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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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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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3
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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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4
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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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5
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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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6
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Copeland CR, McGray CD, Ilic BR, Geist J, Stavis SM. Accurate localization microscopy by intrinsic aberration calibration. Nat Commun 2021; 12:3925. [PMID: 34168121 PMCID: PMC8225824 DOI: 10.1038/s41467-021-23419-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Accepted: 04/28/2021] [Indexed: 02/02/2023] Open
Abstract
A standard paradigm of localization microscopy involves extension from two to three dimensions by engineering information into emitter images, and approximation of errors resulting from the field dependence of optical aberrations. We invert this standard paradigm, introducing the concept of fully exploiting the latent information of intrinsic aberrations by comprehensive calibration of an ordinary microscope, enabling accurate localization of single emitters in three dimensions throughout an ultrawide and deep field. To complete the extraction of spatial information from microscale bodies ranging from imaging substrates to microsystem technologies, we introduce a synergistic concept of the rigid transformation of the positions of multiple emitters in three dimensions, improving precision, testing accuracy, and yielding measurements in six degrees of freedom. Our study illuminates the challenge of aberration effects in localization microscopy, redefines the challenge as an opportunity for accurate, precise, and complete localization, and elucidates the performance and reliability of a complex microelectromechanical system.
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Affiliation(s)
- Craig R Copeland
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Craig D McGray
- Quantum Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - B Robert Ilic
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
- CNST NanoFab, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Jon Geist
- Quantum Measurement Division, National Institute of Standards and Technology, Gaithersburg, MD, USA
| | - Samuel M Stavis
- Microsystems and Nanotechnology Division, National Institute of Standards and Technology, Gaithersburg, MD, USA.
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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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8
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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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9
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AlQattan B, Benton D, Yetisen AK, Butt H. Conformable Holographic Photonic Ink Sensors Based on Adhesive Tapes for Strain Measurements. ACS APPLIED MATERIALS & INTERFACES 2019; 11:29147-29157. [PMID: 31318192 DOI: 10.1021/acsami.9b08545] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Buildings, bridges, and aircrafts are frequently exposed to fluctuation loads, which could start with a fine crack that instantly leads to unpredictable structure failures. The stationary strain sensors can be utilized, but they are costly and only detect limited deformation forms and sizes. Here, we fabricated photonic strain sensors on adhesive tapes, which can provide real-time monitoring of irregular surfaces. Holographic interference patterning was used to produce nonlinear curved nanostructures of one dimensional (1D) (900 nm × 880 nm) and two dimensional (2D) from a black dye film on a robust uniform adhesive layer and heat resistance tape. The patterned structure of the black dye was stable in broad pH environments. Diffracted light from the curved nanostructure detected the signal during structural damage, a shift or material tear of 5 με at less than 1.3 N cm-2. Additionally, the 2D nanostructure detected a surface change from x or y axis. Tilting the 1D structure within a range of 0.3° to 14.2° provided visible wavelength changes under broadband light to reveal early deflection signs. The curved nanopatterns could be also used for transferable holographic symbol design. Photonic nanopatterns on an adhesive tape could be used as a rapid response, conformable, lightweight, and low-cost dynamic strain sensor.
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Affiliation(s)
- Bader AlQattan
- School of Engineering , University of Birmingham , Birmingham B15 2TT , U.K
| | - David Benton
- Aston Institute of Photonics Technologies , Aston University , Birmingham B4 7ET , U.K
| | - Ali K Yetisen
- Department of Chemical Engineering , Imperial College London , London SW7 2AZ , U.K
| | - Haider Butt
- Department of Mechanical and Materials Engineering , Khalifa University, Masdar City Campus , Abu Dhabi 127788 , United Arab Emirates
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10
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Park S, Zhang J, Reyer MA, Zareba J, Troy AA, Fei J. Conducting Multiple Imaging Modes with One Fluorescence Microscope. J Vis Exp 2018. [PMID: 30417870 DOI: 10.3791/58320] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Fluorescence microscopy is a powerful tool to detect biological molecules in situ and monitor their dynamics and interactions in real-time. In addition to conventional epi-fluorescence microscopy, various imaging techniques have been developed to achieve specific experimental goals. Some of the widely used techniques include single-molecule fluorescence resonance energy transfer (smFRET), which can report conformational changes and molecular interactions with angstrom resolution, and single-molecule detection-based super-resolution (SR) imaging, which can enhance the spatial resolution approximately ten to twentyfold compared to diffraction-limited microscopy. Here we present a customer-designed integrated system, which merges multiple imaging methods in one microscope, including conventional epi-fluorescent imaging, single-molecule detection-based SR imaging, and multi-color single-molecule detection, including smFRET imaging. Different imaging methods can be achieved easily and reproducibly by switching optical elements. This set-up is easy to adopt by any research laboratory in biological sciences with a need for routine and diverse imaging experiments at a reduced cost and space relative to building separate microscopes for individual purposes.
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Affiliation(s)
- Seongjin Park
- Department of Biochemistry and Molecular Biology, University of Chicago
| | - Jiacheng Zhang
- The Institute for Biophysical Dynamics, University of Chicago
| | - Matthew A Reyer
- The Institute for Biophysical Dynamics, University of Chicago
| | - Joanna Zareba
- Department of Biochemistry and Molecular Biology, University of Chicago; Faculty of Chemistry, Wrocław University of Science and Technology
| | | | - Jingyi Fei
- Department of Biochemistry and Molecular Biology, University of Chicago; The Institute for Biophysical Dynamics, University of Chicago;
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11
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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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