1
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Acher O, de Abreu MB, Grigoriev A, de Bettignies P, Vilotta M, Nguyên TL. Identifying and fixing in-plane positioning and stability issues on a microscope using machine-readable patterned position scales. Sci Rep 2023; 13:19521. [PMID: 37945927 PMCID: PMC10636118 DOI: 10.1038/s41598-023-46950-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 11/07/2023] [Indexed: 11/12/2023] Open
Abstract
Investigations of the in-plane positioning capabilities of microscopes using machine-readable encoded patterned scales are presented. The scales have patterns that contain absolute position information, and adequate software accurately determines the in-plane position from the scale images captured by the microscope camera. This makes in-plane positioning experiments simple and fast. The scales and software used in this study are commercially available. We investigated different microscopy systems and found that positioning performance is a system issue that is not determined solely by stage performance. In some cases, our experiments revealed software or hardware glitches that limited the positioning performance, which we easily fixed. We have also shown that it is possible to investigate vibrations using this approach and quantify their impact on image blurring. This is, for example, useful for experimentally determining the settling time after a stage movement.
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Affiliation(s)
- Olivier Acher
- HORIBA France SAS, 14 Bd Thomas Gobert, 91120, Palaiseau, France.
| | | | | | | | - Maxime Vilotta
- HORIBA France SAS, 455 Avenue Eugène Avinée, 59120, Palaiseau, France
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2
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Li K, Ni J, Tan X, Zhou Q, Chen D, Cao B, Lin J, Lin T, Zhao P, Yuan X, Ni Y. Motion screening of fiducial marker for improved localization precision and resolution in SMLM. OPTICS EXPRESS 2023; 31:26764-26776. [PMID: 37710528 DOI: 10.1364/oe.496761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/13/2023] [Indexed: 09/16/2023]
Abstract
Single-molecule localization microscopy (SMLM) provides unmatched high resolution but relies on accurate drift correction due to the long acquisition time for each field of view. A popular drift correction is implemented via referencing to fiducial markers that are assumed to be firmly immobilized and remain stationary relative to the imaged sample. However, there is so far lack of efficient approaches for evaluating other motions except sample drifting of immobilized markers and for addressing their potential impacts on images. Here, we developed a new approach for quantitatively assessing the motions of fiducial markers relative to the sample via mean squared displacement (MSD) analysis. Our findings revealed that over 90% of immobilized fluorescent beads in the SMLM imaging buffer exhibited higher MSDs compared to stationary beads in dry samples and displayed varying degrees of wobbling relative to the imaged field. By excluding extremely high-MSD beads in each field from drift correction, we optimized drift correction and experimentally measured localization precision. In SMLM experiments of cellular microtubules, we also found that including only relatively low-MSD beads for drift correction significantly improved the image resolution and quality. Our study presents a simple and effective approach to assess the potential relative motions of fiducial markers and emphasizes the importance of pre-screening fiducial markers for improved image quality and resolution in SMLM imaging.
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3
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Øvrebø Ø, Ojansivu M, Kartasalo K, Barriga HMG, Ranefall P, Holme MN, Stevens MM. RegiSTORM: channel registration for multi-color stochastic optical reconstruction microscopy. BMC Bioinformatics 2023; 24:237. [PMID: 37277712 DOI: 10.1186/s12859-023-05320-1] [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: 03/28/2022] [Accepted: 05/04/2023] [Indexed: 06/07/2023] Open
Abstract
BACKGROUND Stochastic optical reconstruction microscopy (STORM), a super-resolution microscopy technique based on single-molecule localizations, has become popular to characterize sub-diffraction limit targets. However, due to lengthy image acquisition, STORM recordings are prone to sample drift. Existing cross-correlation or fiducial marker-based algorithms allow correcting the drift within each channel, but misalignment between channels remains due to interchannel drift accumulating during sequential channel acquisition. This is a major drawback in multi-color STORM, a technique of utmost importance for the characterization of various biological interactions. RESULTS We developed RegiSTORM, a software for reducing channel misalignment by accurately registering STORM channels utilizing fiducial markers in the sample. RegiSTORM identifies fiducials from the STORM localization data based on their non-blinking nature and uses them as landmarks for channel registration. We first demonstrated accurate registration on recordings of fiducials only, as evidenced by significantly reduced target registration error with all the tested channel combinations. Next, we validated the performance in a more practically relevant setup on cells multi-stained for tubulin. Finally, we showed that RegiSTORM successfully registers two-color STORM recordings of cargo-loaded lipid nanoparticles without fiducials, demonstrating the broader applicability of this software. CONCLUSIONS The developed RegiSTORM software was demonstrated to be able to accurately register multiple STORM channels and is freely available as open-source (MIT license) at https://github.com/oystein676/RegiSTORM.git and https://doi.org/10.5281/zenodo.5509861 (archived), and runs as a standalone executable (Windows) or via Python (Mac OS, Linux).
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Affiliation(s)
- Øystein Øvrebø
- Department of Materials, Imperial College London, London, SW7 2AZ, UK
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK
- Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK
| | - Miina Ojansivu
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Kimmo Kartasalo
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Hanna M G Barriga
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Petter Ranefall
- SciLifeLab BioImage Informatics Facility, and Department of Information Technology, Uppsala University, 751 05, Uppsala, Sweden
| | - Margaret N Holme
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77, Stockholm, Sweden
| | - Molly M Stevens
- Department of Materials, Imperial College London, London, SW7 2AZ, UK.
- Department of Bioengineering, Imperial College London, London, SW7 2AZ, UK.
- Institute of Biomedical Engineering, Imperial College London, London, SW7 2AZ, UK.
- Department of Medical Biochemistry and Biophysics, Karolinska Institute, 171 77, Stockholm, Sweden.
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4
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Yao J, Guo H, Yin Z, Liu C, Da B, Liu Z, Chu Y, Zhong L, Sun L. Application of optical flow algorithm for drift correction in electron microscopy images. THE REVIEW OF SCIENTIFIC INSTRUMENTS 2023; 94:2890458. [PMID: 37184348 DOI: 10.1063/5.0129291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 04/25/2023] [Indexed: 05/16/2023]
Abstract
Transmission electron microscopy (TEM) image drift correction has been effectively addressed using diverse approaches, including the cross correlation algorithm (CC) and other strategies. However, most of the strategies fall short of achieving sufficient accuracy or cannot strike a balance between time consumption and accuracy. The present study proposes a TEM image drift correction strategy that enhances accuracy without any additional time consumption. Unlike the CC algorithm that matches pixels one by one, our approach involves the extraction of multiple feature points from the first TEM image and then uses the Lucas-Kanade (LK) optical flow algorithm to calculate the optical field of these feature points in the subsequent TEM images. The LK algorithm is used to calculate the instantaneous velocity of these feature points, which can help track the movement of the TEM image series. In addition, a high-precision sub-pixel level correction strategy by the utilization of linear interpolation during the correction process is developed in this work. Experimental results confirm that this strategy offers superior accuracy in comparison with the CC algorithm and also is insensitive to the size of the image. Furthermore, we offer a semantic segmentation neural network for electron microscope image pre-processing, thereby expanding the applicability of our methodology.
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Affiliation(s)
- JiaHao Yao
- SEU-FEI Nano-Pico Center, Key Laboratory of MEMS of Ministry of Education, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Hongxuan Guo
- SEU-FEI Nano-Pico Center, Key Laboratory of MEMS of Ministry of Education, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Ziqing Yin
- SEU-FEI Nano-Pico Center, Key Laboratory of MEMS of Ministry of Education, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Chang Liu
- SEU-FEI Nano-Pico Center, Key Laboratory of MEMS of Ministry of Education, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Bo Da
- Research and Services Division of Materials Data and Integrated System, National Institute for Materials Science, Ibaraki 305-0044, Japan
| | - Zheng Liu
- National Graphene Products Quality Inspection and Testing Center (Jiangsu), Wuxi 214174, People's Republic of China
| | - Yajie Chu
- School of Materials Science and Engineering, Nanjing Institute of Technology, Nanjing 211167, People's Republic of China
- Jiangsu Key Laboratory of Advanced Structure Materials and Application Technology, Nanjing 211167, People's Republic of China
| | - Li Zhong
- SEU-FEI Nano-Pico Center, Key Laboratory of MEMS of Ministry of Education, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, People's Republic of China
| | - Litao Sun
- SEU-FEI Nano-Pico Center, Key Laboratory of MEMS of Ministry of Education, School of Electronic Science and Engineering, Southeast University, Nanjing 210096, People's Republic of China
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5
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Niederauer C, Seynen M, Zomerdijk J, Kamp M, Ganzinger KA. The K2: Open-source simultaneous triple-color TIRF microscope for live-cell and single-molecule imaging. HARDWAREX 2023; 13:e00404. [PMID: 36923558 PMCID: PMC10009532 DOI: 10.1016/j.ohx.2023.e00404] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Imaging the dynamics and interactions of biomolecules at the single-molecule level in live cells and reconstituted systems has generated unprecedented knowledge about the biomolecular processes underlying many cellular functions. To achieve the speed and sensitivity needed to detect and follow individual molecules, these experiments typically require custom-built microscopes or custom modifications of commercial systems. The costs of such single-molecule microscopes, their technical complexity and the lack of open-source documentation on how to build custom setups therefore limit the accessibility of single-molecule imaging techniques. To advance the adaptation of dynamic single-molecule imaging by a wider community, we present the "K2": an open-source, simultaneous triple-color total internal reflection fluorescence (TIRF) microscope specifically designed for live-cell and single-molecule imaging. We explain our design considerations and provide step-by-step building instructions, parts list and full CAD models. The modular design of this TIRF microscope allows users to customize it to their scientific and financial needs, or to re-use parts of our design to improve the capabilities of their existing setups without necessarily having to build a full copy of the K2 microscope.
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6
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Youn Y, Lau GW, Lee Y, Maity BK, Gouaux E, Chung HJ, Selvin PR. Quantitative DNA-PAINT imaging of AMPA receptors in live neurons. CELL REPORTS METHODS 2023; 3:100408. [PMID: 36936077 PMCID: PMC10014303 DOI: 10.1016/j.crmeth.2023.100408] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Revised: 09/25/2022] [Accepted: 01/25/2023] [Indexed: 02/18/2023]
Abstract
DNA-point accumulation for imaging at nanoscale topography (DNA-PAINT) can image fixed biological specimens with nanometer resolution and absolute stoichiometry. In living systems, however, the usage of DNA-PAINT has been limited due to high salt concentration in the buffer required for specific binding of the imager to the docker attached to the target. Here, we used multiple binding motifs of the docker, from 2 to 16, to accelerate the binding speed of the imager under physiological buffer conditions without compromising spatial resolution and maintaining the basal level homeostasis during the measurement. We imaged endogenous α-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid receptor (AMPAR) in cultured neurons-critical proteins involved in nerve communication-by DNA-PAINT in 3-dimensions using a monovalent single-chain variable fragment (scFv) to the GluA1 subunit of AMPAR. We found a heterogeneous distribution of synaptic AMPARs: ≈60% are immobile, primarily in nanodomains, defined as AMPARs that are within 0.3 μm of the Homer1 protein in the postsynaptic density; the other ∼40% of AMPARs have restricted mobility and trajectory.
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Affiliation(s)
- Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Gloria W. Lau
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Yongjae Lee
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Barun Kumar Maity
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Eric Gouaux
- Vollum Institute, Oregon Health & Science University, Portland, OR, USA
- Howard Hughes Medical Institute, Portland, OR, USA
| | - Hee Jung Chung
- Department of Molecular and Integrative Physiology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Neuroscience Program, University of Illinois at Urbana-Champaign, Urbana, IL, USA
| | - Paul R. Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, IL, USA
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7
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Dai Z, Xie X, Gao Z, Li Q. DNA‐PAINT Super‐Resolution Imaging for Characterization of Nucleic Acid Nanostructures. Chempluschem 2022; 87:e202200127. [DOI: 10.1002/cplu.202200127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 07/12/2022] [Indexed: 11/06/2022]
Affiliation(s)
- Zheze Dai
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering CHINA
| | - Xiaodong Xie
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Zhaoshuai Gao
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering 200240 Shanghai CHINA
| | - Qian Li
- Shanghai Jiao Tong University School of Chemistry and Chemical Engineering Dongchuan Road 800中国 200240 Shanghai CHINA
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8
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Shang M, Huang ZL, Wang Y. Influence of drift correction precision on super-resolution localization microscopy. APPLIED OPTICS 2022; 61:3516-3522. [PMID: 36256388 DOI: 10.1364/ao.451561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 03/24/2022] [Indexed: 06/16/2023]
Abstract
Super-resolution localization microscopy (SRLM) breaks the diffraction limit successfully and improves the resolution of optical imaging systems by nearly an order of magnitude. However, SRLM typically takes several minutes or longer to collect a sufficient number of image frames that are required for reconstructing a final super-resolution image. During this long image acquisition period, system drift should be tightly controlled to ensure the imaging quality; thus, several drift correction methods have been developed. However, it is still unclear whether the performance of these methods is able to ensure sufficient image quality in SRLM. Without a clear answer to this question, it is hard to choose a suitable drift correction method for a specific SRLM experiment. In this paper, we use both theoretical analysis and simulation to investigate the relationship among drift correction precision, localization precision, and position estimation precision. We propose a concept of relative localization precision for evaluating the effect of drift correction on imaging resolution, which would help to select an appropriate drift correction method for a specific experiment.
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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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Wester MJ, Schodt DJ, Mazloom-Farsibaf H, Fazel M, Pallikkuth S, Lidke KA. Robust, fiducial-free drift correction for super-resolution imaging. Sci Rep 2021; 11:23672. [PMID: 34880301 PMCID: PMC8655078 DOI: 10.1038/s41598-021-02850-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 11/15/2021] [Indexed: 11/09/2022] Open
Abstract
We describe a robust, fiducial-free method of drift correction for use in single molecule localization-based super-resolution methods. The method combines periodic 3D registration of the sample using brightfield images with a fast post-processing algorithm that corrects residual registration errors and drift between registration events. The method is robust to low numbers of collected localizations, requires no specialized hardware, and provides stability and drift correction for an indefinite time period.
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Affiliation(s)
- Michael J Wester
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Mathematics and Statistics, University of New Mexico, Albuquerque, NM, 87131, USA
| | - David J Schodt
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Hanieh Mazloom-Farsibaf
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, 87131, USA.,Lyda Hill Department of Bioinformatics, UT Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Mohamadreza Fazel
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, 87131, USA.,Department of Physics, Center for Biological Physics, Arizona State University, Tempe, AZ, 85287, USA
| | - Sandeep Pallikkuth
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, 87131, USA
| | - Keith A Lidke
- Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM, 87131, USA.
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11
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Shang M, Zhou Z, Kuang W, Wang Y, Xin B, Huang ZL. High-precision 3D drift correction with differential phase contrast images. OPTICS EXPRESS 2021; 29:34641-34655. [PMID: 34809249 DOI: 10.1364/oe.438160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Accepted: 10/01/2021] [Indexed: 06/13/2023]
Abstract
Single molecule localization microscopy (SMLM) usually requires long image acquisition time at the order of minutes and thus suffers from sample drift, which deteriorates image quality. A drift estimation method with high precision is typically used in SMLM, which can be further combined with a drift compensation device to enable active microscope stabilization. Among all the reported methods, the drift estimation method based on bright-field image correlation requires no extra sample preparation or complicated modification to the imaging setup. However, the performance of this method is limited by the contrast of bright-field images, especially for the structures without sufficient features. In this paper, we proposed to use differential phase contrast (DPC) microscopy to enhance the image contrast and presented a 3D drift correction method with higher precision and robustness. This DPC-based drift correction method is suitable even for biological samples without clear morphological features. We demonstrated that this method can achieve a correction precision of < 6 nm in both the lateral direction and axial direction. Using SMLM imaging of microtubules, we verified that this method provides a comparable drift estimation performance as redundant cross-correlation.
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12
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Cnossen J, Cui TJ, Joo C, Smith C. Drift correction in localization microscopy using entropy minimization. OPTICS EXPRESS 2021; 29:27961-27974. [PMID: 34614938 DOI: 10.1364/oe.426620] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 07/05/2021] [Indexed: 06/13/2023]
Abstract
Localization microscopy offers resolutions down to a single nanometer but currently requires additional dedicated hardware or fiducial markers to reduce resolution loss from the drift of the sample. Drift estimation without fiducial markers is typically implemented using redundant cross correlation (RCC). We show that RCC has sub-optimal precision and bias, which leaves room for improvement. Here, we minimize a bound on the entropy of the obtained localizations to efficiently compute a precise drift estimate. Within practical compute-time constraints, simulations show a 5x improvement in drift estimation precision over the widely used RCC algorithm. The algorithm operates directly on fluorophore localizations and is tested on simulated and experimental datasets in 2D and 3D. An open source implementation is provided, implemented in Python and C++, and can utilize a GPU if available.
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13
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Ying Q, Zhang J, Zhang H, Yan M, Ruan Z. Highly stable measurement for nanoparticle extinction cross section by analyzing aperture-edge blurriness. OPTICS EXPRESS 2021; 29:16323-16333. [PMID: 34154198 DOI: 10.1364/oe.426163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/03/2021] [Indexed: 06/13/2023]
Abstract
In order to stabilize the extinction cross section measurement of a single nanoparticle, we propose to analyze the blurriness parameter of aperture edge images in real time, which provides a feedback to lock the sample position. Unlike the conventional spatial modulation spectroscopy (SMS) technique, a probe beam experiences both the spatial modulation by a piezo stage and the temporal modulation by a chopper. We experimentally demonstrate that the measurement uncertainty is one order magnitude less than that in the previous report. The proposed method can be readily implemented in conventional SMS systems and can help to achieve high stability for sensing based on light extinction by a single nanoparticle, which alleviate the impact from laboratory environment and increase the experimental sensitivity.
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14
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Aaron J, Chew TL. A guide to accurate reporting in digital image processing - can anyone reproduce your quantitative analysis? J Cell Sci 2021; 134:134/6/jcs254151. [PMID: 33785609 DOI: 10.1242/jcs.254151] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022] Open
Abstract
Considerable attention has been recently paid to improving replicability and reproducibility in life science research. This has resulted in commendable efforts to standardize a variety of reagents, assays, cell lines and other resources. However, given that microscopy is a dominant tool for biologists, comparatively little discussion has been offered regarding how the proper reporting and documentation of microscopy relevant details should be handled. Image processing is a critical step of almost any microscopy-based experiment; however, improper, or incomplete reporting of its use in the literature is pervasive. The chosen details of an image processing workflow can dramatically determine the outcome of subsequent analyses, and indeed, the overall conclusions of a study. This Review aims to illustrate how proper reporting of image processing methodology improves scientific reproducibility and strengthens the biological conclusions derived from the results.
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Affiliation(s)
- Jesse Aaron
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
| | - Teng-Leong Chew
- Advanced Imaging Center, Howard Hughes Medical Institute Janelia Research Campus, Ashburn, VA 20147, USA
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15
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Analysing errors in single-molecule localisation microscopy. Int J Biochem Cell Biol 2021; 134:105931. [PMID: 33609748 DOI: 10.1016/j.biocel.2021.105931] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/06/2021] [Accepted: 01/13/2021] [Indexed: 11/21/2022]
Abstract
In single molecule localisation microscopy (SMLM) a super-resolution image of the distribution of fluorophores in the sample is built up from the localised positions of many individual molecules. It has become widely used due to its experimental simplicity and the high resolution that can be achieved. However, the factors which limit resolution in a reconstructed image, and the artefacts which can be present, are completely different to those present in standard fluorescent microscopy techniques. Artefacts may be difficult for users to identify, particularly as they can cause images to appear falsely sharp, an effect called artificial sharpening. Here we discuss the different sources of error and bias in SMLM, and the methods available for avoiding or detecting them.
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16
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Lelek M, Gyparaki MT, Beliu G, Schueder F, Griffié J, Manley S, Jungmann R, Sauer M, Lakadamyali M, Zimmer C. Single-molecule localization microscopy. NATURE REVIEWS. METHODS PRIMERS 2021; 1:39. [PMID: 35663461 PMCID: PMC9160414 DOI: 10.1038/s43586-021-00038-x] [Citation(s) in RCA: 279] [Impact Index Per Article: 93.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Single-molecule localization microscopy (SMLM) describes a family of powerful imaging techniques that dramatically improve spatial resolution over standard, diffraction-limited microscopy techniques and can image biological structures at the molecular scale. In SMLM, individual fluorescent molecules are computationally localized from diffraction-limited image sequences and the localizations are used to generate a super-resolution image or a time course of super-resolution images, or to define molecular trajectories. In this Primer, we introduce the basic principles of SMLM techniques before describing the main experimental considerations when performing SMLM, including fluorescent labelling, sample preparation, hardware requirements and image acquisition in fixed and live cells. We then explain how low-resolution image sequences are computationally processed to reconstruct super-resolution images and/or extract quantitative information, and highlight a selection of biological discoveries enabled by SMLM and closely related methods. We discuss some of the main limitations and potential artefacts of SMLM, as well as ways to alleviate them. Finally, we present an outlook on advanced techniques and promising new developments in the fast-evolving field of SMLM. We hope that this Primer will be a useful reference for both newcomers and practitioners of SMLM.
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Affiliation(s)
- Mickaël Lelek
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
| | - Melina T. Gyparaki
- Department of Biology, University of Pennsylvania,
Philadelphia, PA, USA
| | - Gerti Beliu
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
| | - Florian Schueder
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
| | - Juliette Griffié
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
| | - Suliana Manley
- Laboratory of Experimental Biophysics, Institute of
Physics, École Polytechnique Fédérale de Lausanne (EPFL),
Lausanne, Switzerland
- ;
;
;
;
| | - Ralf Jungmann
- Faculty of Physics and Center for Nanoscience, Ludwig
Maximilian University, Munich, Germany
- Max Planck Institute of Biochemistry, Martinsried,
Germany
- ;
;
;
;
| | - Markus Sauer
- Department of Biotechnology and Biophysics Biocenter,
University of Würzburg, Würzburg, Germany
- ;
;
;
;
| | - Melike Lakadamyali
- Department of Physiology, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- Department of Cell and Developmental Biology, Perelman
School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Epigenetics Institute, Perelman School of Medicine,
University of Pennsylvania, Philadelphia, PA, USA
- ;
;
;
;
| | - Christophe Zimmer
- Imaging and Modeling Unit, Department of Computational
Biology, Institut Pasteur, Paris, France
- CNRS, UMR 3691, Paris, France
- ;
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17
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Fan X, Gensch T, Büldt G, Zhang Y, Musha Z, Zhang W, Roncarati R, Huang R. Three dimensional drift control at nano-scale in single molecule localization microscopy. OPTICS EXPRESS 2020; 28:32750-32763. [PMID: 33114953 DOI: 10.1364/oe.404123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 10/04/2020] [Indexed: 06/11/2023]
Abstract
Super-resolution imaging based on single molecule localization of cellular structures on nanometer scale requires to record a series of wide-field or TIRF images resulting in a considerable recording time (typically of minutes). Therefore, sample drift becomes a critical problem and will lower the imaging precision. Herein we utilized morphological features of the specimen (mammalian cells) itself as reference markers replacing the traditionally used markers (e.g., artificial fiduciary markers, fluorescent beads, or metal nanoparticles) for sample drift compensation. We achieved sub-nanometer localization precision <1.0 nm in lateral direction and <6.0 nm in axial direction, which is well comparable with the precision achieved with the established methods using artificial position markers added to the specimen. Our method does not require complex hardware setup, extra labelling or markers, and has the additional advantage of the absence of photobleaching, which caused precision decrease during the course of super-resolution measurement. The achieved improvement of quality and resolution in reconstructed super-resolution images by application of our drift-correction method is demonstrated by single molecule localization-based super-resolution imaging of F-actin in fixed A549 cells.
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18
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Liu S, Huh H, Lee SH, Huang F. Three-Dimensional Single-Molecule Localization Microscopy in Whole-Cell and Tissue Specimens. Annu Rev Biomed Eng 2020; 22:155-184. [PMID: 32243765 PMCID: PMC7430714 DOI: 10.1146/annurev-bioeng-060418-052203] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Super-resolution microscopy techniques are versatile and powerful tools for visualizing organelle structures, interactions, and protein functions in biomedical research. However, whole-cell and tissue specimens challenge the achievable resolution and depth of nanoscopy methods. We focus on three-dimensional single-molecule localization microscopy and review some of the major roadblocks and developing solutions to resolving thick volumes of cells and tissues at the nanoscale in three dimensions. These challenges include background fluorescence, system- and sample-induced aberrations, and information carried by photons, as well as drift correction, volume reconstruction, and photobleaching mitigation. We also highlight examples of innovations that have demonstrated significant breakthroughs in addressing the abovementioned challenges together with their core concepts as well as their trade-offs.
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Affiliation(s)
- Sheng Liu
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
| | - Hyun Huh
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
| | - Sang-Hyuk Lee
- Institute for Quantitative Biomedicine, Rutgers University, Piscataway, New Jersey 08854, USA
- Department of Physics and Astronomy, Rutgers University, Piscataway, New Jersey 08854, USA;
| | - Fang Huang
- Weldon School of Biomedical Engineering, Purdue University, West Lafayette, Indiana 47907, USA;
- Purdue Institute for Integrative Neuroscience, Purdue University, West Lafayette, Indiana 47907, USA
- Purdue Institute of Inflammation, Immunology, and Infectious Disease, Purdue University, West Lafayette, Indiana 47907, USA
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19
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Godeau AL, Delanoë-Ayari H, Riveline D. Generation of fluorescent cell-derived-matrix to study 3D cell migration. Methods Cell Biol 2020; 156:185-203. [PMID: 32222219 DOI: 10.1016/bs.mcb.2019.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/24/2023]
Abstract
Cell migration is involved in key phenomena in biology, ranging from development to cancer. Fibroblasts move between organs in 3D polymeric networks. So far, motile cells were mainly tracked in vitro on Petri dishes or on coverslips, i.e., 2D flat surfaces, which made the extrapolation to 3D physiological environments difficult. We therefore prepared 3D Cell Derived Matrices (CDM) with specific characteristics with the goal of extracting the main readouts required to measure and characterize cell motion: cell specific matrix deformation through the tracking of fluorescent fibronectin within CDM, focal contacts as the cell anchor and acto-myosin cytoskeleton which applies cellular forces. We report our method for generating this assay of physiological-like gel with relevant readouts together with its potential impact in explaining cell motility in vivo.
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Affiliation(s)
- Amélie Luise Godeau
- Laboratory of Cell Physics ISIS/IGBMC, CNRS and University of Strasbourg, Strasbourg, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France; Université de Strasbourg, Illkirch, France
| | - Hélène Delanoë-Ayari
- University of Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, Villeurbanne, France
| | - Daniel Riveline
- Laboratory of Cell Physics ISIS/IGBMC, CNRS and University of Strasbourg, Strasbourg, France; Institut de Génétique et de Biologie Moléculaire et Cellulaire, Illkirch, France; Centre National de la Recherche Scientifique, UMR7104, Illkirch, France; Institut National de la Santé et de la Recherche Médicale, U964, Illkirch, France; Université de Strasbourg, Illkirch, France.
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20
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Chen SY, Heintzmann R, Cremer C. Sample drift estimation method based on speckle patterns formed by backscattered laser light. BIOMEDICAL OPTICS EXPRESS 2019; 10:6462-6475. [PMID: 31853411 PMCID: PMC6913400 DOI: 10.1364/boe.10.006462] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Revised: 10/28/2019] [Accepted: 11/04/2019] [Indexed: 05/06/2023]
Abstract
Single molecule localization microscopy (SMLM) has been established to acquire images with unprecedented resolution down to several nanometers. A typical time scale for image acquisition is several minutes to hours. Yet it is difficult to avoid completely sample drift for long time measurements. To estimate drift, we present a method based on the evaluation of speckle patterns formed by backscattered laser light from the cells using a single molecule localization microscope setup. A z-stack of unique speckle patterns is recorded prior to the measurements as a three-dimensional position reference. During the experiment, images of scattered laser light were acquired, and correlated individually with each of the images of the speckle reference stack to estimate x, y and z drift. Our method shows highly comparable results with a fiducial marker approach, achieving a precision of several nanometers. This method allows for high precision three dimensional drift correction of microscope systems without any additional sample preparation.
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Affiliation(s)
| | - Rainer Heintzmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, Germany
- Leibniz Institute of Photonic Technology, Jena, Germany
| | - Christoph Cremer
- Institute of Molecular Biology, Mainz, Germany
- Department of Physics, University of Mainz (JGU), Mainz, Germany
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21
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Gao J, Wo X, Wang Y, Li M, Zhou C, Wang W. Postrecording Pixel-Reconstruction Approach for Correcting the Lateral Drifts in Surface Plasmon Resonance Microscope. Anal Chem 2019; 91:13620-13626. [PMID: 31612709 DOI: 10.1021/acs.analchem.9b02804] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Surface plasmon resonance microscope (SPRM) sample stage inevitably suffers from lateral drifts as a result of many environmental factors including thermal fluctuation, mechanical vibration, and relaxation. It places great obstacles to time-lapsed imaging and measurements that need high spatial resolution or long recording time. Existing solutions often require experimental efforts such as the addition of optical markers together with piezoelectric stage-based active feedback configurations. Herein, we propose an all-digital, postrecording image-processing method to remove the lateral drift in a series of time-lapsed SPRM images. The method first calculates the value of lateral drift at subpixel accuracy by combining image cross-correlation analysis and superlocalization strategy. It subsequently reconstructed the drift-free image sequences in a pixel-by-pixel and frame-by-frame manner, according to the linear decomposition and reconstruction principle. This method purely relies on image processing, and it does not require any experimental efforts or hardware. In addition to SPRM, we further demonstrated the applicability of the present method in other types of optical imaging techniques including bright-field transmission microscope and dark-field scattering microscope.
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Affiliation(s)
- Jia Gao
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Xiang Wo
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Yongjie Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Minghe Li
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
| | - Chunyuan Zhou
- Nikon Instruments (Shanghai) Co., Ltd. , Shanghai 200120 , P. R. China
| | - Wei Wang
- State Key Laboratory of Analytical Chemistry for Life Science, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing 210023 , P. R. China
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22
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Kozgunova E, Goshima G. A versatile microfluidic device for highly inclined thin illumination microscopy in the moss Physcomitrella patens. Sci Rep 2019; 9:15182. [PMID: 31645620 PMCID: PMC6811556 DOI: 10.1038/s41598-019-51624-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/03/2019] [Indexed: 12/26/2022] Open
Abstract
High-resolution microscopy is a valuable tool for studying cellular processes, such as signalling, membrane trafficking, or cytoskeleton remodelling. Several techniques of inclined illumination microscopy allow imaging at a near single molecular level; however, the application of these methods to plant cells is limited, owing to thick cell walls as well as the necessity to excise a part of the tissue for sample preparation. In this study, we utilised a simple, easy-to-use microfluidic device for highly inclined and laminated optical sheet (HILO) microscopy using a model plant Physcomitrella patens. We demonstrated that the shallow microfluidic device can be used for long-term culture of living cells and enables high-resolution HILO imaging of microtubules without perturbing their dynamics. In addition, our microdevice allows the supply and robust washout of compounds during HILO microscopy imaging, for example, to perform a microtubule regrowth assay. Furthermore, we tested long-term (48 h) HILO imaging using a microdevice and visualised the developmental changes in the microtubule dynamics during tissue regeneration. These novel applications of the microfluidic device provide a valuable resource for studying molecular dynamics in living plant cells.
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Affiliation(s)
- Elena Kozgunova
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan.
| | - Gohta Goshima
- Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi, 464-8602, Japan
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23
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Li L, Xin B, Kuang W, Zhou Z, Huang ZL. Divide and conquer: real-time maximum likelihood fitting of multiple emitters for super-resolution localization microscopy. OPTICS EXPRESS 2019; 27:21029-21049. [PMID: 31510188 DOI: 10.1364/oe.27.021029] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2019] [Accepted: 06/29/2019] [Indexed: 05/25/2023]
Abstract
Multi-emitter localization has great potential for maximizing the imaging speed of super-resolution localization microscopy. However, the slow image analysis speed of reported multi-emitter localization algorithms limits their usage in mostly off-line image processing with small image size. Here we adopt the well-known divide and conquer strategy in computer science and present a fitting-based method called QC-STORM for fast multi-emitter localization. Using simulated and experimental data, we verify that QC-STORM is capable of providing real-time full image processing on raw images with 100 µm × 100 µm field of view and 10 ms exposure time, with comparable spatial resolution as the popular fitting-based ThunderSTORM and the up-to-date non-iterative WindSTORM. This study pushes the development and practical use of super-resolution localization microscopy in high-throughput or high-content imaging of cell-to-cell differences or discovering rare events in a large cell population.
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24
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Wu X, Kim M, Qu H, Wang Y. Single-defect spectroscopy in the shortwave infrared. Nat Commun 2019; 10:2672. [PMID: 31209262 PMCID: PMC6572808 DOI: 10.1038/s41467-019-10788-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2019] [Accepted: 05/28/2019] [Indexed: 11/09/2022] Open
Abstract
Chemical defects that fluoresce in the shortwave infrared open exciting opportunities in deep-penetration bioimaging, chemically specific sensing, and quantum technologies. However, the atomic size of defects and the high noise of infrared detectors have posed significant challenges to the studies of these unique emitters. Here we demonstrate high throughput single-defect spectroscopy in the shortwave infrared capable of quantitatively and spectrally resolving chemical defects at the single defect level. By cooling an InGaAs detector array down to -190 °C and implementing a nondestructive readout scheme, we are able to capture low light fluorescent events in the shortwave infrared with a signal-to-noise ratio improved by more than three orders-of-magnitude. As a demonstration, we show it is possible to resolve individual chemical defects in carbon nanotube semiconductors, simultaneously collecting a full spectrum for each defect within the entire field of view at the single defect limit.
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Affiliation(s)
- Xiaojian Wu
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regent Drive, College Park, MD, 20742, USA
| | - Mijin Kim
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regent Drive, College Park, MD, 20742, USA
| | - Haoran Qu
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regent Drive, College Park, MD, 20742, USA
| | - YuHuang Wang
- Department of Chemistry and Biochemistry, University of Maryland, 8051 Regent Drive, College Park, MD, 20742, USA.
- Maryland NanoCenter, University of Maryland, College Park, MD, 20742, USA.
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25
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Schmidt PD, Reichert BH, Lajoie JG, Sivasankar S. Method for high frequency tracking and sub-nm sample stabilization in single molecule fluorescence microscopy. Sci Rep 2018; 8:13912. [PMID: 30224660 PMCID: PMC6141618 DOI: 10.1038/s41598-018-32012-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2018] [Accepted: 08/31/2018] [Indexed: 12/15/2022] Open
Abstract
While fluorescence microscopes and atomic force microscopes are widely used to visualize, track, and manipulate single biomolecules, the resolution of these methods is limited by sample drift. To minimize drift, active feedback methods have recently been used to stabilize single molecule microscopes on the sub-nanometer scale. However, these methods require high intensity lasers which limits their application in single molecule fluorescence measurements. Furthermore, these feedback methods do not track user-defined regions of the sample, but rather monitor the relative displacement of an unknown point on a fiducial marker, which limits their use in biological force measurements. To overcome these limitations, we have developed a novel method to image, track and stabilize a sample using low laser intensities. We demonstrate the capabilities of our approach by tracking a user-chosen point on a fiducial marker at 8.6 kHz and stabilizing it with sub-nanometer resolution. We further showcase the application of our method in single molecule fluorescence microscopy by imaging and stabilizing individual fluorescently-tagged streptavidin proteins under biologically relevant conditions. We anticipate that our method can be easily used to improve the resolution of a wide range of single molecule fluorescence microscopy and integrated force-fluorescence applications.
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Affiliation(s)
- Patrick D Schmidt
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA
| | - Benjamin H Reichert
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA
| | - John G Lajoie
- Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA
| | - Sanjeevi Sivasankar
- Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, 50011, USA. .,Department of Physics and Astronomy, Iowa State University, Ames, IA, 50011, USA. .,Department of Biomedical Engineering, University of California, Davis, CA, 95616, USA.
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26
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Copeland CR, Geist J, McGray CD, Aksyuk VA, Liddle JA, Ilic BR, Stavis SM. Subnanometer localization accuracy in widefield optical microscopy. LIGHT, SCIENCE & APPLICATIONS 2018; 7:31. [PMID: 30839614 PMCID: PMC6107003 DOI: 10.1038/s41377-018-0031-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Revised: 04/24/2018] [Accepted: 05/01/2018] [Indexed: 05/16/2023]
Abstract
The common assumption that precision is the limit of accuracy in localization microscopy and the typical absence of comprehensive calibration of optical microscopes lead to a widespread issue-overconfidence in measurement results with nanoscale statistical uncertainties that can be invalid due to microscale systematic errors. In this article, we report a comprehensive solution to this underappreciated problem. We develop arrays of subresolution apertures into the first reference materials that enable localization errors approaching the atomic scale across a submillimeter field. We present novel methods for calibrating our microscope system using aperture arrays and develop aberration corrections that reach the precision limit of our reference materials. We correct and register localization data from multiple colors and test different sources of light emission with equal accuracy, indicating the general applicability of our reference materials and calibration methods. In a first application of our new measurement capability, we introduce the concept of critical-dimension localization microscopy, facilitating tests of nanofabrication processes and quality control of aperture arrays. In a second application, we apply these stable reference materials to answer open questions about the apparent instability of fluorescent nanoparticles that commonly serve as fiducial markers. Our study establishes a foundation for subnanometer localization accuracy in widefield optical microscopy.
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Affiliation(s)
- Craig R. Copeland
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
- Maryland NanoCenter, University of Maryland, College Park, MD 20742 USA
| | - Jon Geist
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Craig D. McGray
- Engineering Physics Division, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Vladimir A. Aksyuk
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - J. Alexander Liddle
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - B. Robert Ilic
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
| | - Samuel M. Stavis
- Center for Nanoscale Science and Technology, National Institute of Standards and Technology, Gaithersburg, MD 20899 USA
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27
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Suresh K, Sharma DK, Chulliyil R, Sarode KD, Kumar VR, Chowdhury A, Kumaraswamy G. Single-Particle Tracking To Probe the Local Environment in Ice-Templated Crosslinked Colloidal Assemblies. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2018; 34:4603-4613. [PMID: 29554800 DOI: 10.1021/acs.langmuir.7b04120] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
We use single-particle tracking to investigate colloidal dynamics in hybrid assemblies comprising colloids enmeshed in a crosslinked polymer network. These assemblies are prepared using ice templating and are macroporous monolithic structures. We investigate microstructure-property relations in assemblies that appear chemically identical but show qualitatively different mechanical response. Specifically, we contrast elastic assemblies that can recover from large compressive deformations with plastic assemblies that fail on being compressed. Particle tracking provides insights into the microstructural differences that underlie the different mechanical response of elastic and plastic assemblies. Since colloidal motions in these assemblies are sluggish, particle tracking is especially sensitive to imaging artifacts such as stage drift. We demonstrate that the use of wavelet transforms applied to trajectories of probe particles from fluorescence microscopy eliminates stage drift, allowing a spatial resolution of about 2 nm. In elastic and plastic scaffolds, probe particles are surrounded by other particles-thus, their motion is caged. We present mean square displacement and van Hove distributions for particle motions and demonstrate that plastic assemblies are characterized by significantly larger spatial heterogeneity when compared with the elastic sponges. In elastic assemblies, particle diffusivities are peaked around a mean value, whereas in plastic assemblies, there is a wide distribution of diffusivities with no clear peak. Both elastic and plastic assemblies show a frequency independent solid modulus from particle tracking microrheology. Here too, there is a much wider distribution of modulus values for plastic scaffolds as compared to elastic, in contrast to bulk rheological measurements where both assemblies exhibit a similar response. We interpret our results in terms of the spatial distribution of crosslinks in the polymer mesh in the colloidal assemblies.
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Affiliation(s)
| | - Dharmendar Kumar Sharma
- Department of Chemistry , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , Maharashtra , India
| | - Ramya Chulliyil
- Department of Chemistry , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , Maharashtra , India
| | | | | | - Arindam Chowdhury
- Department of Chemistry , Indian Institute of Technology Bombay , Powai , Mumbai 400076 , Maharashtra , India
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28
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Youn Y, Ishitsuka Y, Jin C, Selvin PR. Thermal nanoimprint lithography for drift correction in super-resolution fluorescence microscopy. OPTICS EXPRESS 2018; 26:1670-1680. [PMID: 29402038 PMCID: PMC5901072 DOI: 10.1364/oe.26.001670] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Localization-based super-resolution microscopy enables imaging of biological structures with sub-diffraction-limited accuracy, but generally requires extended acquisition time. Consequently, stage drift often limits the spatial precision. Previously, we reported a simple method to correct for this by creating an array of 1 μm3 fiducial markers, every ~8 μm, on the coverslip, using UV-nanoimprint lithography (UV-NIL). While this allowed reliable and accurate 3D drift correction, it suffered high autofluorescence background with shorter wavelength illumination, unstable adsorption to the substrate glass surface, and suboptimal biocompatibility. Here, we present an improved fiducial micro-pattern prepared by thermal nanoimprint lithography (T-NIL). The new pattern is made of a thermal plastic material with low fluorescence backgrounds across the wide excitation range, particularly in the blue-region; robust structural stability under cell culturing condition; and a high bio-compatibility in terms of cell viability and adhesion. We demonstrate drift precision to 1.5 nm for lateral (x, y) and 6.1 nm axial (z) axes every 0.2 seconds for a total of 1 min long image acquisition. As a proof of principle, we acquired 4-color wide-field fluorescence images of live mammalian cells; we also acquired super-resolution images of fixed hippocampal neurons, and super-resolution images of live glutamate receptors and postsynaptic density proteins.
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Affiliation(s)
- Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- These authors contributed equally to this work
| | - Yuji Ishitsuka
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- These authors contributed equally to this work
| | - Chaoyi Jin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
| | - Paul R. Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Center for the Physics of Living Cells, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, USA
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29
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Tas RP, Bos TGAA, Kapitein LC. Purification and Application of a Small Actin Probe for Single-Molecule Localization Microscopy. Methods Mol Biol 2018; 1665:155-171. [PMID: 28940069 DOI: 10.1007/978-1-4939-7271-5_9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The cytoskeleton is involved in many cellular processes. Over the last decade, super-resolution microscopy has become widely available to image cytoskeletal structures, such as microtubules and actin, with great detail. For example, Single-Molecule Localization Microscopy (SMLM) achieves resolutions of 5-50 nm through repetitive sparse labeling of samples, followed by Point-Spread-Function analysis of individual fluorophores. Whereas initially this approach depended on the controlled photoswitching of fluorophores targeted to the structure of interest, alternative techniques now depend on the transient binding of fluorescently labeled probes, such as the small polypeptide lifeAct that can transiently interact with polymerized actin. These techniques allow for simple multicolor imaging and are no longer limited by a fluorophore's blinking properties. Here we describe a detailed step-by-step protocol to purify, label, and utilize the lifeAct fragment for SMLM. This purification and labeling strategy can potentially be extended to a variety of protein fragments compatible with SMLM.
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Affiliation(s)
- Roderick P Tas
- Cell Biology, Faculty of Science, Utrecht University, Utrecht, The Netherlands
| | - Trusanne G A A Bos
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, Room N511, Utrecht, 3584, The Netherlands
| | - Lukas C Kapitein
- Cell Biology, Faculty of Science, Utrecht University, Padualaan 8, Room N511, Utrecht, 3584, The Netherlands.
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30
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Ma H, Xu J, Jin J, Huang Y, Liu Y. A Simple Marker-Assisted 3D Nanometer Drift Correction Method for Superresolution Microscopy. Biophys J 2017; 112:2196-2208. [PMID: 28538156 DOI: 10.1016/j.bpj.2017.04.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Revised: 04/18/2017] [Accepted: 04/20/2017] [Indexed: 11/15/2022] Open
Abstract
High-precision fluorescence microscopy such as superresolution imaging or single-particle tracking often requires an online drift correction method to maintain the stability of the three-dimensional (3D) position of the sample at a nanometer precision throughout the entire data acquisition process. Current online drift correction methods require modification of the existing two-dimensional (2D) fluorescence microscope with additional optics and detectors, which can be cumbersome and limit its use in many biological laboratories. Here we report a simple marker-assisted online drift correction method in which all 3D positions can be derived from fiducial markers on the coverslip of the sample on a standard 2D fluorescence microscope without additional optical components. We validate this method by tracking the long-term 3D stability of single-molecule localization microscopy at a precision of <2 and 5 nm in the lateral and axial dimension, respectively. We then provide three examples to evaluate the performance of the marker-assisted drift correction method. Finally, we give an example of a biological application of superresolution imaging of spatiotemporal alteration for a DNA replication structure with both low-abundance newly synthesized DNAs at the early onset of DNA synthesis and gradually condensed DNA structures during DNA replication. Using an isogenic breast cancer progression cell line model that recapitulates normal-like, precancerous, and tumorigenic stages, we characterize a distinction in the DNA replication process in normal, precancerous, and tumorigenic cells.
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Affiliation(s)
- Hongqiang Ma
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jianquan Xu
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Jingyi Jin
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania; School of Medicine, Tsinghua University, Haidian District, Beijing, China
| | - Yi Huang
- University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
| | - Yang Liu
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania; University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania.
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31
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Lee SH, Jin C, Cai E, Ge P, Ishitsuka Y, Teng KW, de Thomaz AA, Nall D, Baday M, Jeyifous O, Demonte D, Dundas CM, Park S, Delgado JY, Green WN, Selvin PR. Super-resolution imaging of synaptic and Extra-synaptic AMPA receptors with different-sized fluorescent probes. eLife 2017; 6:27744. [PMID: 28749340 PMCID: PMC5779237 DOI: 10.7554/elife.27744] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2017] [Accepted: 07/26/2017] [Indexed: 12/13/2022] Open
Abstract
Previous studies tracking AMPA receptor (AMPAR) diffusion at synapses observed a large mobile extrasynaptic AMPAR pool. Using super-resolution microscopy, we examined how fluorophore size and photostability affected AMPAR trafficking outside of, and within, post-synaptic densities (PSDs) from rats. Organic fluorescent dyes (≈4 nm), quantum dots, either small (≈10 nm diameter; sQDs) or big (>20 nm; bQDs), were coupled to AMPARs via different-sized linkers. We find that >90% of AMPARs labeled with fluorescent dyes or sQDs were diffusing in confined nanodomains in PSDs, which were stable for 15 min or longer. Less than 10% of sQD-AMPARs were extrasynaptic and highly mobile. In contrast, 5-10% of bQD-AMPARs were in PSDs and 90-95% were extrasynaptic as previously observed. Contrary to the hypothesis that AMPAR entry is limited by the occupancy of open PSD 'slots', our findings suggest that AMPARs rapidly enter stable 'nanodomains' in PSDs with lifetime >15 min, and do not accumulate in extrasynaptic membranes.
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Affiliation(s)
- Sang Hak Lee
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Chaoyi Jin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - En Cai
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Pinghua Ge
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Yuji Ishitsuka
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Kai Wen Teng
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Andre A de Thomaz
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Duncan Nall
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Murat Baday
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
| | - Okunola Jeyifous
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Daniel Demonte
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Christopher M Dundas
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Sheldon Park
- Department of Chemical and Biological Engineering, University at Buffalo, Buffalo, United States
| | - Jary Y Delgado
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - William N Green
- Department of Neurobiology, University of Chicago and the Marine Biological Laboratory, Chicago, United States
| | - Paul R Selvin
- Department of Physics, Center for Biophysics, and Quantitative Biology, and Center for the Physics of Living Cells, University of Illinois, Urbana-Champaign, Champaign, United States
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32
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Xu J, Ma H, Liu Y. Stochastic Optical Reconstruction Microscopy (STORM). CURRENT PROTOCOLS IN CYTOMETRY 2017; 81:12.46.1-12.46.27. [PMID: 28678417 PMCID: PMC5663316 DOI: 10.1002/cpcy.23] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Super-resolution (SR) fluorescence microscopy, a class of optical microscopy techniques at a spatial resolution below the diffraction limit, has revolutionized the way we study biology, as recognized by the Nobel Prize in Chemistry in 2014. Stochastic optical reconstruction microscopy (STORM), a widely used SR technique, is based on the principle of single molecule localization. STORM routinely achieves a spatial resolution of 20 to 30 nm, a ten-fold improvement compared to conventional optical microscopy. Among all SR techniques, STORM offers a high spatial resolution with simple optical instrumentation and standard organic fluorescent dyes, but it is also prone to image artifacts and degraded image resolution due to improper sample preparation or imaging conditions. It requires careful optimization of all three aspects-sample preparation, image acquisition, and image reconstruction-to ensure a high-quality STORM image, which will be extensively discussed in this unit. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Jianquan Xu
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Hongqiang Ma
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Yang Liu
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, University of Pittsburgh Cancer Institute, Pittsburgh, Pennsylvania
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33
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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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34
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Kwon J, Hwang D, Lee JW, Zoh I, Kang J, Kim SK. Generation of highly luminescent micro rings by optical irradiation. Chem Commun (Camb) 2017. [DOI: 10.1039/c7cc01409k] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We report light-induced generation of a circular, highly luminescent and robust microstructure strongly adhered to a glass surface.
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Affiliation(s)
- Jiwoong Kwon
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Doyk Hwang
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jong Woo Lee
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Inhae Zoh
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Jooyoun Kang
- Department of Chemistry
- Seoul National University
- Seoul 08826
- Republic of Korea
| | - Seong Keun Kim
- Department of Biophysics and Chemical Biology
- Seoul National University
- Seoul 08826
- Republic of Korea
- Department of Chemistry
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35
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Teng KW, Ishitsuka Y, Ren P, Youn Y, Deng X, Ge P, Lee SH, Belmont AS, Selvin PR. Labeling proteins inside living cells using external fluorophores for microscopy. eLife 2016; 5. [PMID: 27935478 PMCID: PMC5148600 DOI: 10.7554/elife.20378] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2016] [Accepted: 11/21/2016] [Indexed: 12/31/2022] Open
Abstract
Site-specific fluorescent labeling of proteins inside live mammalian cells has been achieved by employing Streptolysin O, a bacterial toxin which forms temporary pores in the membrane and allows delivery of virtually any fluorescent probes, ranging from labeled IgG’s to small ligands, with high efficiency (>85% of cells). The whole process, including recovery, takes 30 min, and the cell is ready to be imaged immediately. A variety of cell viability tests were performed after treatment with SLO to ensure that the cells have intact membranes, are able to divide, respond normally to signaling molecules, and maintains healthy organelle morphology. When combined with Oxyrase, a cell-friendly photostabilizer, a ~20x improvement in fluorescence photostability is achieved. By adding in glutathione, fluorophores are made to blink, enabling super-resolution fluorescence with 20–30 nm resolution over a long time (~30 min) under continuous illumination. Example applications in conventional and super-resolution imaging of native and transfected cells include p65 signal transduction activation, single molecule tracking of kinesin, and specific labeling of a series of nuclear and cytoplasmic protein complexes. DOI:http://dx.doi.org/10.7554/eLife.20378.001
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Affiliation(s)
- Kai Wen Teng
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Yuji Ishitsuka
- Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pin Ren
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Yeoan Youn
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Xiang Deng
- Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Pinghua Ge
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Sang Hak Lee
- Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Andrew S Belmont
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Paul R Selvin
- Center for Biophysics and Quantitative Biology, University of Illinois at Urbana-Champaign, Urbana, United States.,Center for Physics of Living Cell, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States.,Department of Cell and Developmental Biology, University of Illinois at Urbana-Champaign, Urbana, United States
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36
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Tafteh R, Abraham L, Seo D, Lu HY, Gold MR, Chou KC. Real-time 3D stabilization of a super-resolution microscope using an electrically tunable lens. OPTICS EXPRESS 2016; 24:22959-22970. [PMID: 27828362 DOI: 10.1364/oe.24.022959] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Single-molecule localization microscopy (SMLM) has become an essential tool for examining a wide variety of biological structures and processes. However, the relatively long acquisition time makes SMLM prone to drift-induced artifacts. Here we report an optical design with an electrically tunable lens (ETL) that actively stabilizes a SMLM in three dimensions and nearly eliminates the mechanical drift (RMS ~0.7 nm lateral and ~2.7 nm axial). The bifocal design that employed fiducial markers on the coverslip was able to stabilize the sample regardless of the imaging depth. The effectiveness of the ETL was demonstrated by imaging endosomal transferrin receptors near the apical surface of B-lymphocytes at a depth of 8 µm. The drift-free images obtained with the stabilization system showed that the transferrin receptors were present in distinct but heterogeneous clusters with a bimodal size distribution. In contrast, the images obtained without the stabilization system showed a broader unimodal size distribution. Thus, this stabilization system enables a more accurate analysis of cluster topology. Additionally, this ETL-based stabilization system is cost-effective and can be integrated into existing microscopy systems.
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37
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McGray C, Copeland CR, Stavis SM, Geist J. Centroid precision and orientation precision of planar localization microscopy. J Microsc 2016; 263:238-49. [PMID: 26970565 PMCID: PMC11025010 DOI: 10.1111/jmi.12384] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Accepted: 01/09/2016] [Indexed: 11/27/2022]
Abstract
The concept of localization precision, which is essential to localization microscopy, is formally extended from optical point sources to microscopic rigid bodies. Measurement functions are presented to calculate the planar pose and motion of microscopic rigid bodies from localization microscopy data. Physical lower bounds on the associated uncertainties - termed centroid precision and orientation precision - are derived analytically in terms of the characteristics of the optical measurement system and validated numerically by Monte Carlo simulations. The practical utility of these expressions is demonstrated experimentally by an analysis of the motion of a microelectromechanical goniometer indicated by a sparse constellation of fluorescent nanoparticles. Centroid precision and orientation precision, as developed here, are useful concepts due to the generality of the expressions and the widespread interest in localization microscopy for super-resolution imaging and particle tracking.
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Affiliation(s)
- C McGray
- Engineering Physics Division, NIST, Gaithersburg, Maryland, U.S.A
- Modern Microsystems, Silver Spring, Maryland, U.S.A
| | - C R Copeland
- Center for Nanoscale Science and Technology, NIST, Gaithersburg, Maryland, U.S.A
- Maryland Nanocenter, University of Maryland, College Park, Maryland, U.S.A
| | - S M Stavis
- Center for Nanoscale Science and Technology, NIST, Gaithersburg, Maryland, U.S.A
| | - J Geist
- Engineering Physics Division, NIST, Gaithersburg, Maryland, U.S.A
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38
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Elmokadem A, Yu J. Optimal Drift Correction for Superresolution Localization Microscopy with Bayesian Inference. Biophys J 2016; 109:1772-80. [PMID: 26536254 DOI: 10.1016/j.bpj.2015.09.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/02/2015] [Accepted: 09/16/2015] [Indexed: 01/18/2023] Open
Abstract
Single-molecule-localization-based superresolution microscopy requires accurate sample drift correction to achieve good results. Common approaches for drift compensation include using fiducial markers and direct drift estimation by image correlation. The former increases the experimental complexity and the latter estimates drift at a reduced temporal resolution. Here, we present, to our knowledge, a new approach for drift correction based on the Bayesian statistical framework. The technique has the advantage of being able to calculate the drifts for every image frame of the data set directly from the single-molecule coordinates. We present the theoretical foundation of the algorithm and an implementation that achieves significantly higher accuracy than image-correlation-based estimations.
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Affiliation(s)
- Ahmed Elmokadem
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut
| | - Ji Yu
- Center for Cell Analysis and Modeling, University of Connecticut Health Center, Farmington, Connecticut.
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39
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Grover G, Mohrman W, Piestun R. Real-time adaptive drift correction for super-resolution localization microscopy. OPTICS EXPRESS 2015; 23:23887-23898. [PMID: 26368482 DOI: 10.1364/oe.23.023887] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Super-resolution localization microscopy involves acquiring thousands of image frames of sparse collections of single molecules in the sample. The long acquisition time makes the imaging setup prone to drift, affecting accuracy and precision. Localization accuracy is generally improved by a posteriori drift correction. However, localization precision lost due to sample drifting out of focus cannot be recovered as the signal is originally detected at a lower peak signal. Here, we demonstrate a method of stabilizing a super-resolution localization microscope in three dimensions for extended periods of time with nanometer precision. Hence, no localization correction after the experiment is required to obtain super-resolved reconstructions. The method incorporates a closed-loop with a feedback signal generated from camera images and actuation on a 3D nanopositioning stage holding the sample.
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40
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Bon P, Bourg N, Lécart S, Monneret S, Fort E, Wenger J, Lévêque-Fort S. Three-dimensional nanometre localization of nanoparticles to enhance super-resolution microscopy. Nat Commun 2015. [PMID: 26212705 PMCID: PMC4525210 DOI: 10.1038/ncomms8764] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Meeting the nanometre resolution promised by super-resolution microscopy techniques (pointillist: PALM, STORM, scanning: STED) requires stabilizing the sample drifts in real time during the whole acquisition process. Metal nanoparticles are excellent probes to track the lateral drifts as they provide crisp and photostable information. However, achieving nanometre axial super-localization is still a major challenge, as diffraction imposes large depths-of-fields. Here we demonstrate fast full three-dimensional nanometre super-localization of gold nanoparticles through simultaneous intensity and phase imaging with a wavefront-sensing camera based on quadriwave lateral shearing interferometry. We show how to combine the intensity and phase information to provide the key to the third axial dimension. Presently, we demonstrate even in the occurrence of large three-dimensional fluctuations of several microns, unprecedented sub-nanometre localization accuracies down to 0.7 nm in lateral and 2.7 nm in axial directions at 50 frames per second. We demonstrate that nanoscale stabilization greatly enhances the image quality and resolution in direct stochastic optical reconstruction microscopy imaging.
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Affiliation(s)
- Pierre Bon
- Laboratoire Photonique Numérique et Nanosciences (LP2N), CNRS UMR5298, Institut d'Optique Graduate School, Bordeaux University, Rue Francois Mitterand, 33400 Talence, France.,Institut Langevin, ESPCI ParisTech, CNRS UMR 7587, PSL Research University, 1 rue Jussieu, Paris 75238, France.,Institut des Sciences Moléculaires d'Orsay (ISMO), University Paris-Sud, CNRS UMR 8214, Orsay 91405, France
| | - Nicolas Bourg
- Institut des Sciences Moléculaires d'Orsay (ISMO), University Paris-Sud, CNRS UMR 8214, Orsay 91405, France
| | - Sandrine Lécart
- Centre de photonique Biomédicale (CPBM/CLUPS/LUMAT) FR2764, University Paris-Sud, Orsay 91405, France
| | - Serge Monneret
- CNRS, Aix Marseille Université, Ecole Centrale Marseille, Institut Fresnel UMR7249, 13013 Marseille, France
| | - Emmanuel Fort
- Institut Langevin, ESPCI ParisTech, CNRS UMR 7587, PSL Research University, 1 rue Jussieu, Paris 75238, France
| | - Jérôme Wenger
- CNRS, Aix Marseille Université, Ecole Centrale Marseille, Institut Fresnel UMR7249, 13013 Marseille, France
| | - Sandrine Lévêque-Fort
- Institut des Sciences Moléculaires d'Orsay (ISMO), University Paris-Sud, CNRS UMR 8214, Orsay 91405, France
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41
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Walder R, Paik DH, Bull MS, Sauer C, Perkins TT. Ultrastable measurement platform: sub-nm drift over hours in 3D at room temperature. OPTICS EXPRESS 2015; 23:16554-16564. [PMID: 26191667 DOI: 10.1364/oe.23.016554] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Advanced optical traps can probe single molecules with Ångstrom-scale precision, but drift limits the utility of these instruments. To achieve Å-scale stability, a differential measurement scheme between a pair of laser foci was introduced that substantially exceeds the inherent mechanical stability of various types of microscopes at room temperature. By using lock-in detection to measure both lasers with a single quadrant photodiode, we enhanced the differential stability of this optical reference frame and thereby stabilized an optical-trapping microscope to 0.2 Å laterally over 100 s based on the Allan deviation. In three dimensions, we achieved stabilities of 1 Å over 1,000 s and 1 nm over 15 h. This stability was complemented by high measurement bandwidth (100 kHz). Overall, our compact back-scattered detection enables an ultrastable measurement platform compatible with optical traps, atomic force microscopy, and optical microscopy, including super-resolution techniques.
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42
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Diffraction-unlimited imaging: from pretty pictures to hard numbers. Cell Tissue Res 2015; 360:151-78. [DOI: 10.1007/s00441-014-2109-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Accepted: 12/22/2014] [Indexed: 10/23/2022]
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43
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Nanoscale imaging of caveolin-1 membrane domains in vivo. PLoS One 2015; 10:e0117225. [PMID: 25646724 PMCID: PMC4315472 DOI: 10.1371/journal.pone.0117225] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2014] [Accepted: 12/20/2014] [Indexed: 11/26/2022] Open
Abstract
Light microscopy enables noninvasive imaging of fluorescent species in biological specimens, but resolution is generally limited by diffraction to ~200–250 nm. Many biological processes occur on smaller length scales, highlighting the importance of techniques that can image below the diffraction limit and provide valuable single-molecule information. In recent years, imaging techniques have been developed which can achieve resolution below the diffraction limit. Utilizing one such technique, fluorescence photoactivation localization microscopy (FPALM), we demonstrated its ability to construct super-resolution images from single molecules in a living zebrafish embryo, expanding the realm of previous super-resolution imaging to a living vertebrate organism. We imaged caveolin-1 in vivo, in living zebrafish embryos. Our results demonstrate the successful image acquisition of super-resolution images in a living vertebrate organism, opening several opportunities to answer more dynamic biological questions in vivo at the previously inaccessible nanoscale.
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44
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Häußler AJ, Heller P, McGuinness LP, Naydenov B, Jelezko F. Optical depth localization of nitrogen-vacancy centers in diamond with nanometer accuracy. OPTICS EXPRESS 2014; 22:29986-29995. [PMID: 25606928 DOI: 10.1364/oe.22.029986] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Precise positioning of nitrogen-vacancy (NV) centers is crucial for their application in sensing and quantum information. Here we present a new purely optical technique enabling determination of the NV position with nanometer resolution. We use a confocal microscope to determine the position of individual emitters along the optical axis. Using two separate detection channels, it is possible to simultaneously measure reflected light from the diamond surface and fluorescent light from the NV center and statistically evaluate both signals. An accuracy of 2.6 nm for shallow NV centers was achieved and is consistent with other techniques for depth determination.
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45
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Tang Y, Wang X, Zhang X, Li J, Dai L. Sub-nanometer drift correction for super-resolution imaging. OPTICS LETTERS 2014; 39:5685-5688. [PMID: 25360959 DOI: 10.1364/ol.39.005685] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Spatial resolution of conventional far-field fluorescence microscopy is limited by diffraction of light. Single-molecule localization microscopy (SMLM), such as (direct) stochastic optical reconstruction microscopy (dSTORM/STORM), and (fluorescence) photoactivation localization microscopy (fPALM/PALM), can break this barrier by localizing single emitters and reconstructing super-resolution image with much higher precision. Nevertheless, a SMLM measurement needs to record a large number of image frames and takes considerable recording time. In this process, sample drift becomes a critical problem and cannot be neglected. In this Letter, we present a sub-nanometer precision, low-cost sample drift correction method based on minimizing normalized root-mean-square error (NRMSE) between bright field images. Two optical configurations are suggested for recording bright field and fluorescence images simultaneously or alternately. The method was demonstrated on simulated data, and better than 0.3 nm drift correction precision was achieved. It was also applied on dSTORM imaging of F-actins of 3T3 cell, and the quality of reconstructed super-resolution image was improved observably. This method does not require special hardware, extra labelling or markers, and no precision decline due to photobleaching. It can be applied as an add-on for SMLM setups and achieves sub-nanometer precision drift correction for post-measurement or real time drift compensation.
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46
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Wang Y, Schnitzbauer J, Hu Z, Li X, Cheng Y, Huang ZL, Huang B. Localization events-based sample drift correction for localization microscopy with redundant cross-correlation algorithm. OPTICS EXPRESS 2014; 22:15982-91. [PMID: 24977854 PMCID: PMC4162368 DOI: 10.1364/oe.22.015982] [Citation(s) in RCA: 97] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Revised: 06/14/2014] [Accepted: 06/16/2014] [Indexed: 05/23/2023]
Abstract
Highly accurate sample drift correction is essential in super-resolution localization microscopy to guarantee a high spatial resolution, especially when the technique is used to visualize small cell organelle. Here we present a localization events-based drift correction method using a redundant cross-correlation algorithm originally developed to correct beam-induced motion in cryo-electron microscopy. With simulated, synthesized as well as experimental data, we have demonstrated its superior precision compared to previously published localization events-based drift correction methods. The major advantage of this method is the robustness when the number of localization events is low, either because a short correction time step is required or because the imaged structure is small and sparse. This method has allowed us to improve the effective resolution when imaging Golgi apparatus in mammalian cells.
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Affiliation(s)
- Yina Wang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
- These authors contributed equally to this work
| | - Joerg Schnitzbauer
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158,
USA
- These authors contributed equally to this work
| | - Zhe Hu
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
- These authors contributed equally to this work
| | - Xueming Li
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158,
USA
| | - Yifan Cheng
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158,
USA
| | - Zhen-Li Huang
- Britton Chance Center for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics-Huazhong University of Science and Technology, Wuhan 430074,
China
- MoE Key Laboratory for Biomedical Photonics, Department of Biomedical Engineering, Huazhong University of Science and Technology, Wuhan 430074,
China
| | - Bo Huang
- Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA 94158,
USA
- Department of Biochemistry and Biophysics, University of California, San Francisco, San Francisco, CA 94158,
USA
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Precisely and accurately localizing single emitters in fluorescence microscopy. Nat Methods 2014; 11:253-66. [PMID: 24577276 DOI: 10.1038/nmeth.2843] [Citation(s) in RCA: 295] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/21/2014] [Indexed: 12/19/2022]
Abstract
Methods based on single-molecule localization and photophysics have brought nanoscale imaging with visible light into reach. This has enabled single-particle tracking applications for studying the dynamics of molecules and nanoparticles and contributed to the recent revolution in super-resolution localization microscopy techniques. Crucial to the optimization of such methods are the precision and accuracy with which single fluorophores and nanoparticles can be localized. We present a lucid synthesis of the developments on this localization precision and accuracy and their practical implications in order to guide the increasing number of researchers using single-particle tracking and super-resolution localization microscopy.
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Gramlich MW, Bae J, Hayward RC, Ross JL. Fluorescence imaging of nanoscale domains in polymer blends using stochastic optical reconstruction microscopy (STORM). OPTICS EXPRESS 2014; 22:8438-8450. [PMID: 24718217 DOI: 10.1364/oe.22.008438] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
High-resolution fluorescence techniques that provide spatial resolution below the diffraction limit are attractive new methods for structural characterization of nanostructured materials. For the first time, we apply the super-resolution technique of Stochastic Optical Reconstruction Microscopy (STORM), to characterize nanoscale structures within polymer blend films. The STORM technique involves temporally separating the fluorescence signals from individual labeled polymers, allowing their positions to be localized with high accuracy, yielding a high-resolution composite image of the material. Here, we describe the application of the technique to demixed blend films of polystyrene (PS) and poly(methyl methacrylate) (PMMA), and find that STORM provides comparable structural characteristics as those determined by Atomic Force Microscopy (AFM) and scanning electron microscopy (SEM), but with all of the advantages of a far-field optical technique.
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49
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Super-resolution microscopy of live cells using single molecule localization. CHINESE SCIENCE BULLETIN-CHINESE 2013. [DOI: 10.1007/s11434-013-6088-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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50
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Pavlides SC, Huang KT, Reid DA, Wu L, Blank SV, Mittal K, Guo L, Rothenberg E, Rueda B, Cardozo T, Gold LI. Inhibitors of SCF-Skp2/Cks1 E3 ligase block estrogen-induced growth stimulation and degradation of nuclear p27kip1: therapeutic potential for endometrial cancer. Endocrinology 2013; 154:4030-45. [PMID: 24035998 PMCID: PMC3800755 DOI: 10.1210/en.2013-1757] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
In many human cancers, the tumor suppressor, p27(kip1) (p27), a cyclin-dependent kinase inhibitor critical to cell cycle arrest, undergoes perpetual ubiquitin-mediated proteasomal degradation by the E3 ligase complex SCF-Skp2/Cks1 and/or cytoplasmic mislocalization. Lack of nuclear p27 causes aberrant cell cycle progression, and cytoplasmic p27 mediates cell migration/metastasis. We previously showed that mitogenic 17-β-estradiol (E2) induces degradation of p27 by the E3 ligase Skp1-Cullin1-F-Box- S phase kinase-associated protein2/cyclin dependent kinase regulatory subunit 1 in primary endometrial epithelial cells and endometrial carcinoma (ECA) cell lines, suggesting a pathogenic mechanism for type I ECA, an E2-induced cancer. The current studies show that treatment of endometrial carcinoma cells-1 (ECC-1) with small molecule inhibitors of Skp2/Cks1 E3 ligase activity (Skp2E3LIs) stabilizes p27 in the nucleus, decreases p27 in the cytoplasm, and prevents E2-induced proliferation and degradation of p27 in endometrial carcinoma cells-1 and primary ECA cells. Furthermore, Skp2E3LIs increase p27 half-life by 6 hours, inhibit cell proliferation (IC50, 14.3μM), block retinoblastoma protein (pRB) phosphorylation, induce G1 phase block, and are not cytotoxic. Similarly, using super resolution fluorescence localization microscopy and quantification, Skp2E3LIs increase p27 protein in the nucleus by 1.8-fold. In vivo, injection of Skp2E3LIs significantly increases nuclear p27 and reduces proliferation of endometrial epithelial cells by 42%-62% in ovariectomized E2-primed mice. Skp2E3LIs are specific inhibitors of proteolytic degradation that pharmacologically target the binding interaction between the E3 ligase, SCF-Skp2/Cks1, and p27 to stabilize nuclear p27 and prevent cell cycle progression. These targeted inhibitors have the potential to be an important therapeutic advance over general proteasome inhibitors for cancers characterized by SCF-Skp2/Cks1-mediated destruction of nuclear p27.
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Affiliation(s)
- Savvas C Pavlides
- PhD, Department of Medicine, Division of Translational Medicine, 550 First Avenue, NB17E4, New York, NY 10016.
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