1
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Zhu FY, Mei LJ, Tian R, Li C, Wang YL, Xiang SL, Zhu MQ, Tang BZ. Recent advances in super-resolution optical imaging based on aggregation-induced emission. Chem Soc Rev 2024; 53:3350-3383. [PMID: 38406832 DOI: 10.1039/d3cs00698k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Super-resolution imaging has rapidly emerged as an optical microscopy technique, offering advantages of high optical resolution over the past two decades; achieving improved imaging resolution requires significant efforts in developing super-resolution imaging agents characterized by high brightness, high contrast and high sensitivity to fluorescence switching. Apart from technical requirements in optical systems and algorithms, super-resolution imaging relies on fluorescent dyes with special photophysical or photochemical properties. The concept of aggregation-induced emission (AIE) was proposed in 2001, coinciding with unprecedented advancements and innovations in super-resolution imaging technology. AIE probes offer many advantages, including high brightness in the aggregated state, low background signal, a larger Stokes shift, ultra-high photostability, and excellent biocompatibility, making them highly promising for applications in super-resolution imaging. In this review, we summarize the progress in implementation methods and provide insights into the mechanism of AIE-based super-resolution imaging, including fluorescence switching resulting from photochemically-converted aggregation-induced emission, electrostatically controlled aggregation-induced emission and specific binding-regulated aggregation-induced emission. Particularly, the aggregation-induced emission principle has been proposed to achieve spontaneous fluorescence switching, expanding the selection and application scenarios of super-resolution imaging probes. By combining the aggregation-induced emission principle and specific molecular design, we offer some comprehensive insights to facilitate the applications of AIEgens (AIE-active molecules) in super-resolution imaging.
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Affiliation(s)
- Feng-Yu Zhu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Li-Jun Mei
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Rui Tian
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Chong Li
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
| | - Ya-Long Wang
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Shi-Li Xiang
- Hubei Jiufengshan Laboratory, Wuhan, 430206, China
| | - Ming-Qiang Zhu
- Wuhan National Laboratory for Optoelectronics, School of Optical and Electronic Information, College of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Key Laboratory of Biomedical Engineering of Hainan Province, School of Biomedical Engineering, Hainan University, Haikou, 570228, China
| | - Ben Zhong Tang
- School of Science and Engineering, Shenzhen Institute of Aggregate Science and Technology, The Chinese University of Hong Kong, Shenzhen (CUHK-Shenzhen), Guangdong 518172, China.
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2
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Wang H, Lee D, Cao Y, Bi X, Du J, Miao K, Wei L. Bond-selective fluorescence imaging with single-molecule sensitivity. NATURE PHOTONICS 2023; 17:846-855. [PMID: 38162388 PMCID: PMC10756635 DOI: 10.1038/s41566-023-01243-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Accepted: 05/25/2023] [Indexed: 01/03/2024]
Abstract
Bioimaging harnessing optical contrasts and chemical specificity is of vital importance in probing complex biology. Vibrational spectroscopy based on mid-infrared (mid-IR) excitation can reveal rich chemical information about molecular distributions. However, its full potential for bioimaging is hindered by the achievable sensitivity. Here, we report bond selective fluorescence-detected infrared-excited (BonFIRE) spectral microscopy. BonFIRE employs two-photon excitation in the mid-IR and near-IR to upconvert vibrational excitations to electronic states for fluorescence detection, thus encoding vibrational information into fluorescence. The system utilizes tuneable narrowband picosecond pulses to ensure high sensitivity, biocompatibility, and robustness for bond-selective biological interrogations over a wide spectrum of reporter molecules. We demonstrate BonFIRE spectral imaging in both fingerprint and cell-silent spectroscopic windows with single-molecule sensitivity for common fluorescent dyes. We then demonstrate BonFIRE imaging on various intracellular targets in fixed and live cells, neurons, and tissues, with promises for further vibrational multiplexing. For dynamic bioanalysis in living systems, we implement a high-frequency modulation scheme and demonstrate time-lapse BonFIRE microscopy of live HeLa cells. We expect BonFIRE to expand the bioimaging toolbox by providing a new level of bond-specific vibrational information and facilitate functional imaging and sensing for biological investigations.
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Affiliation(s)
- Haomin Wang
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Dongkwan Lee
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Yulu Cao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Xiaotian Bi
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Jiajun Du
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Kun Miao
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - Lu Wei
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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3
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Shivanna K, Astumian M, Raut P, Ngo VN, Hess ST, Henry C. Super-Resolution Imaging Reveals the Nanoscale Distributions of Dystroglycan and Integrin Itga7 in Zebrafish Muscle Fibers. Biomedicines 2023; 11:1941. [PMID: 37509580 PMCID: PMC10377463 DOI: 10.3390/biomedicines11071941] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 06/30/2023] [Accepted: 07/06/2023] [Indexed: 07/30/2023] Open
Abstract
Cell signaling is determined partially by the localization and abundance of proteins. Dystroglycan and integrin are both transmembrane receptors that connect the cytoskeleton inside muscle cells to the extracellular matrix outside muscle cells, maintaining proper adhesion and function of muscle. The position and abundance of Dystroglycan relative to integrins is thought to be important for muscle adhesion and function. The subcellular localization and quantification of these receptor proteins can be determined at the nanometer scale by FPALM super-resolution microscopy. We used FPALM to determine localizations of Dystroglycan and integrin proteins in muscle fibers of intact zebrafish (Danio rerio). Results were consistent with confocal imaging data, but illuminate further details at the nanoscale and show the feasibility of using FPALM to quantify interactions of two proteins in a whole organism.
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Affiliation(s)
- Komala Shivanna
- Department of Physics & Astronomy, University of Maine, 5709 Bennett Hall, Orono, ME 04469-5709, USA; (K.S.); (P.R.); (V.-N.N.)
| | - Mary Astumian
- School of Biology and Ecology, University of Maine, 217 Hitchner Hall, Orono, ME 04469-5751, USA;
| | - Prakash Raut
- Department of Physics & Astronomy, University of Maine, 5709 Bennett Hall, Orono, ME 04469-5709, USA; (K.S.); (P.R.); (V.-N.N.)
| | - Vinh-Nhan Ngo
- Department of Physics & Astronomy, University of Maine, 5709 Bennett Hall, Orono, ME 04469-5709, USA; (K.S.); (P.R.); (V.-N.N.)
| | - Samuel T. Hess
- Department of Physics & Astronomy, University of Maine, 5709 Bennett Hall, Orono, ME 04469-5709, USA; (K.S.); (P.R.); (V.-N.N.)
| | - Clarissa Henry
- School of Biology and Ecology, University of Maine, 217 Hitchner Hall, Orono, ME 04469-5751, USA;
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4
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Xu LW, Sgouralis I, Kilic Z, Pressé S. BNP-Track: A framework for multi-particle superresolved tracking. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535440. [PMID: 37066179 PMCID: PMC10104013 DOI: 10.1101/2023.04.03.535440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/18/2023]
Abstract
When tracking fluorescently labeled molecules (termed "emitters") under widefield microscopes, point spread function overlap of neighboring molecules is inevitable in both dilute and especially crowded environments. In such cases, superresolution methods leveraging rare photophysical events to distinguish static targets nearby in space introduce temporal delays that compromise tracking. As we have shown in a companion manuscript, for dynamic targets, information on neighboring fluorescent molecules is encoded as spatial intensity correlations across pixels and temporal correlations in intensity patterns across time frames. We then demonstrated how we used all spatiotemporal correlations encoded in the data to achieve superresolved tracking. That is, we showed the results of full posterior inference over both the number of emitters and their associated tracks simultaneously and self-consistently through Bayesian nonparametrics. In this companion manuscript we focus on testing the robustness of our tracking tool, BNP-Track, across sets of parameter regimes and compare BNP-Track to competing tracking methods in the spirit of a prior Nature Methods tracking competition. We explore additional features of BNP-Track including how a stochastic treatment of background yields greater accuracy in emitter number determination and how BNP-Track corrects for point spread function blur (or "aliasing") introduced by intraframe motion in addition to propagating error originating from myriad sources (such as criss-crossing tracks, out-of-focus particles, pixelation, shot and camera artefact, stochastic background) in posterior inference over emitter numbers and their associated tracks. While head-to-head comparison with other tracking methods is not possible (as competitors cannot simultaneously learn molecule numbers and associated tracks), we can give competing methods some advantages in order to perform approximate head-to-head comparison. We show that even under such optimistic scenarios, BNP-Track is capable of tracking multiple diffraction-limited point emitters conventional tracking methods cannot resolve thereby extending the superresolution paradigm to dynamical targets.
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Affiliation(s)
- Lance W.Q. Xu
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
| | - Ioannis Sgouralis
- Department of Mathematics, University of Tennessee, Knoxville, TN 37996, USA
| | - Zeliha Kilic
- Single-Molecule Imaging Center, Department of Structural Biology, St. Jude Children’s Research Hospital, Memphis, TN 38105, USA
| | - Steve Pressé
- Center for Biological Physics, Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- Department of Physics, Arizona State University, Tempe, AZ 85287, USA
- School of Molecular Science, Arizona State University, Tempe, AZ 85287, USA
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5
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Laitenberger O, Aspelmeier T, Staudt T, Geisler C, Munk A, Egner A. Towards Unbiased Fluorophore Counting in Superresolution Fluorescence Microscopy. NANOMATERIALS (BASEL, SWITZERLAND) 2023; 13:459. [PMID: 36770420 PMCID: PMC9921631 DOI: 10.3390/nano13030459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Revised: 01/16/2023] [Accepted: 01/18/2023] [Indexed: 06/18/2023]
Abstract
With the advent of fluorescence superresolution microscopy, nano-sized structures can be imaged with a previously unprecedented accuracy. Therefore, it is rapidly gaining importance as an analytical tool in the life sciences and beyond. However, the images obtained so far lack an absolute scale in terms of fluorophore numbers. Here, we use, for the first time, a detailed statistical model of the temporal imaging process which relies on a hidden Markov model operating on two timescales. This allows us to extract this information from the raw data without additional calibration measurements. We show this on the basis of added data from experiments on single Alexa 647 molecules as well as GSDIM/dSTORM measurements on DNA origami structures with a known number of labeling positions.
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Affiliation(s)
- Oskar Laitenberger
- Department of Optical Nanoscopy, Institut für Nanophotonik e.V., 37077 Göttingen, Germany
| | - Timo Aspelmeier
- Institute for Mathematical Stochastics, Georg-August-University of Göttingen, 37073 Göttingen, Germany
| | - Thomas Staudt
- Institute for Mathematical Stochastics, Georg-August-University of Göttingen, 37073 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Claudia Geisler
- Department of Optical Nanoscopy, Institut für Nanophotonik e.V., 37077 Göttingen, Germany
| | - Axel Munk
- Institute for Mathematical Stochastics, Georg-August-University of Göttingen, 37073 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
| | - Alexander Egner
- Department of Optical Nanoscopy, Institut für Nanophotonik e.V., 37077 Göttingen, Germany
- Cluster of Excellence “Multiscale Bioimaging: from Molecular Machines to Networks of Excitable Cells” (MBExC), University of Göttingen, 37075 Göttingen, Germany
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6
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Hung ST, Llobet Rosell A, Jurriens D, Siemons M, Soloviev O, Kapitein LC, Grußmayer K, Neukomm LJ, Verhaegen M, Smith C. Adaptive optics in single objective inclined light sheet microscopy enables three-dimensional localization microscopy in adult Drosophila brains. Front Neurosci 2022; 16:954949. [PMID: 36278016 PMCID: PMC9583434 DOI: 10.3389/fnins.2022.954949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 09/01/2022] [Indexed: 11/24/2022] Open
Abstract
Single-molecule localization microscopy (SMLM) enables the high-resolution visualization of organelle structures and the precise localization of individual proteins. However, the expected resolution is not achieved in tissue as the imaging conditions deteriorate. Sample-induced aberrations distort the point spread function (PSF), and high background fluorescence decreases the localization precision. Here, we synergistically combine sensorless adaptive optics (AO), in-situ 3D-PSF calibration, and a single-objective lens inclined light sheet microscope (SOLEIL), termed (AO-SOLEIL), to mitigate deep tissue-induced deteriorations. We apply AO-SOLEIL on several dSTORM samples including brains of adult Drosophila. We observed a 2x improvement in the estimated axial localization precision with respect to widefield without aberration correction while we used synergistic solution. AO-SOLEIL enhances the overall imaging resolution and further facilitates the visualization of sub-cellular structures in tissue.
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Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Arnau Llobet Rosell
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience, Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Lukas J. Neukomm
- Department of Fundamental Neurosciences, University of Lausanne, Lausanne, Switzerland
| | - Michel Verhaegen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Carlas Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
- *Correspondence: Carlas Smith
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7
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Li W, Kaminski Schierle GS, Lei B, Liu Y, Kaminski CF. Fluorescent Nanoparticles for Super-Resolution Imaging. Chem Rev 2022; 122:12495-12543. [PMID: 35759536 PMCID: PMC9373000 DOI: 10.1021/acs.chemrev.2c00050] [Citation(s) in RCA: 50] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Super-resolution imaging techniques that overcome the diffraction limit of light have gained wide popularity for visualizing cellular structures with nanometric resolution. Following the pace of hardware developments, the availability of new fluorescent probes with superior properties is becoming ever more important. In this context, fluorescent nanoparticles (NPs) have attracted increasing attention as bright and photostable probes that address many shortcomings of traditional fluorescent probes. The use of NPs for super-resolution imaging is a recent development and this provides the focus for the current review. We give an overview of different super-resolution methods and discuss their demands on the properties of fluorescent NPs. We then review in detail the features, strengths, and weaknesses of each NP class to support these applications and provide examples from their utilization in various biological systems. Moreover, we provide an outlook on the future of the field and opportunities in material science for the development of probes for multiplexed subcellular imaging with nanometric resolution.
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Affiliation(s)
- Wei Li
- Key
Laboratory for Biobased Materials and Energy of Ministry of Education,
College of Materials and Energy, South China
Agricultural University, Guangzhou 510642, People’s Republic
of China,Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom
| | | | - Bingfu Lei
- Key
Laboratory for Biobased Materials and Energy of Ministry of Education,
College of Materials and Energy, South China
Agricultural University, Guangzhou 510642, People’s Republic
of China,B. Lei.
| | - Yingliang Liu
- Key
Laboratory for Biobased Materials and Energy of Ministry of Education,
College of Materials and Energy, South China
Agricultural University, Guangzhou 510642, People’s Republic
of China
| | - Clemens F. Kaminski
- Department
of Chemical Engineering and Biotechnology, University of Cambridge, Cambridge CB3 0AS, United Kingdom,C. F. Kaminski.
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8
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Hung ST, Cnossen J, Fan D, Siemons M, Jurriens D, Grußmayer K, Soloviev O, Kapitein LC, Smith CS. SOLEIL: single-objective lens inclined light sheet localization microscopy. BIOMEDICAL OPTICS EXPRESS 2022; 13:3275-3294. [PMID: 35781973 PMCID: PMC9208595 DOI: 10.1364/boe.451634] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 06/15/2023]
Abstract
High-NA light sheet illumination can improve the resolution of single-molecule localization microscopy (SMLM) by reducing the background fluorescence. These approaches currently require custom-made sample holders or additional specialized objectives, which makes the sample mounting or the optical system complex and therefore reduces the usability of these approaches. Here, we developed a single-objective lens-inclined light sheet microscope (SOLEIL) that is capable of 2D and 3D SMLM in thick samples. SOLEIL combines oblique illumination with point spread function PSF engineering to enable dSTORM imaging in a wide variety of samples. SOLEIL is compatible with standard sample holders and off-the-shelve optics and standard high NA objectives. To accomplish optimal optical sectioning we show that there is an ideal oblique angle and sheet thickness. Furthermore, to show what optical sectioning delivers for SMLM we benchmark SOLEIL against widefield and HILO microscopy with several biological samples. SOLEIL delivers in 15 μm thick Caco2-BBE cells a 374% higher intensity to background ratio and a 54% improvement in the estimated CRLB compared to widefield illumination, and a 184% higher intensity to background ratio and a 20% improvement in the estimated CRLB compared to HILO illumination.
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Affiliation(s)
- Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Jelmer Cnossen
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Daniel Fan
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
| | - Marijn Siemons
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Daphne Jurriens
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Kristin Grußmayer
- Department of Bionanoscience and Kavli Institute of Nanoscience Delft, Delft University of Technology, Delft, Netherlands
| | - Oleg Soloviev
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Flexible Optical B.V., Polakweg 10-11, 2288 GG Rijswijk, Netherlands
| | - Lukas C. Kapitein
- Cell Biology, Neurobiology and Biophysics, Department of Biology, Faculty of Science, Utrecht University, Utrecht, Netherlands
| | - Carlas S. Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, Netherlands
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9
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Novel Tools to Measure Single Molecules Colocalization in Fluorescence Nanoscopy by Image Cross Correlation Spectroscopy. NANOMATERIALS 2022; 12:nano12040686. [PMID: 35215014 PMCID: PMC8875509 DOI: 10.3390/nano12040686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 02/14/2022] [Accepted: 02/16/2022] [Indexed: 01/27/2023]
Abstract
Super Resolution Microscopy revolutionized the approach to the study of molecular interactions by providing new quantitative tools to describe the scale below 100 nanometers. Single Molecule Localization Microscopy (SMLM) reaches a spatial resolution less than 50 nm with a precision in calculating molecule coordinates between 10 and 20 nanometers. However new procedures are required to analyze data from the list of molecular coordinates created by SMLM. We propose new tools based on Image Cross Correlation Spectroscopy (ICCS) to quantify the colocalization of fluorescent signals at single molecule level. These analysis procedures have been inserted into an experimental pipeline to optimize the produced results. We show that Fluorescent NanoDiamonds targeted to an intracellular compartment can be employed (i) to correct spatial drift to maximize the localization precision and (ii) to register confocal and SMLM images in correlative multiresolution, multimodal imaging. We validated the ICCS based approach on defined biological control samples and showed its ability to quantitatively map area of interactions inside the cell. The produced results show that the ICCS analysis is an efficient tool to measure relative spatial distribution of different molecular species at the nanoscale.
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10
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Kratz J, Geisler C, Egner A. ISM-assisted tomographic STED microscopy. OPTICS EXPRESS 2022; 30:939-956. [PMID: 35209272 DOI: 10.1364/oe.445441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Stimulated emission depletion (STED) microscopy theoretically provides unlimited resolution. However, in practice the achievable resolution in biological samples is essentially limited by photobleaching. One method which overcomes this problem is tomographic STED (tomoSTED) microscopy. In tomoSTED microscopy, one-dimensional depletion patterns facing in different directions are successively applied in order to acquire a highly-resolved image in two dimensions. In this context, the number of addressed directions depends on the desired angular homogeneity of the point spread function or the optical transfer function and thus on the resolution increase as compared to diffraction-limited imaging. At a reasonable angular homogeneity the light dose and thus bleaching can be reduced, as compared to conventional STED microscopy. Here, we propose and demonstrate for the first time, to our knowledge, that the number of required depletion pattern orientations can be reduced by combining tomoSTED microscopy with the concept of image scanning microscopy (ISM). With our realization of an ISM-tomoSTED microscope, we show that approximately a factor of 2 lower number of orientations are required to achieve the same resolution and image quality as in tomoSTED microscopy.
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11
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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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12
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Kulaitis G, Munk A, Werner F. What is resolution? A statistical minimax testing perspective on superresolution microscopy. Ann Stat 2021. [DOI: 10.1214/20-aos2037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Affiliation(s)
- Gytis Kulaitis
- Institute for Mathematical Stochastics, University of Göttingen
| | - Axel Munk
- Institute for Mathematical Stochastics, University of Göttingen
| | - Frank Werner
- Institute of Mathematics, University of Würzburg
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13
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Heller JP, Odii T, Zheng K, Rusakov DA. Imaging tripartite synapses using super-resolution microscopy. Methods 2020; 174:81-90. [PMID: 31153907 PMCID: PMC7144327 DOI: 10.1016/j.ymeth.2019.05.024] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 05/03/2019] [Accepted: 05/28/2019] [Indexed: 01/02/2023] Open
Abstract
Astroglia are vital facilitators of brain development, homeostasis, and metabolic support. In addition, they are also essential to the formation and regulation of synaptic circuits. Due to the extraordinary complex, nanoscopic morphology of astrocytes, the underlying cellular mechanisms have been poorly understood. In particular, fine astrocytic processes that can be found in the vicinity of synapses have been difficult to study using traditional imaging techniques. Here, we describe a 3D three-colour super-resolution microscopy approach to unravel the nanostructure of tripartite synapses. The method is based on the SMLM technique direct stochastic optical reconstruction microscopy (dSTORM) which uses conventional fluorophore-labelled antibodies. This approach enables reconstructing the nanoscale localisation of individual astrocytic glutamate transporter (GLT-1) molecules surrounding presynaptic (bassoon) and postsynaptic (Homer1) protein localisations in fixed mouse brain sections. However, the technique is readily adaptable to other types of targets and tissues.
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Affiliation(s)
- Janosch Peter Heller
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; FutureNeuro Research Centre, Royal College of Surgeons in Ireland, Dublin, Ireland.
| | - Tuamoru Odii
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom; Department of Physiology, Faculty of Basic Medical Sciences, Alex Ekwueme Federal University Ndufu-Alike Ikwo, PMB 1010 Abakaliki, Nigeria
| | - Kaiyu Zheng
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom
| | - Dmitri A Rusakov
- UCL Queen Square Institute of Neurology, University College London, London, United Kingdom.
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Staudt T, Aspelmeier T, Laitenberger O, Geisler C, Egner A, Munk A. Statistical Molecule Counting in Super-Resolution Fluorescence Microscopy: Towards Quantitative Nanoscopy. Stat Sci 2020. [DOI: 10.1214/19-sts753] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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15
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Lee SA, Biteen JS. Spectral Reshaping of Single Dye Molecules Coupled to Single Plasmonic Nanoparticles. J Phys Chem Lett 2019; 10:5764-5769. [PMID: 31508965 DOI: 10.1021/acs.jpclett.9b02480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Fluorescent molecules are highly susceptible to their local environment. Thus, a fluorescent molecule near a plasmonic nanoparticle can experience changes in local electric field and local density of states that reshape its intrinsic emission spectrum. By avoiding ensemble averaging while simultaneously measuring the super-resolved position of the fluorophore and its emission spectrum, single-molecule hyperspectral imaging is uniquely suited to differentiate changes in the spectrum from heterogeneous ensemble effects. Thus, we uncover for the first time single-molecule fluorescence emission spectrum reshaping upon near-field coupling to individual gold nanoparticles using hyperspectral super-resolution fluorescence imaging, and we resolve this spectral reshaping as a function of the nanoparticle/dye spectral overlap and separation distance. We find that dyes bluer than the plasmon resonance maximum are red-shifted and redder dyes are blue-shifted. The primary vibronic peak transition probabilities shift to favor secondary vibronic peaks, leading to effective emission maxima shifts in excess of 50 nm, and we understand these light-matter interactions by combining super-resolution hyperspectral imaging and full-field electromagnetic simulations.
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Affiliation(s)
- Stephen A Lee
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
| | - Julie S Biteen
- Department of Chemistry , University of Michigan , Ann Arbor , Michigan 48109 , United States
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16
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Tameling C, Sommerfeld M, Munk A. Empirical optimal transport on countable metric spaces: Distributional limits and statistical applications. ANN APPL PROBAB 2019. [DOI: 10.1214/19-aap1463] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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17
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Jradi FM, Lavis LD. Chemistry of Photosensitive Fluorophores for Single-Molecule Localization Microscopy. ACS Chem Biol 2019; 14:1077-1090. [PMID: 30997987 DOI: 10.1021/acschembio.9b00197] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Development of single-molecule localization microscopy (SMLM) has sparked a revolution in biological imaging, allowing "super-resolution" fluorescence microscopy below the diffraction limit of light. The past decade has seen an explosion in not only optical hardware for SMLM but also the development or repurposing of fluorescent proteins and small-molecule fluorescent probes for this technique. In this review, written by chemists for chemists, we detail the history of single-molecule localization microscopy and collate the collection of probes with demonstrated utility in SMLM. We hope it will serve as a primer for probe choice in localization microscopy as well as an inspiration for the development of new fluorophores that enable imaging of biological samples with exquisite detail.
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Affiliation(s)
- Fadi M. Jradi
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
| | - Luke D. Lavis
- Janelia Research Campus, Howard Hughes Medical Institute, 19700 Helix Drive, Ashburn, Virginia 20147, United States
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18
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Correlative cryo super-resolution light and electron microscopy on mammalian cells using fluorescent proteins. Sci Rep 2019; 9:1369. [PMID: 30718653 PMCID: PMC6362030 DOI: 10.1038/s41598-018-37728-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/12/2018] [Indexed: 11/22/2022] Open
Abstract
Sample fixation by vitrification is critical for the optimal structural preservation of biomolecules and subsequent high-resolution imaging by cryo-correlative light and electron microscopy (cryoCLEM). There is a large resolution gap between cryo fluorescence microscopy (cryoFLM), ~400-nm, and the sub-nanometre resolution achievable with cryo-electron microscopy (cryoEM), which hinders interpretation of cryoCLEM data. Here, we present a general approach to increase the resolution of cryoFLM using cryo-super-resolution (cryoSR) microscopy that is compatible with successive cryoEM investigation in the same region. We determined imaging parameters to avoid devitrification of the cryosamples without the necessity for cryoprotectants. Next, we examined the applicability of various fluorescent proteins (FPs) for single-molecule localisation cryoSR microscopy and found that all investigated FPs display reversible photoswitchable behaviour, and demonstrated cryoSR on lipid nanotubes labelled with rsEGFP2 and rsFastLime. Finally, we performed SR-cryoCLEM on mammalian cells expressing microtubule-associated protein-2 fused to rsEGFP2 and performed 3D cryo-electron tomography on the localised areas. The method we describe exclusively uses commercially available equipment to achieve a localisation precision of 30-nm. Furthermore, all investigated FPs displayed behaviour compatible with cryoSR microscopy, making this technique broadly available without requiring specialised equipment and will improve the applicability of this emerging technique for cellular and structural biology.
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19
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Sahl SJ, Schönle A, Hell SW. Fluorescence Microscopy with Nanometer Resolution. SPRINGER HANDBOOK OF MICROSCOPY 2019. [DOI: 10.1007/978-3-030-00069-1_22] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Roubinet B, Bischoff M, Nizamov S, Yan S, Geisler C, Stoldt S, Mitronova GY, Belov VN, Bossi ML, Hell SW. Photoactivatable Rhodamine Spiroamides and Diazoketones Decorated with “Universal Hydrophilizer” or Hydroxyl Groups. J Org Chem 2018; 83:6466-6476. [DOI: 10.1021/acs.joc.8b00756] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Benôit Roubinet
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Matthias Bischoff
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Shamil Nizamov
- Abberior GmbH, Hans-Adolf-Krebs-Weg 1, 37077 Göttingen, Germany
| | - Sergey Yan
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Claudia Geisler
- Department of Optical Nanoscopy, Laser-Laboratorium Göttingen e.V., 37077 Göttingen, Germany
| | - Stefan Stoldt
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Gyuzel Y. Mitronova
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Vladimir N. Belov
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Mariano L. Bossi
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
| | - Stefan W. Hell
- Department of Nanobiophotonics, Max Planck Institute for Biophysical Chemistry, Am Fassberg 11, 37077 Göttingen, Germany
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21
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Bernhem K, Blom H, Brismar H. Quantification of endogenous and exogenous protein expressions of Na,K-ATPase with super-resolution PALM/STORM imaging. PLoS One 2018; 13:e0195825. [PMID: 29694368 PMCID: PMC5918999 DOI: 10.1371/journal.pone.0195825] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Accepted: 03/30/2018] [Indexed: 01/19/2023] Open
Abstract
Transient transfection of fluorescent fusion proteins is a key enabling technology in fluorescent microscopy to spatio-temporally map cellular protein distributions. Transient transfection of proteins may however bypass normal regulation of expression, leading to overexpression artefacts like misallocations and excess amounts. In this study we investigate the use of STORM and PALM microscopy to quantitatively monitor endogenous and exogenous protein expression. Through incorporation of an N-terminal hemagglutinin epitope to a mMaple3 fused Na,K-ATPase (α1 isoform), we analyze the spatial and quantitative changes of plasma membrane Na,K-ATPase localization during competitive transient expression. Quantification of plasma membrane protein density revealed a time dependent increase of Na,K-ATPase, but no increase in size of protein clusters. Results show that after 41h transfection, the total plasma membrane density of Na,K-ATPase increased by 63% while the endogenous contribution was reduced by 16%.
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Affiliation(s)
- Kristoffer Bernhem
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Hans Blom
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
| | - Hjalmar Brismar
- Science for Life Laboratory, Department of Applied Physics, Royal Institute of Technology, Stockholm, Sweden
- Science for Life Laboratory, Department of Women’s and Children’s Health, Karolinska Institutet, Stockholm, Sweden
- * E-mail:
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22
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Abstract
Fluorescence nanoscopy uniquely combines minimally invasive optical access to the internal nanoscale structure and dynamics of cells and tissues with molecular detection specificity. While the basic physical principles of 'super-resolution' imaging were discovered in the 1990s, with initial experimental demonstrations following in 2000, the broad application of super-resolution imaging to address cell-biological questions has only more recently emerged. Nanoscopy approaches have begun to facilitate discoveries in cell biology and to add new knowledge. One current direction for method improvement is the ambition to quantitatively account for each molecule under investigation and assess true molecular colocalization patterns via multi-colour analyses. In pursuing this goal, the labelling of individual molecules to enable their visualization has emerged as a central challenge. Extending nanoscale imaging into (sliced) tissue and whole-animal contexts is a further goal. In this Review we describe the successes to date and discuss current obstacles and possibilities for further development.
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Cremer C, Szczurek A, Schock F, Gourram A, Birk U. Super-resolution microscopy approaches to nuclear nanostructure imaging. Methods 2017; 123:11-32. [PMID: 28390838 DOI: 10.1016/j.ymeth.2017.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
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Affiliation(s)
- Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany. http://www.optics.imb-mainz.de
| | - Aleksander Szczurek
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Florian Schock
- Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Amine Gourram
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
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25
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Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples. Nat Protoc 2017; 12:916-946. [PMID: 28384138 DOI: 10.1038/nprot.2017.017] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM data sets for aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. The choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replication creates high-contrast, 3D images of the cytoplasmic surface of the plasma membrane but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (∼10-50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2-7 d, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology.
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26
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Cheng D, Schwartzman A. MULTIPLE TESTING OF LOCAL MAXIMA FOR DETECTION OF PEAKS IN RANDOM FIELDS. Ann Stat 2017; 45:529-556. [PMID: 31527989 PMCID: PMC6746560 DOI: 10.1214/16-aos1458] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A topological multiple testing scheme is presented for detecting peaks in images under stationary ergodic Gaussian noise, where tests are performed at local maxima of the smoothed observed signals. The procedure generalizes the one-dimensional scheme of [31] to Euclidean domains of arbitrary dimension. Two methods are developed according to two different ways of computing p-values: (i) using the exact distribution of the height of local maxima, available explicitly when the noise field is isotropic [9, 10]; (ii) using an approximation to the overshoot distribution of local maxima above a pre-threshold, applicable when the exact distribution is unknown, such as when the stationary noise field is non-isotropic [9]. The algorithms, combined with the Benjamini-Hochberg procedure for thresholding p-values, provide asymptotic strong control of the False Discovery Rate (FDR) and power consistency, with specific rates, as the search space and signal strength get large. The optimal smoothing bandwidth and optimal pre-threshold are obtained to achieve maximum power. Simulations show that FDR levels are maintained in non-asymptotic conditions. The methods are illustrated in the analysis of functional magnetic resonance images of the brain.
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Affiliation(s)
- Dan Cheng
- Division of Biostatistics, University of California, San Diego
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27
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Colomb W, Czerski J, Sau JD, Sarkar SK. Estimation of microscope drift using fluorescent nanodiamonds as fiducial markers. J Microsc 2017; 266:298-306. [PMID: 28328030 DOI: 10.1111/jmi.12539] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2016] [Revised: 01/16/2017] [Accepted: 01/25/2017] [Indexed: 01/10/2023]
Abstract
Fiducial markers are used to correct the microscope drift and should be photostable, be usable at multiple wavelengths and be compatible for multimodal imaging. Fiducial markers such as beads, gold nanoparticles, microfabricated patterns and organic fluorophores lack one or more of these criteria. Moreover, the localization accuracy and drift correction can be degraded by other fluorophores, instrument noise and artefacts due to image processing and tracking algorithms. Estimating mechanical drift by assuming Gaussian distributed noise is not suitable under these circumstances. Here we present a method that uses fluorescent nanodiamonds as fiducial markers and uses an improved maximum likelihood algorithm to estimate the drift with both accuracy and precision within the range 1.55-5.75 nm.
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Affiliation(s)
- W Colomb
- Department of Physics, Colorado School of Mines, Golden, Colorado, U.S.A
| | - J Czerski
- Department of Physics, Colorado School of Mines, Golden, Colorado, U.S.A
| | - J D Sau
- Department of Physics, University of Maryland, College Park, MD, U.S.A
| | - S K Sarkar
- Department of Physics, Colorado School of Mines, Golden, Colorado, U.S.A
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28
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Affiliation(s)
- Hans Blom
- Royal Institute of Technology (KTH), Dept Applied Physics, SciLifeLab, 17165 Solna, Sweden
| | - Jerker Widengren
- Royal Institute of Technology (KTH), Dept Applied Physics, Albanova Univ Center, 10691 Stockholm, Sweden
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29
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Prakash K. Investigating Chromatin Organisation Using Single Molecule Localisation Microscopy. ACTA ACUST UNITED AC 2017. [DOI: 10.1007/978-3-319-52183-1_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
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30
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Hauser M, Wojcik M, Kim D, Mahmoudi M, Li W, Xu K. Correlative Super-Resolution Microscopy: New Dimensions and New Opportunities. Chem Rev 2017; 117:7428-7456. [PMID: 28045508 DOI: 10.1021/acs.chemrev.6b00604] [Citation(s) in RCA: 101] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Correlative microscopy, the integration of two or more microscopy techniques performed on the same sample, produces results that emphasize the strengths of each technique while offsetting their individual weaknesses. Light microscopy has historically been a central method in correlative microscopy due to its widespread availability, compatibility with hydrated and live biological samples, and excellent molecular specificity through fluorescence labeling. However, conventional light microscopy can only achieve a resolution of ∼300 nm, undercutting its advantages in correlations with higher-resolution methods. The rise of super-resolution microscopy (SRM) over the past decade has drastically improved the resolution of light microscopy to ∼10 nm, thus creating exciting new opportunities and challenges for correlative microscopy. Here we review how these challenges are addressed to effectively correlate SRM with other microscopy techniques, including light microscopy, electron microscopy, cryomicroscopy, atomic force microscopy, and various forms of spectroscopy. Though we emphasize biological studies, we also discuss the application of correlative SRM to materials characterization and single-molecule reactions. Finally, we point out current limitations and discuss possible future improvements and advances. We thus demonstrate how a correlative approach adds new dimensions of information and provides new opportunities in the fast-growing field of SRM.
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Affiliation(s)
- Meghan Hauser
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Michal Wojcik
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Doory Kim
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Morteza Mahmoudi
- Center for Nanomedicine and Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
| | - Wan Li
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California , Berkeley, California 94720, United States.,Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
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31
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Cristino L, Imperatore R, Di Marzo V. Techniques for the Cellular and Subcellular Localization of Endocannabinoid Receptors and Enzymes in the Mammalian Brain. Methods Enzymol 2017; 593:61-98. [DOI: 10.1016/bs.mie.2017.05.003] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
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32
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Barr VA, Yi J, Samelson LE. Super-resolution Analysis of TCR-Dependent Signaling: Single-Molecule Localization Microscopy. Methods Mol Biol 2017; 1584:183-206. [PMID: 28255704 PMCID: PMC6676910 DOI: 10.1007/978-1-4939-6881-7_13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Single-molecule localization microscopy (SMLM) comprises methods that produce super-resolution images from molecular locations of single molecules. These techniques mathematically determine the center of a diffraction-limited spot produced by a fluorescent molecule, which represents the most likely location of the molecule. Only a small cohort of well-separated molecules is visualized in a single image, and then many images are obtained from a single sample. The localizations from all the images are combined to produce a super-resolution picture of the sample. Here we describe the application of two methods, photoactivation localization microscopy (PALM) and direct stochastic optical reconstruction microscopy (dSTORM), to the study of signaling microclusters in T cells.
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Affiliation(s)
- Valarie A Barr
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Jason Yi
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA
| | - Lawrence E Samelson
- Laboratory of Cellular and Molecular Biology, Center for Cancer Research, National Cancer Institute, Bethesda, MD, 20892-4256, USA.
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33
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Gelissen APH, Oppermann A, Caumanns T, Hebbeker P, Turnhoff SK, Tiwari R, Eisold S, Simon U, Lu Y, Mayer J, Richtering W, Walther A, Wöll D. 3D Structures of Responsive Nanocompartmentalized Microgels. NANO LETTERS 2016; 16:7295-7301. [PMID: 27701865 DOI: 10.1021/acs.nanolett.6b03940] [Citation(s) in RCA: 77] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Compartmentalization in soft matter is important for segregating and coordinating chemical reactions, sequestering (re)active components, and integrating multifunctionality. Advances depend crucially on quantitative 3D visualization in situ with high spatiotemporal resolution. Here, we show the direct visualization of different compartments within adaptive microgels using a combination of in situ electron and super-resolved fluorescence microscopy. We unravel new levels of structural details and address the challenge of reconstructing 3D information from 2D projections for nonuniform soft matter as opposed to monodisperse proteins. Moreover, we visualize the thermally induced shrinkage of responsive core-shell microgels live in water. This strategy opens doors for systematic in situ studies of soft matter systems and their application as smart materials.
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Affiliation(s)
- Arjan P H Gelissen
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Alex Oppermann
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Tobias Caumanns
- GFE Central Facility for Electron Microscopy, RWTH Aachen University , Mies-van-der-Rohe-Straße 59, D-52074 Aachen, Germany
| | - Pascal Hebbeker
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Sarah K Turnhoff
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Rahul Tiwari
- DWI - Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, D-52074 Aachen, Germany
| | - Sabine Eisold
- Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Ulrich Simon
- Institute of Inorganic Chemistry, RWTH Aachen University , Landoltweg 1, D-52056 Aachen, Germany
| | - Yan Lu
- Soft Matter and Functional Materials, Helmholtz-Zentrum Berlin für Materialien und Energie , Hahn-Meitner-Platz 1, D-14109 Berlin, Germany
| | - Joachim Mayer
- GFE Central Facility for Electron Microscopy, RWTH Aachen University , Mies-van-der-Rohe-Straße 59, D-52074 Aachen, Germany
| | - Walter Richtering
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
| | - Andreas Walther
- DWI - Leibniz-Institute for Interactive Materials , Forckenbeckstraße 50, D-52074 Aachen, Germany
| | - Dominik Wöll
- Institute of Physical Chemistry, RWTH Aachen University , Landoltweg 2, D-52056 Aachen, Germany
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35
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Abstract
Fluorescence microscopy is an invaluable tool to visualize molecules in their biological context with ease and flexibility. However, studies using conventional light microscopy have been limited to the resolution that light diffraction allows (i.e., ~200 nm). This limitation has been recently circumvented by several types of advanced fluorescence microscopy techniques, which have achieved resolutions of up to ~10 nm. The resulting enhanced imaging precision has helped to find important cellular details that were not visible using diffraction-limited instruments. However, it has also revealed that conventional stainings using large affinity tags, such as antibodies, are not accurate enough for these imaging techniques. Since aptamers are substantially smaller than antibodies, they could provide a real advantage in super-resolution imaging. Here we compare the live staining of transferrin receptors (TfnR) obtained with different fluorescently labeled affinity probes: aptamers, specific monoclonal antibodies, or the natural receptor ligand transferrin. We observed negligible differences between these staining strategies when imaging is performed with conventional light microscopy (i.e., laser scanning confocal microscopy). However, a clear superiority of the aptamer tag over antibodies became apparent in super-resolved images obtained with stimulated emission depletion (STED) microscopy.
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Affiliation(s)
- Maria Angela Gomes de Castro
- Department of Neuro- and Sensory Physiology, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University of Göttingen Medical Center, Humboldtallee 23, 37073, Göttingen, Germany
| | - Burkhard Rammner
- Department of Neuro- and Sensory Physiology, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University of Göttingen Medical Center, Humboldtallee 23, 37073, Göttingen, Germany
| | - Felipe Opazo
- Department of Neuro- and Sensory Physiology, Cluster of Excellence Nanoscale Microscopy and Molecular Physiology of the Brain, University of Göttingen Medical Center, Humboldtallee 23, 37073, Göttingen, Germany.
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Sialic Acid Glycobiology Unveils Trypanosoma cruzi Trypomastigote Membrane Physiology. PLoS Pathog 2016; 12:e1005559. [PMID: 27058585 PMCID: PMC4825991 DOI: 10.1371/journal.ppat.1005559] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/18/2016] [Indexed: 01/25/2023] Open
Abstract
Trypanosoma cruzi, the flagellate protozoan agent of Chagas disease or American trypanosomiasis, is unable to synthesize sialic acids de novo. Mucins and trans-sialidase (TS) are substrate and enzyme, respectively, of the glycobiological system that scavenges sialic acid from the host in a crucial interplay for T. cruzi life cycle. The acquisition of the sialyl residue allows the parasite to avoid lysis by serum factors and to interact with the host cell. A major drawback to studying the sialylation kinetics and turnover of the trypomastigote glycoconjugates is the difficulty to identify and follow the recently acquired sialyl residues. To tackle this issue, we followed an unnatural sugar approach as bioorthogonal chemical reporters, where the use of azidosialyl residues allowed identifying the acquired sugar. Advanced microscopy techniques, together with biochemical methods, were used to study the trypomastigote membrane from its glycobiological perspective. Main sialyl acceptors were identified as mucins by biochemical procedures and protein markers. Together with determining their shedding and turnover rates, we also report that several membrane proteins, including TS and its substrates, both glycosylphosphatidylinositol-anchored proteins, are separately distributed on parasite surface and contained in different and highly stable membrane microdomains. Notably, labeling for α(1,3)Galactosyl residues only partially colocalize with sialylated mucins, indicating that two species of glycosylated mucins do exist, which are segregated at the parasite surface. Moreover, sialylated mucins were included in lipid-raft-domains, whereas TS molecules are not. The location of the surface-anchored TS resulted too far off as to be capable to sialylate mucins, a role played by the shed TS instead. Phosphatidylinositol-phospholipase-C activity is actually not present in trypomastigotes. Therefore, shedding of TS occurs via microvesicles instead of as a fully soluble form.
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Abstract
The majority of studies of the living cell rely on capturing images using fluorescence microscopy. Unfortunately, for centuries, diffraction of light was limiting the spatial resolution in the optical microscope: structural and molecular details much finer than about half the wavelength of visible light (~200 nm) could not be visualized, imposing significant limitations on this otherwise so promising method. The surpassing of this resolution limit in far-field microscopy is currently one of the most momentous developments for studying the living cell, as the move from microscopy to super-resolution microscopy or 'nanoscopy' offers opportunities to study problems in biophysical and biomedical research at a new level of detail. This review describes the principles and modalities of present fluorescence nanoscopes, as well as their potential for biophysical and cellular experiments. All the existing nanoscopy variants separate neighboring features by transiently preparing their fluorescent molecules in states of different emission characteristics in order to make the features discernible. Usually these are fluorescent 'on' and 'off' states causing the adjacent molecules to emit sequentially in time. Each of the variants can in principle reach molecular spatial resolution and has its own advantages and disadvantages. Some require specific transitions and states that can be found only in certain fluorophore subfamilies, such as photoswitchable fluorophores, while other variants can be realized with standard fluorescent labels. Similar to conventional far-field microscopy, nanoscopy can be utilized for dynamical, multi-color and three-dimensional imaging of fixed and live cells, tissues or organisms. Lens-based fluorescence nanoscopy is poised for a high impact on future developments in the life sciences, with the potential to help solve long-standing quests in different areas of scientific research.
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Abstract
The characteristic lengths of molecular arrangement in primary cilia are below the diffraction limit of light, challenging structural and functional studies of ciliary proteins. Superresolution microscopy can reach up to a 20 nm resolution, significantly improving the ability to map molecules in primary cilia. Here we describe detailed experimental procedure of STED microscopy imaging and dSTORM imaging, two of the most powerful superresolution imaging techniques. Specifically, we emphasize the use of these two methods on imaging proteins in primary cilia.
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Affiliation(s)
- T Tony Yang
- Institute of Atomic and Molecular Sciences, Academia Sinica, No 1, Roosevelt Rd. Sec 4, Taipei, 10617, Taiwan
| | - Weng Man Chong
- Institute of Atomic and Molecular Sciences, Academia Sinica, No 1, Roosevelt Rd. Sec 4, Taipei, 10617, Taiwan
| | - Jung-Chi Liao
- Institute of Atomic and Molecular Sciences, Academia Sinica, No 1, Roosevelt Rd. Sec 4, Taipei, 10617, Taiwan.
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Abstract
The field of fluorescent proteins (FPs) is constantly developing. The use of FPs changed the field of life sciences completely, starting a new era of direct observation and quantification of cellular processes. The broad spectrum of FPs (see Fig. 1) with a wide range of characteristics allows their use in many different experiments. This review discusses the use of FPs for imaging in budding yeast (Saccharomyces cerevisiae) and fission yeast Schizosaccharomyces pombe). The information included in this review is relevant for both species unless stated otherwise.
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Affiliation(s)
- Maja Bialecka-Fornal
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA
| | - Tatyana Makushok
- Department of Biochemistry and Biophysics, University of California, San Francisco, 600 16th Street, San Francisco, CA, 94158, USA
| | - Susanne M Rafelski
- Department of Developmental and Cell Biology, Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
- Center for Complex Biological Systems, University of California, Irvine, CA, 92697, USA.
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Lehmann M, Gottschalk B, Puchkov D, Schmieder P, Schwagerus S, Hackenberger CPR, Haucke V, Schmoranzer J. Multicolor Caged dSTORM Resolves the Ultrastructure of Synaptic Vesicles in the Brain. Angew Chem Int Ed Engl 2015; 54:13230-5. [DOI: 10.1002/anie.201505138] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2015] [Revised: 08/04/2015] [Indexed: 01/31/2023]
Affiliation(s)
- Martin Lehmann
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Freie Universität Berlin, Department of Biochemistry, Takustrasse 6, 14195 Berlin (Germany)
| | - Benjamin Gottschalk
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Dmytro Puchkov
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Peter Schmieder
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Sergej Schwagerus
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Christian P. R. Hackenberger
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department of Chemistry, Brook‐Taylor‐Strasse. 2, 12489 Berlin (Germany)
| | - Volker Haucke
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Freie Universität Berlin, Department of Biochemistry, Takustrasse 6, 14195 Berlin (Germany)
| | - Jan Schmoranzer
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Freie Universität Berlin, Department of Biochemistry, Takustrasse 6, 14195 Berlin (Germany)
- Charité ‐ Universitätsmedizin Berlin, Charité Campus Mitte, Virchowweg 6, 10117 Berlin (Germany)
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Lehmann M, Gottschalk B, Puchkov D, Schmieder P, Schwagerus S, Hackenberger CPR, Haucke V, Schmoranzer J. Multicolor Caged dSTORM Resolves the Ultrastructure of Synaptic Vesicles in the Brain. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201505138] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Martin Lehmann
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Freie Universität Berlin, Department of Biochemistry, Takustrasse 6, 14195 Berlin (Germany)
| | - Benjamin Gottschalk
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Dmytro Puchkov
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Peter Schmieder
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Sergej Schwagerus
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
| | - Christian P. R. Hackenberger
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Humboldt Universität zu Berlin, Department of Chemistry, Brook‐Taylor‐Strasse. 2, 12489 Berlin (Germany)
| | - Volker Haucke
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Freie Universität Berlin, Department of Biochemistry, Takustrasse 6, 14195 Berlin (Germany)
| | - Jan Schmoranzer
- Leibniz Institut für Molekulare Pharmakologie (FMP), Robert‐Roessle‐Strasse 10, 13125 Berlin (Germany)
- Freie Universität Berlin, Department of Biochemistry, Takustrasse 6, 14195 Berlin (Germany)
- Charité ‐ Universitätsmedizin Berlin, Charité Campus Mitte, Virchowweg 6, 10117 Berlin (Germany)
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Schneider J, Zahn J, Maglione M, Sigrist SJ, Marquard J, Chojnacki J, Kräusslich HG, Sahl SJ, Engelhardt J, Hell SW. Ultrafast, temporally stochastic STED nanoscopy of millisecond dynamics. Nat Methods 2015. [DOI: 10.1038/nmeth.3481] [Citation(s) in RCA: 85] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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43
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Hartmann A, Huckemann S, Dannemann J, Laitenberger O, Geisler C, Egner A, Munk A. Drift estimation in sparse sequential dynamic imaging, with application to nanoscale fluorescence microscopy. J R Stat Soc Series B Stat Methodol 2015. [DOI: 10.1111/rssb.12128] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
| | | | | | | | | | | | - Axel Munk
- Georg-August-Universität; Göttingen Germany
- Max Planck Institute for Biophysical Chemistry; Göttingen Germany
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Almada P, Culley S, Henriques R. PALM and STORM: Into large fields and high-throughput microscopy with sCMOS detectors. Methods 2015; 88:109-21. [PMID: 26079924 DOI: 10.1016/j.ymeth.2015.06.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 05/28/2015] [Accepted: 06/03/2015] [Indexed: 01/05/2023] Open
Abstract
Single Molecule Localization Microscopy (SMLM) techniques such as Photo-Activation Localization Microscopy (PALM) and Stochastic Optical Reconstruction Microscopy (STORM) enable fluorescence microscopy super-resolution: the overcoming of the resolution barrier imposed by the diffraction of light. These techniques are based on acquiring hundreds or thousands of images of single molecules, locating them and reconstructing a higher-resolution image from the high-precision localizations. These methods generally imply a considerable trade-off between imaging speed and resolution, limiting their applicability to high-throughput workflows. Recent advancements in scientific Complementary Metal-Oxide Semiconductor (sCMOS) camera sensors and localization algorithms reduce the temporal requirements for SMLM, pushing it toward high-throughput microscopy. Here we outline the decisions researchers face when considering how to adapt hardware on a new system for sCMOS sensors with high-throughput in mind.
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Affiliation(s)
- Pedro Almada
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, United Kingdom
| | - Siân Culley
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, United Kingdom
| | - Ricardo Henriques
- Quantitative Imaging and NanoBiophysics Group, MRC Laboratory for Molecular Cell Biology and Department of Cell and Developmental Biology, University College London, Gower Street, WC1E 6BT London, United Kingdom.
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45
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Quantification of Internalized Silica Nanoparticles via STED Microscopy. BIOMED RESEARCH INTERNATIONAL 2015; 2015:961208. [PMID: 26125028 PMCID: PMC4466362 DOI: 10.1155/2015/961208] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Accepted: 02/24/2015] [Indexed: 01/11/2023]
Abstract
The development of safe engineered nanoparticles (NPs) requires a detailed understanding of their interaction mechanisms on a cellular level. Therefore, quantification of NP internalization is crucial to predict the potential impact of intracellular NP doses, providing essential information for risk assessment as well as for drug delivery applications. In this study, the internalization of 25 nm and 85 nm silica nanoparticles (SNPs) in alveolar type II cells (A549) was quantified by application of super-resolution STED (stimulated emission depletion) microscopy. Cells were exposed to equal particle number concentrations (9.2 × 1010 particles mL−1) of each particle size and the sedimentation of particles during exposure was taken into account. Microscopy images revealed that particles of both sizes entered the cells after 5 h incubation in serum supplemented and serum-free medium. According to the in vitro sedimentation, diffusion, and dosimetry (ISDD) model 20–27% of the particles sedimented. In comparison, 102-103 NPs per cell were detected intracellularly serum-containing medium. Furthermore, in the presence of serum, no cytotoxicity was induced by the SNPs. In serum-free medium, large agglomerates of both particle sizes covered the cells whereas only high concentrations (≥ 3.8 × 1012 particles mL−1) of the smaller particles induced cytotoxicity.
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46
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Lin Y, Long JJ, Huang F, Duim WC, Kirschbaum S, Zhang Y, Schroeder LK, Rebane AA, Velasco MGM, Virrueta A, Moonan DW, Jiao J, Hernandez SY, Zhang Y, Bewersdorf J. Quantifying and optimizing single-molecule switching nanoscopy at high speeds. PLoS One 2015; 10:e0128135. [PMID: 26011109 PMCID: PMC4444241 DOI: 10.1371/journal.pone.0128135] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2014] [Accepted: 04/23/2015] [Indexed: 12/12/2022] Open
Abstract
Single-molecule switching nanoscopy overcomes the diffraction limit of light by stochastically switching single fluorescent molecules on and off, and then localizing their positions individually. Recent advances in this technique have greatly accelerated the data acquisition speed and improved the temporal resolution of super-resolution imaging. However, it has not been quantified whether this speed increase comes at the cost of compromised image quality. The spatial and temporal resolution depends on many factors, among which laser intensity and camera speed are the two most critical parameters. Here we quantitatively compare the image quality achieved when imaging Alexa Fluor 647-immunolabeled microtubules over an extended range of laser intensities and camera speeds using three criteria - localization precision, density of localized molecules, and resolution of reconstructed images based on Fourier Ring Correlation. We found that, with optimized parameters, single-molecule switching nanoscopy at high speeds can achieve the same image quality as imaging at conventional speeds in a 5-25 times shorter time period. Furthermore, we measured the photoswitching kinetics of Alexa Fluor 647 from single-molecule experiments, and, based on this kinetic data, we developed algorithms to simulate single-molecule switching nanoscopy images. We used this software tool to demonstrate how laser intensity and camera speed affect the density of active fluorophores and influence the achievable resolution. Our study provides guidelines for choosing appropriate laser intensities for imaging Alexa Fluor 647 at different speeds and a quantification protocol for future evaluations of other probes and imaging parameters.
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Affiliation(s)
- Yu Lin
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Jane J. Long
- Yale College, Yale University, New Haven, Connecticut, United States of America
| | - Fang Huang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Whitney C. Duim
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Stefanie Kirschbaum
- Institute for Molecular Biophysics, The Jackson Laboratory, Bar Harbor, Maine, United States of America
| | - Yongdeng Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Lena K. Schroeder
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
| | - Aleksander A. Rebane
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Physics, Yale University, New Haven, Connecticut, United States of America
| | - Mary Grace M. Velasco
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Alejandro Virrueta
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Mechanical Engineering and Material Science, Yale University, New Haven, Connecticut, United States of America
| | - Daniel W. Moonan
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut, United States of America
| | - Junyi Jiao
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Sandy Y. Hernandez
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Yongli Zhang
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
| | - Joerg Bewersdorf
- Department of Cell Biology, Yale University School of Medicine, New Haven, Connecticut, United States of America
- Department of Biomedical Engineering, Yale University, New Haven, Connecticut, United States of America
- Integrated Graduate Program in Physical and Engineering Biology, Yale University, New Haven, Connecticut, United States of America
- * E-mail:
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47
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Ranchon H, Picot V, Bancaud A. Metrology of confined flows using wide field nanoparticle velocimetry. Sci Rep 2015; 5:10128. [PMID: 25974654 PMCID: PMC4431396 DOI: 10.1038/srep10128] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 03/31/2015] [Indexed: 01/10/2023] Open
Abstract
The manipulation of fluids in micro/nanofabricated systems opens new avenues to engineer the transport of matter at the molecular level. Yet the number of methods for the in situ characterization of fluid flows in shallow channels is limited. Here we establish a simple method called nanoparticle velocimetry distribution analysis (NVDA) that relies on wide field microscopy to measure the flow rate and channel height based on the fitting of particle velocity distributions along and across the flow direction. NVDA is validated by simulations, showing errors in velocity and height determination of less than 1% and 8% respectively, as well as with experiments, in which we monitor the behavior of 200 nm nanoparticles conveyed in channels of ~1.8 μm in height. We then show the relevance of this assay for the characterization of flows in bulging channels, and prove its suitability to characterize the concentration of particles across the channel height in the context of visco-elastic focusing. Our method for rapid and quantitative flow characterization has therefore a broad spectrum of applications in micro/nanofluidics, and a strong potential for the optimization of Lab-on-Chips modules in which engineering of confined transport is necessary.
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Affiliation(s)
- Hubert Ranchon
- 1] CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France [2] Univ de Toulouse, LAAS, F-31400 Toulouse, France
| | - Vincent Picot
- 1] CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France [2] Univ de Toulouse, LAAS, F-31400 Toulouse, France
| | - Aurélien Bancaud
- 1] CNRS, LAAS, 7 avenue du colonel Roche, F-31400 Toulouse, France [2] Univ de Toulouse, LAAS, F-31400 Toulouse, France
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48
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Zhong H. Applying superresolution localization-based microscopy to neurons. Synapse 2015; 69:283-94. [PMID: 25648102 DOI: 10.1002/syn.21806] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2014] [Revised: 01/19/2015] [Accepted: 01/26/2015] [Indexed: 01/15/2023]
Abstract
Proper brain function requires the precise localization of proteins and signaling molecules on a nanometer scale. The examination of molecular organization at this scale has been difficult in part because it is beyond the reach of conventional, diffraction-limited light microscopy. The recently developed method of superresolution, localization-based fluorescent microscopy (LBM), such as photoactivated localization microscopy (PALM) and stochastic optical reconstruction microscopy (STORM), has demonstrated a resolving power at a 10 nm scale and is poised to become a vital tool in modern neuroscience research. Indeed, LBM has revealed previously unknown cellular architectures and organizational principles in neurons. Here, we discuss the principles of LBM, its current applications in neuroscience, and the challenges that must be met before its full potential is achieved. We also present the unpublished results of our own experiments to establish a sample preparation procedure for applying LBM to study brain tissue.
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Affiliation(s)
- Haining Zhong
- Vollum Institute, Oregon Health & Science University, Portland, Oregon, 97239; Howard Hughes Medical Institute, Janelia Research Campus, Ashburn, Virginia, 20147
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49
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Broeken J, Johnson H, Lidke DS, Liu S, Nieuwenhuizen RPJ, Stallinga S, Lidke KA, Rieger B. Resolution improvement by 3D particle averaging in localization microscopy. Methods Appl Fluoresc 2015; 3:014003. [PMID: 25866640 DOI: 10.1088/2050-6120/3/1/014003] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Abstract
Inspired by recent developments in localization microscopy that applied averaging of identical particles in 2D for increasing the resolution even further, we discuss considerations for alignment (registration) methods for particles in general and for 3D in particular. We detail that traditional techniques for particle registration from cryo electron microscopy based on cross-correlation are not suitable, as the underlying image formation process is fundamentally different. We argue that only localizations, i.e. a set of coordinates with associated uncertainties, are recorded and not a continuous intensity distribution. We present a method that owes to this fact and that is inspired by the field of statistical pattern recognition. In particular we suggest to use an adapted version of the Bhattacharyya distance as a merit function for registration. We evaluate the method in simulations and demonstrate it on three-dimensional super-resolution data of Alexa 647 labelled to the Nup133 protein in the nuclear pore complex of Hela cells. From the simulations we find suggestions that for successful registration the localization uncertainty must be smaller than the distance between labeling sites on a particle. These suggestions are supported by theoretical considerations concerning the attainable resolution in localization microscopy and its scaling behavior as a function of labeling density and localization precision.
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Affiliation(s)
- Jordi Broeken
- Quantitative Imaging Group, Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 RE Delft, The Netherlands
| | - Hannah Johnson
- Department of Pathology, University of New Mexico, Albuquerque, NM 87106, USA
| | - Diane S Lidke
- Department of Pathology, University of New Mexico, Albuquerque, NM 87106, USA
| | - Sheng Liu
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87106, USA
| | - Robert P J Nieuwenhuizen
- Quantitative Imaging Group, Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 RE Delft, The Netherlands
| | - Sjoerd Stallinga
- Quantitative Imaging Group, Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 RE Delft, The Netherlands
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87106, USA
| | - Bernd Rieger
- Quantitative Imaging Group, Department of Imaging Physics, Delft University of Technology, Lorentzweg 1, 2628 RE Delft, The Netherlands
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50
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Han R, Wang L, Xu F, Zhang Y, Zhang M, Liu Z, Ren F, Zhang F. Drift correction for single-molecule imaging by molecular constraint field, a distance minimum metric. BMC BIOPHYSICS 2015; 8:1. [PMID: 25649266 PMCID: PMC4306247 DOI: 10.1186/s13628-014-0015-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 11/26/2014] [Indexed: 11/30/2022]
Abstract
Background The recent developments of far-field optical microscopy (single molecule imaging techniques) have overcome the diffraction barrier of light and improve image resolution by a factor of ten compared with conventional light microscopy. These techniques utilize the stochastic switching of probe molecules to overcome the diffraction limit and determine the precise localizations of molecules, which often requires a long image acquisition time. However, long acquisition times increase the risk of sample drift. In the case of high resolution microscopy, sample drift would decrease the image resolution. Results In this paper, we propose a novel metric based on the distance between molecules to solve the drift correction. The proposed metric directly uses the position information of molecules to estimate the frame drift. We also designed an algorithm to implement the metric for the general application of drift correction. There are two advantages of our method: First, because our method does not require space binning of positions of molecules but directly operates on the positions, it is more natural for single molecule imaging techniques. Second, our method can estimate drift with a small number of positions in each temporal bin, which may extend its potential application. Conclusions The effectiveness of our method has been demonstrated by both simulated data and experiments on single molecular images.
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Affiliation(s)
- Renmin Han
- Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China ; University of Chinese Academy of Sciences, Beijing, China
| | | | - Fan Xu
- Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China ; University of Chinese Academy of Sciences, Beijing, China
| | - Yongdeng Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Mingshu Zhang
- Institute of Biophysics, Chinese Academy of Sciences, Beijing, 100101 China
| | - Zhiyong Liu
- State Key Lab for Computer Architecture, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China
| | - Fei Ren
- Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China
| | - Fa Zhang
- Key Lab of Intelligent Information Processing and Advanced Computing Research Lab, Institute of Computing Technology, Chinese Academy of Sciences, Beijing, 100190 China
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