, or cells labeled for multiple targets. We then assess if crosstalk can affect the detection of biologically relevant subdiffraction patterns. Extending these approaches to three-dimensional acquisition and SD-dSTORM to three-color imaging, we show that spectral demixing is an attractive option for robust and versatile multicolor SMLM investigations.
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Affiliation(s)
- Karoline Friedl
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France; Abbelight, 191 Avenue Aristide Briand, 94230 Cachan, France
| | - Adrien Mau
- Abbelight, 191 Avenue Aristide Briand, 94230 Cachan, France; Université Paris Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Fanny Boroni-Rueda
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France
| | | | - Nicolas Bourg
- Abbelight, 191 Avenue Aristide Briand, 94230 Cachan, France
| | - Sandrine Lévêque-Fort
- Université Paris Saclay, CNRS, Institut des Sciences Moléculaires d'Orsay, 91405 Orsay, France
| | - Christophe Leterrier
- Aix Marseille Université, CNRS, INP UMR7051, NeuroCyto, 13005 Marseille, France.
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2
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Lévêque O, Kulcsár C, Cognet L, Goudail F. On the equivalence of binary phase masks optimized for localization or detection in extended depth-of-field localization microscopy. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2023; 40:1753-1761. [PMID: 37707012 DOI: 10.1364/josaa.492654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Accepted: 07/30/2023] [Indexed: 09/15/2023]
Abstract
Binary annular masks have recently been proposed to extend the depth of field (DoF) of single-molecule localization microscopy. A strategy for designing optimal masks has been introduced based on maximizing the emitter localization accuracy, expressed in terms of Fisher information, over a targeted DoF range. However, the complete post-processing pipeline to localize a single emitter consists of two successive steps: detection, where the regions containing emitters are determined, and localization, where the sub-pixel position of each detected emitter is estimated. Phase masks usually optimize only this second step. The presence of a phase mask also affecting detection, the purpose of this paper is to quantify and mitigate this effect. Using a rigorous framework built from a detection-oriented information theoretical criterion (Bhattacharyya distance), we demonstrate that in most cases of practical significance, annular binary phase masks maximizing Fisher information also maximize the detection probability. This result supports the common design practice consisting of optimizing a phase mask by maximizing Fisher information only.
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3
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Wu T, Guillon M, Gentner C, Rigneault H, Tessier G, Bon P, Berto P. 3D nanoparticle superlocalization with a thin diffuser. OPTICS LETTERS 2022; 47:3079-3082. [PMID: 35709055 DOI: 10.1364/ol.453813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/23/2022] [Indexed: 06/15/2023]
Abstract
We report on the use of a thin diffuser placed in the close vicinity of a camera sensor as a simple and effective way to superlocalize plasmonic nanoparticles in 3D. This method is based on holographic reconstruction via quantitative phase and intensity measurements of a light field after its interaction with nanoparticles. We experimentally demonstrate that this thin diffuser can be used as a simple add-on to a standard bright-field microscope to allow the localization of 100 nm gold nanoparticles at video rate with nanometer precision (1.3 nm laterally and 6.3 nm longitudinally). We exemplify the approach by revealing the dynamic Brownian trajectory of a gold nanoparticle trapped in various pockets within an agarose gel. The proposed method provides a simple but highly performant way to track nanoparticles in 3D.
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4
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Hinterer F, Schneider MC, Hubmer S, López-Martinez M, Zelger P, Jesacher A, Ramlau R, Schütz GJ. Robust and bias-free localization of individual fixed dipole emitters achieving the Cramér Rao bound for applications in cryo-single molecule localization microscopy. PLoS One 2022; 17:e0263500. [PMID: 35120171 PMCID: PMC8815875 DOI: 10.1371/journal.pone.0263500] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 01/20/2022] [Indexed: 11/18/2022] Open
Abstract
Single molecule localization microscopy (SMLM) has the potential to resolve structural details of biological samples at the nanometer length scale. Compared to room temperature experiments, SMLM performed under cryogenic temperature achieves higher photon yields and, hence, higher localization precision. However, to fully exploit the resolution it is crucial to account for the anisotropic emission characteristics of fluorescence dipole emitters with fixed orientation. In case of slight residual defocus, localization estimates may well be biased by tens of nanometers. We show here that astigmatic imaging in combination with information about the dipole orientation allows to extract the position of the dipole emitters without localization bias and down to a precision of 1 nm, thereby reaching the corresponding Cramér Rao bound. The approach is showcased with simulated data for various dipole orientations, and parameter settings realistic for real life experiments.
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Affiliation(s)
- Fabian Hinterer
- Institute of Industrial Mathematics, Johannes Kepler University Linz, Linz, Austria
| | | | | | | | - Philipp Zelger
- Division for Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Alexander Jesacher
- Division for Biomedical Physics, Medical University of Innsbruck, Innsbruck, Austria
| | - Ronny Ramlau
- Institute of Industrial Mathematics, Johannes Kepler University Linz, Linz, Austria
- Johann Radon Institute Linz, Linz, Austria
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5
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Bond C, Santiago-Ruiz AN, Tang Q, Lakadamyali M. Technological advances in super-resolution microscopy to study cellular processes. Mol Cell 2022; 82:315-332. [PMID: 35063099 PMCID: PMC8852216 DOI: 10.1016/j.molcel.2021.12.022] [Citation(s) in RCA: 27] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/22/2023]
Abstract
Since its initial demonstration in 2000, far-field super-resolution light microscopy has undergone tremendous technological developments. In parallel, these developments have opened a new window into visualizing the inner life of cells at unprecedented levels of detail. Here, we review the technical details behind the most common implementations of super-resolution microscopy and highlight some of the recent, promising advances in this field.
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Affiliation(s)
- Charles Bond
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adriana N Santiago-Ruiz
- Department of Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Qing Tang
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Cell and Developmental Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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6
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Velas L, Brameshuber M, Huppa JB, Kurz E, Dustin ML, Zelger P, Jesacher A, Schütz GJ. Three-Dimensional Single Molecule Localization Microscopy Reveals the Topography of the Immunological Synapse at Isotropic Precision below 15 nm. NANO LETTERS 2021; 21:9247-9255. [PMID: 34709845 PMCID: PMC8587899 DOI: 10.1021/acs.nanolett.1c03160] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
T-cells engage with antigen-presenting cells in search for antigenic peptides and form transient interfaces termed immunological synapses. Synapse topography affects receptor binding rates and the mutual segregation of proteins due to size exclusion effects. It is hence important to determine the 3D topography of the immunological synapse at high precision. Current methods provide only rather coarse images of the protein distribution within the synapse. Here, we applied supercritical angle fluorescence microscopy combined with defocused imaging, which allows three-dimensional single molecule localization microscopy (3D-SMLM) at an isotropic localization precision below 15 nm. Experiments were performed on hybrid synapses between primary T-cells and functionalized glass-supported lipid bilayers. We used 3D-SMLM to quantify the cleft size within the synapse by mapping the position of the T-cell receptor (TCR) with respect to the supported lipid bilayer, yielding average distances of 18 nm up to 31 nm for activating and nonactivating bilayers, respectively.
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Affiliation(s)
- Lukas Velas
- Institute
of Applied Physics, TU Wien, 1040 Vienna, Austria
| | | | - Johannes B. Huppa
- Institute
for Hygiene and Applied Immunology, Center for Pathophysiology, Infectiology
and Immunology, Medical University of Vienna, 1090 Vienna, Austria
| | - Elke Kurz
- Kennedy
Institute of Rheumatology, University of
Oxford, OX3 7FY Oxford, United Kingdom
| | - Michael L. Dustin
- Kennedy
Institute of Rheumatology, University of
Oxford, OX3 7FY Oxford, United Kingdom
| | - Philipp Zelger
- Division
for Biomedical Physics, Medical University
of Innsbruck, 6020 Innsbruck, Austria
| | - Alexander Jesacher
- Division
for Biomedical Physics, Medical University
of Innsbruck, 6020 Innsbruck, Austria
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7
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Abstract
Fluorescence imaging techniques play a pivotal role in our understanding of the nervous system. The emergence of various super-resolution microscopy methods and specialized fluorescent probes enables direct insight into neuronal structure and protein arrangements in cellular subcompartments with so far unmatched resolution. Super-resolving visualization techniques in neurons unveil a novel understanding of cytoskeletal composition, distribution, motility, and signaling of membrane proteins, subsynaptic structure and function, and neuron-glia interaction. Well-defined molecular targets in autoimmune and neurodegenerative disease models provide excellent starting points for in-depth investigation of disease pathophysiology using novel and innovative imaging methodology. Application of super-resolution microscopy in human brain samples and for testing clinical biomarkers is still in its infancy but opens new opportunities for translational research in neurology and neuroscience. In this review, we describe how super-resolving microscopy has improved our understanding of neuronal and brain function and dysfunction in the last two decades.
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Affiliation(s)
- Christian Werner
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, University of Würzburg, 97074 Würzburg, Germany
| | - Christian Geis
- Section Translational Neuroimmunology, Department of Neurology, Jena University Hospital, Am Klinikum 1, 07747 Jena, Germany
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8
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 296] [Impact Index Per Article: 98.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
;
;
;
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9
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Lévêque O, Kulcsár C, Lee A, Sauer H, Aleksanyan A, Bon P, Cognet L, Goudail F. Co-designed annular binary phase masks for depth-of-field extension in single-molecule localization microscopy. OPTICS EXPRESS 2020; 28:32426-32446. [PMID: 33114929 DOI: 10.1364/oe.402752] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 09/27/2020] [Indexed: 06/11/2023]
Abstract
Single-molecule localization microscopy has become a prominent approach to study structural and dynamic arrangements of nanometric objects well beyond the diffraction limit. To maximize localization precision, high numerical aperture objectives must be used; however, this inherently strongly limits the depth-of-field (DoF) of the microscope images. In this work, we present a framework inspired by "optical co-design" to optimize and benchmark phase masks, which, when placed in the exit pupil of the microscope objective, can extend the DoF in the realistic context of single fluorescent molecule detection. Using the Cramér-Rao bound (CRB) on localization accuracy as a criterion, we optimize annular binary phase masks for various DoF ranges, compare them to Incoherently Partitioned Pupil masks and show that they significantly extend the DoF of single-molecule localization microscopes. In particular we propose different designs including a simple and easy-to-realize two-ring binary mask to extend the DoF. Moreover, we demonstrate that a simple maximum likelihood-based localization algorithm can reach the localization accuracy predicted by the CRB. The framework developed in this paper is based on an explicit and general information theoretic criterion, and can thus be used as an engineering tool to optimize and compare any type of DoF-enhancing phase mask in high resolution microscopy on a quantitative basis.
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10
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Genuage: visualize and analyze multidimensional single-molecule point cloud data in virtual reality. Nat Methods 2020; 17:1100-1102. [PMID: 32958921 DOI: 10.1038/s41592-020-0946-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/10/2020] [Indexed: 01/10/2023]
Abstract
Experimentally recorded point cloud data, such as those generated by single-molecule localization microscopy, are continuously increasing in size and dimension. Gaining an intuitive understanding and facilitating the analysis of such multidimensional data remains challenging. Here we report a new open-source software platform, Genuage, that enables the easy perception of, interaction with and analysis of multidimensional point clouds in virtual reality. Genuage is compatible with arbitrary multidimensional data extending beyond single-molecule localization microscopy.
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11
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Innovative particle standards and long-lived imaging for 2D and 3D dSTORM. Sci Rep 2019; 9:17967. [PMID: 31784555 PMCID: PMC6884466 DOI: 10.1038/s41598-019-53528-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2018] [Accepted: 10/23/2019] [Indexed: 12/21/2022] Open
Abstract
Direct stochastic optical reconstruction microscopy (dSTORM), developed in the last decade, has revolutionised optical microscopy by enabling scientists to visualise objects beyond the resolution provided by conventional microscopy (200 nm). We developed an innovative method based on blinking particle standards and conditions for long-lived imaging over several weeks. Stable localisation precisions within the 10 nm-range were achieved for single virions and in cellulo 2D imaging of centrosomes, as well as their reliable reconstruction in 3D dSTORM.
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12
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Wollman AJM, Hedlund EG, Shashkova S, Leake MC. Towards mapping the 3D genome through high speed single-molecule tracking of functional transcription factors in single living cells. Methods 2019; 170:82-89. [PMID: 31252059 PMCID: PMC6971689 DOI: 10.1016/j.ymeth.2019.06.021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Accepted: 06/22/2019] [Indexed: 10/26/2022] Open
Abstract
How genomic DNA is organized in the nucleus is a long-standing question. We describe a single-molecule bioimaging method utilizing super-localization precision coupled to fully quantitative image analysis tools, towards determining snapshots of parts of the 3D genome architecture of model eukaryote budding yeast Saccharomyces cerevisiae with exceptional millisecond time resolution. We employ astigmatism imaging to enable robust extraction of 3D position data on genomically encoded fluorescent protein reporters that bind to DNA. Our relatively straightforward method enables snippets of 3D architectures of likely single genome conformations to be resolved captured via DNA-sequence specific binding proteins in single functional living cells.
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Affiliation(s)
- Adam J M Wollman
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Erik G Hedlund
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Sviatlana Shashkova
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
| | - Mark C Leake
- Biological Physical Science Institute, Departments of Physics and Biology, University of York, YO10 5DD York, UK.
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13
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Mateos N, Molenaar R, Claessens MMAE, Blum C. Photonic emitter manipulation to sample nanoscale topography. OPTICS EXPRESS 2019; 27:11698-11708. [PMID: 31053012 DOI: 10.1364/oe.27.011698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Accepted: 03/22/2019] [Indexed: 06/09/2023]
Abstract
We demonstrate that photonic emitter manipulation can be used to image the nanoscale topography of a fluorescently labeled layer in confocal imaging. We exploit the fact that a metallic probe manipulates a fluorophore's photonic environment, and thereby its fluorescent lifetime, in a strongly distance-dependent manner. To image surface topography, a metallic probe that is not in contact with the surface is rasterscanned over a fluorescently labeled sample. The axial position of the probe is kept constant. At each lateral probe position, the fluorescence decay is recorded and analyzed to obtain probe - sample distances and hence, the topography of the sample. We present images resolving a microfabricated step of 14 nm in topography, with the probe positioned at different axial positions.
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14
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El Beheiry M, Doutreligne S, Caporal C, Ostertag C, Dahan M, Masson JB. Virtual Reality: Beyond Visualization. J Mol Biol 2019; 431:1315-1321. [DOI: 10.1016/j.jmb.2019.01.033] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/13/2019] [Accepted: 01/22/2019] [Indexed: 12/29/2022]
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15
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Gruβmayer KS, Yserentant K, Herten DP. Photons in - numbers out: perspectives in quantitative fluorescence microscopy for in situ protein counting. Methods Appl Fluoresc 2019; 7:012003. [DOI: 10.1088/2050-6120/aaf2eb] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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16
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Lambert TJ, Waters JC. Navigating challenges in the application of superresolution microscopy. J Cell Biol 2017; 216:53-63. [PMID: 27920217 PMCID: PMC5223610 DOI: 10.1083/jcb.201610011] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 11/15/2016] [Accepted: 11/18/2016] [Indexed: 11/22/2022] Open
Abstract
In 2014, the Nobel Prize in Chemistry was awarded to three scientists who have made groundbreaking contributions to the field of superresolution (SR) microscopy (SRM). The first commercial SR microscope came to market a decade earlier, and many other commercial options have followed. As commercialization has lowered the barrier to using SRM and the awarding of the Nobel Prize has drawn attention to these methods, biologists have begun adopting SRM to address a wide range of questions in many types of specimens. There is no shortage of reviews on the fundamental principles of SRM and the remarkable achievements made with these methods. We approach SRM from another direction: we focus on the current practical limitations and compromises that must be made when designing an SRM experiment. We provide information and resources to help biologists navigate through common pitfalls in SRM specimen preparation and optimization of image acquisition as well as errors and artifacts that may compromise the reproducibility of SRM data.
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Affiliation(s)
- Talley J Lambert
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
| | - Jennifer C Waters
- Department of Cell Biology, Harvard Medical School, Boston, MA 02115
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17
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Zhang P, Kim K, Lee S, Chakkarapani SK, Fang N, Kang SH. Augmented 3D super-resolution of fluorescence-free nanoparticles using enhanced dark-field illumination based on wavelength-modulation and a least-cubic algorithm. Sci Rep 2016; 6:32863. [PMID: 27619347 PMCID: PMC5020655 DOI: 10.1038/srep32863] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 08/16/2016] [Indexed: 12/19/2022] Open
Abstract
Augmented three-dimensional (3D) subdiffraction-limited resolution of fluorescence-free single-nanoparticles was achieved with wavelength-dependent enhanced dark-field (EDF) illumination and a least-cubic algorithm. Various plasmonic nanoparticles on a glass slide (i.e., gold nanoparticles, GNPs; silver nanoparticles, SNPs; and gold nanorods, GNRs) were imaged and sliced in the z-direction to a thickness of 10 nm. Single-particle images were then compared with simulation data. The 3D coordinates of individual GNP, SNP, and GNR nanoparticles (x, y, z) were resolved by fitting the data with 3D point spread functions using a least-cubic algorithm and collation. Final, 3D super-resolution microscopy (SRM) images were obtained by resolving 3D coordinates and their Cramér-Rao lower bound-based localization precisions in an image space (530 nm × 530 nm × 300 nm) with a specific voxel size (2.5 nm × 2.5 nm × 5 nm). Compared with the commonly used least-square method, the least-cubic method was more useful for finding the center in asymmetric cases (i.e., nanorods) with high precision and accuracy. This novel 3D fluorescence-free SRM technique was successfully applied to resolve the positions of various nanoparticles on glass and gold nanospots (in vitro) as well as in a living single cell (in vivo) with subdiffraction limited resolution in 3D.
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Affiliation(s)
- Peng Zhang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Kyungsoo Kim
- Department of Applied Mathematics, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Seungah Lee
- Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Suresh Kumar Chakkarapani
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
| | - Ning Fang
- Department of Chemistry, Georgia State University, 308 Petit Science Center, Atlanta, GA 30303, USA
| | - Seong Ho Kang
- Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea.,Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 17104, Republic of Korea
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18
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Laine RF, Kaminski Schierle GS, van de Linde S, Kaminski CF. From single-molecule spectroscopy to super-resolution imaging of the neuron: a review. Methods Appl Fluoresc 2016; 4:022004. [PMID: 28809165 PMCID: PMC5390958 DOI: 10.1088/2050-6120/4/2/022004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Revised: 05/09/2016] [Accepted: 05/19/2016] [Indexed: 12/03/2022]
Abstract
For more than 20 years, single-molecule spectroscopy has been providing invaluable insights into nature at the molecular level. The field has received a powerful boost with the development of the technique into super-resolution imaging methods, ca. 10 years ago, which overcome the limitations imposed by optical diffraction. Today, single molecule super-resolution imaging is routinely used in the study of macromolecular function and structure in the cell. Concomitantly, computational methods have been developed that provide information on numbers and positions of molecules at the nanometer-scale. In this overview, we outline the technical developments that have led to the emergence of localization microscopy techniques from single-molecule spectroscopy. We then provide a comprehensive review on the application of the technique in the field of neuroscience research.
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Affiliation(s)
- Romain F Laine
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Gabriele S Kaminski Schierle
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
| | - Sebastian van de Linde
- Department of Biotechnology and Biophysics, Julius-Maximilians-University, Am Hubland, D-97074 Würzburg, Germany
| | - Clemens F Kaminski
- Laser Analytics Group, Department of Chemical Engineering and Biotechnology, Cambridge University, Pembroke Street, Cambridge, CB2 3RA, UK
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Quantitative nanoimmunosensor based on dark-field illumination with enhanced sensitivity and on–off switching using scattering signals. Biosens Bioelectron 2016; 79:709-14. [DOI: 10.1016/j.bios.2016.01.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2015] [Revised: 12/11/2015] [Accepted: 01/02/2016] [Indexed: 11/20/2022]
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Hajj B, El Beheiry M, Dahan M. PSF engineering in multifocus microscopy for increased depth volumetric imaging. BIOMEDICAL OPTICS EXPRESS 2016; 7:726-31. [PMID: 27231584 PMCID: PMC4866451 DOI: 10.1364/boe.7.000726] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 01/27/2016] [Accepted: 01/27/2016] [Indexed: 05/15/2023]
Abstract
Imaging and localizing single molecules with high accuracy in a 3D volume is a challenging task. Here we combine multifocal microscopy, a recently developed volumetric imaging technique, with point spread function engineering to achieve an increased depth for single molecule imaging. Applications in 3D single molecule localization-based super-resolution imaging is shown over an axial depth of 4 µm as well as for the tracking of diffusing beads in a fluid environment over 8 µm.
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Affiliation(s)
- Bassam Hajj
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA;
| | - Mohamed El Beheiry
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA
| | - Maxime Dahan
- Laboratoire Physico-Chimie, Institut Curie, PSL Research University, CNRS UMR168, 75005, Paris, France; Sorbonne Universités, UPMC Univ Paris 06, 75005, Paris, France; Transcription Imaging Consortium, Janelia Research Campus, 19700 Helix Drive, Ashburn VA, 20147, USA;
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Caccianini L, Normanno D, Izeddin I, Dahan M. Single molecule study of non-specific binding kinetics of LacI in mammalian cells. Faraday Discuss 2015; 184:393-400. [PMID: 26387491 DOI: 10.1039/c5fd00112a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Many key cellular processes are controlled by the association of DNA-binding proteins (DBPs) to specific sites. The kinetics of the search process leading to the binding of DBPs to their target locus are largely determined by transient interactions with non-cognate DNA. Using single-molecule microscopy, we studied the dynamics and non-specific binding to DNA of the Lac repressor (LacI) in the environment of mammalian nuclei. We measured the distribution of the LacI-DNA binding times at non-cognate sites and determined the mean residence time to be τ(1D) = 182 ms. This non-specific interaction time, measured in the context of an exogenous system such as that of human U2OS cells, is remarkably different compared to that reported for the LacI in its native environment in E. coli (<5 ms). Such a striking difference (more than 30 fold) suggests that the genome, its organization, and the nuclear environment of mammalian cells play important roles on the dynamics of DBPs and their non-specific DNA interactions. Furthermore, we found that the distribution of off-target binding times follows a power law, similar to what was reported for TetR in U2OS cells. We argue that a possible molecular origin of such a power law distribution of residence times is the large variability of non-cognate sequences found in the mammalian nucleus by the diffusing DBPs.
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Affiliation(s)
- Laura Caccianini
- Laboratoire Physico-Chimie Curie, Institut Curie, PSL Research University, CNRS UMR168, Université Pierre et Marie Curie-Paris 6, 11 rue Pierre et Marie Curie, 75005 Paris, France.
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Schubert V, Weisshart K. Abundance and distribution of RNA polymerase II in Arabidopsis interphase nuclei. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:1687-98. [PMID: 25740920 PMCID: PMC4357323 DOI: 10.1093/jxb/erv091] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
RNA polymerase II (RNAPII) is responsible for the transcription of most eukaryotic protein-coding genes. Analysing the topological distribution and quantification of RNAPII can contribute to understanding its function in interphase nuclei. Previously it was shown that RNAPII molecules in plant nuclei form reticulate structures within euchromatin of differentiated Arabidopsis thaliana nuclei rather than being organized in distinct 'transcription factories' as observed in mammalian nuclei. Immunosignal intensity measurements based on specific antibody labelling in maximum intensity projections of image stacks acquired by structured illumination microscopy (SIM) suggested a relative proportional increase of RNAPII in endopolyploid plant nuclei. Here, photoactivated localization microscopy (PALM) was applied to determine the absolute number and distribution of active and inactive RNAPII molecules in differentiated A. thaliana nuclei. The proportional increase of RNAPII during endopolyploidization is confirmed, but it is also shown that PALM measurements are more reliable than those based on SIM in terms of quantification. The single molecule localization results show that, although RNAPII molecules are globally dispersed within plant euchromatin, they also aggregate within smaller distances as described for mammalian transcription factories.
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Affiliation(s)
- Veit Schubert
- Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, D-06466 Stadt Seeland, Germany
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Whole-cell, multicolor superresolution imaging using volumetric multifocus microscopy. Proc Natl Acad Sci U S A 2014; 111:17480-5. [PMID: 25422417 DOI: 10.1073/pnas.1412396111] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Single molecule-based superresolution imaging has become an essential tool in modern cell biology. Because of the limited depth of field of optical imaging systems, one of the major challenges in superresolution imaging resides in capturing the 3D nanoscale morphology of the whole cell. Despite many previous attempts to extend the application of photo-activated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM) techniques into three dimensions, effective localization depths do not typically exceed 1.2 µm. Thus, 3D imaging of whole cells (or even large organelles) still demands sequential acquisition at different axial positions and, therefore, suffers from the combined effects of out-of-focus molecule activation (increased background) and bleaching (loss of detections). Here, we present the use of multifocus microscopy for volumetric multicolor superresolution imaging. By simultaneously imaging nine different focal planes, the multifocus microscope instantaneously captures the distribution of single molecules (either fluorescent proteins or synthetic dyes) throughout an ∼ 4-µm-deep volume, with lateral and axial localization precisions of ∼ 20 and 50 nm, respectively. The capabilities of multifocus microscopy to rapidly image the 3D organization of intracellular structures are illustrated by superresolution imaging of the mammalian mitochondrial network and yeast microtubules during cell division.
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