1
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Power RM, Tschanz A, Zimmermann T, Ries J. Build and operation of a custom 3D, multicolor, single-molecule localization microscope. Nat Protoc 2024; 19:2467-2525. [PMID: 38702387 DOI: 10.1038/s41596-024-00989-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 02/19/2024] [Indexed: 05/06/2024]
Abstract
Single-molecule localization microscopy (SMLM) enables imaging scientists to visualize biological structures with unprecedented resolution. Particularly powerful implementations of SMLM are capable of three-dimensional, multicolor and high-throughput imaging and can yield key biological insights. However, widespread access to these technologies is limited, primarily by the cost of commercial options and complexity of de novo development of custom systems. Here we provide a comprehensive guide for interested researchers who wish to establish a high-end, custom-built SMLM setup in their laboratories. We detail the initial configuration and subsequent assembly of the SMLM, including the instructions for the alignment of all the optical pathways, the software and hardware integration, and the operation of the instrument. We describe the validation steps, including the preparation and imaging of test and biological samples with structures of well-defined geometries, and assist the user in troubleshooting and benchmarking the system's performance. Additionally, we provide a walkthrough of the reconstruction of a super-resolved dataset from acquired raw images using the Super-resolution Microscopy Analysis Platform. Depending on the instrument configuration, the cost of the components is in the range US$95,000-180,000, similar to other open-source advanced SMLMs, and substantially lower than the cost of a commercial instrument. A builder with some experience of optical systems is expected to require 4-8 months from the start of the system construction to attain high-quality three-dimensional and multicolor biological images.
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Affiliation(s)
- Rory M Power
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany.
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Timo Zimmermann
- EMBL Imaging Centre, EMBL Heidelberg, Heidelberg, Germany
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, EMBL Heidelberg, Heidelberg, Germany.
- Max Perutz Labs, Vienna Biocenter Campus, Vienna, Austria.
- University of Vienna, Center for Molecular Biology, Department of Structural and Computational Biology, Vienna, Austria.
- University of Vienna, Faculty of Physics, Vienna, Austria.
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2
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Almahayni K, Nestola G, Spiekermann M, Möckl L. Simple, Economic, and Robust Rail-Based Setup for Super-Resolution Localization Microscopy. J Phys Chem A 2023; 127:4553-4560. [PMID: 37163339 DOI: 10.1021/acs.jpca.3c01351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
Research during the past 2 decades has showcased the power of single-molecule localization microscopy (SMLM) as a tool for exploring the nanoworld. However, SMLM systems are typically available in specialized laboratories and imaging facilities, owing to their expensiveness as well as complex assembly and alignment procedure. Here, we lay out the blueprint of a sturdy, rail-based, cost-efficient, multicolor SMLM setup that is easy to construct and align in service of simplifying the accessibility of SMLM. We characterize the optical properties of the design and assess its capabilities, robustness, and stability. The performance of the system is assayed using super-resolution imaging of biological samples. We believe that this design will make SMLM more affordable and broaden its availability.
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Affiliation(s)
- Karim Almahayni
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
- Department of Physics, Friedrich-Alexander-University Erlangen-Nuremberg, 91054 Erlangen, Germany
| | - Gianluca Nestola
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
| | - Malte Spiekermann
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
| | - Leonhard Möckl
- Max Planck Institute for the Science of Light, Staudtstr. 2, 91058 Erlangen, Germany
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3
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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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4
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Danial JSH, Lam JYL, Wu Y, Woolley M, Dimou E, Cheetham MR, Emin D, Klenerman D. Constructing a cost-efficient, high-throughput and high-quality single-molecule localization microscope for super-resolution imaging. Nat Protoc 2022; 17:2570-2619. [PMID: 36002768 DOI: 10.1038/s41596-022-00730-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2021] [Accepted: 05/24/2022] [Indexed: 11/09/2022]
Abstract
Single-molecule localization microscopy (SMLM) leverages the power of modern optics to unleash ultra-precise structural nanoscopy of complex biological machines in their native environments as well as ultra-sensitive and high-throughput medical diagnostics with the sensitivity of a single molecule. To achieve this remarkable speed and resolution, SMLM setups are either built by research laboratories with strong expertise in optical engineering or commercially sold at a hefty price tag. The inaccessibility of SMLM to life scientists for technical or financial reasons is detrimental to the progress of biological and biomedical discoveries reliant on super-resolution imaging. In this work, we present the NanoPro, an economic, high-throughput, high-quality and easy-to-assemble SMLM for super-resolution imaging. We show that our instrument performs similarly to the most expensive, best-in-class commercial microscopes and rivals existing open-source microscopes at a lower price and construction complexity. To facilitate its wide adoption, we compiled a step-by-step protocol, accompanied by extensive illustrations, to aid inexperienced researchers in constructing the NanoPro as well as assessing its performance by imaging ground-truth samples as small as 20 nm. The detailed visual instructions make it possible for students with little expertise in microscopy engineering to construct, validate and use the NanoPro in <1 week, provided that all components are available.
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Affiliation(s)
- John S H Danial
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
| | - Jeff Y L Lam
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Yunzhao Wu
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Matthew Woolley
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
| | - Eleni Dimou
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Matthew R Cheetham
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - Derya Emin
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK
| | - David Klenerman
- Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
- UK Dementia Research Institute, University of Cambridge, Cambridge, UK.
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5
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Diekmann R, Deschamps J, Li Y, Deguchi T, Tschanz A, Kahnwald M, Matti U, Ries J. Photon-free (s)CMOS camera characterization for artifact reduction in high- and super-resolution microscopy. Nat Commun 2022; 13:3362. [PMID: 35690614 PMCID: PMC9188588 DOI: 10.1038/s41467-022-30907-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 05/04/2022] [Indexed: 11/09/2022] Open
Abstract
Modern implementations of widefield fluorescence microscopy often rely on sCMOS cameras, but this camera architecture inherently features pixel-to-pixel variations. Such variations lead to image artifacts and render quantitative image interpretation difficult. Although a variety of algorithmic corrections exists, they require a thorough characterization of the camera, which typically is not easy to access or perform. Here, we developed a fully automated pipeline for camera characterization based solely on thermally generated signal, and implemented it in the popular open-source software Micro-Manager and ImageJ/Fiji. Besides supplying the conventional camera maps of noise, offset and gain, our pipeline also gives access to dark current and thermal noise as functions of the exposure time. This allowed us to avoid structural bias in single-molecule localization microscopy (SMLM), which without correction is substantial even for scientific-grade, cooled cameras. In addition, our approach enables high-quality 3D super-resolution as well as live-cell time-lapse microscopy with cheap, industry-grade cameras. As our approach for camera characterization does not require any user interventions or additional hardware implementations, numerous correction algorithms that rely on camera characterization become easily applicable.
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Affiliation(s)
- Robin Diekmann
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- LaVision Biotec GmbH, Bielefeld, Germany
| | - Joran Deschamps
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Fondazione Human Technopole, Milan, Italy
| | - Yiming Li
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Department of Biomedical Engineering, Southern University of Science and Technology, Shenzhen, China
| | - Takahiro Deguchi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Aline Tschanz
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Collaboration for Joint PhD Degree Between EMBL and Heidelberg University, Faculty of Biosciences, Heidelberg, Germany
| | - Maurice Kahnwald
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland
| | - Ulf Matti
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
- Abberior Instruments GmbH, Göttingen, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany.
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6
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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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7
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Jabermoradi A, Yang S, Gobes MI, van Duynhoven JPM, Hohlbein J. Enabling single-molecule localization microscopy in turbid food emulsions. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20200164. [PMID: 0 DOI: 10.1098/rsta.2020.0164] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/20/2021] [Indexed: 05/19/2023]
Abstract
Turbidity poses a major challenge for the microscopic characterization of food systems. Local mismatches in refractive indices, for example, lead to significant image deterioration along sample depth. To mitigate the issue of turbidity and to increase the accessible optical resolution in food microscopy, we added adaptive optics (AO) and flat-field illumination to our previously published open microscopy framework, the miCube. In the detection path, we implemented AO via a deformable mirror to compensate aberrations and to modulate the emission wavefront enabling the engineering of point spread functions (PSFs) for single-molecule localization microscopy (SMLM) in three dimensions. As a model system for a non-transparent food colloid such as mayonnaise, we designed an oil-in-water emulsion containing the ferric ion binding protein phosvitin commonly present in egg yolk. We targeted phosvitin with fluorescently labelled primary antibodies and used PSF engineering to obtain two- and three-dimensional images of phosvitin covered oil droplets with sub 100 nm resolution. Our data indicated that phosvitin is homogeneously distributed at the interface. With the possibility to obtain super-resolved images in depth, our work paves the way for localizing biomacromolecules at heterogeneous colloidal interfaces in food emulsions.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Abbas Jabermoradi
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
| | - Suyeon Yang
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
| | - Martijn I. Gobes
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
| | - John P. M. van Duynhoven
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
- Unilever Global Foods Innovation Centre, Bronland 14, Wageningen 6708, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
- Microspectroscopy Research Facility, Wageningen University and Research, Stippeneng 4, Wageningen 6708, The Netherlands
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8
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Dhiman S, Andrian T, Gonzalez BS, Tholen MME, Wang Y, Albertazzi L. Can super-resolution microscopy become a standard characterization technique for materials chemistry? Chem Sci 2022; 13:2152-2166. [PMID: 35310478 PMCID: PMC8864713 DOI: 10.1039/d1sc05506b] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 12/01/2021] [Indexed: 12/20/2022] Open
Abstract
The characterization of newly synthesized materials is a cornerstone of all chemistry and nanotechnology laboratories. For this purpose, a wide array of analytical techniques have been standardized and are used routinely by laboratories across the globe. With these methods we can understand the structure, dynamics and function of novel molecular architectures and their relations with the desired performance, guiding the development of the next generation of materials. Moreover, one of the challenges in materials chemistry is the lack of reproducibility due to improper publishing of the sample preparation protocol. In this context, the recent adoption of the reporting standard MIRIBEL (Minimum Information Reporting in Bio-Nano Experimental Literature) for material characterization and details of experimental protocols aims to provide complete, reproducible and reliable sample preparation for the scientific community. Thus, MIRIBEL should be immediately adopted in publications by scientific journals to overcome this challenge. Besides current standard spectroscopy and microscopy techniques, there is a constant development of novel technologies that aim to help chemists unveil the structure of complex materials. Among them super-resolution microscopy (SRM), an optical technique that bypasses the diffraction limit of light, has facilitated the study of synthetic materials with multicolor ability and minimal invasiveness at nanometric resolution. Although still in its infancy, the potential of SRM to unveil the structure, dynamics and function of complex synthetic architectures has been highlighted in pioneering reports during the last few years. Currently, SRM is a sophisticated technique with many challenges in sample preparation, data analysis, environmental control and automation, and moreover the instrumentation is still expensive. Therefore, SRM is currently limited to expert users and is not implemented in characterization routines. This perspective discusses the potential of SRM to transition from a niche technique to a standard routine method for material characterization. We propose a roadmap for the necessary developments required for this purpose based on a collaborative effort from scientists and engineers across disciplines.
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Affiliation(s)
- Shikha Dhiman
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
| | - Teodora Andrian
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
| | - Beatriz Santiago Gonzalez
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Marrit M E Tholen
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
| | - Yuyang Wang
- Institute for Complex Molecular Systems, Eindhoven University of Technology P. O. Box 513 5600 MB Eindhoven The Netherlands
- Department of Applied Physics, Eindhoven University of Technology Postbus 513 5600 MB Eindhoven The Netherlands
| | - Lorenzo Albertazzi
- Institute of Bioengineering of Catalonia (IBEC), Barcelona Institute of Science and Technology Barcelona Spain
- Department of Biomedical Engineering, Institute of Complex Molecular Systems, Eindhoven University of Technology Eindhoven The Netherlands
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9
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Vatan T, Minehart JA, Zhang C, Agarwal V, Yang J, Speer CM. Volumetric super-resolution imaging by serial ultrasectioning and stochastic optical reconstruction microscopy in mouse neural tissue. STAR Protoc 2021; 2:100971. [PMID: 34901889 PMCID: PMC8637648 DOI: 10.1016/j.xpro.2021.100971] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Here, we present a protocol for collecting large-volume, four-color, single-molecule localization imaging data from neural tissue. We have applied this technique to map the location and identities of chemical synapses across whole cells in mouse retinae. Our sample preparation approach improves 3D STORM image quality by reducing tissue scattering, photobleaching, and optical distortions associated with deep imaging. This approach can be extended for use on other tissue types enabling life scientists to perform volumetric super-resolution imaging in diverse biological models. For complete details on the use and execution of this protocol, please refer to Sigal et al. (2015).
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Affiliation(s)
- Tarlan Vatan
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Neuroscience and Cognitive Science Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Jacqueline A. Minehart
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Neuroscience and Cognitive Science Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Chenghang Zhang
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Biophysics Graduate Program, University of Maryland, College Park, MD 20742, USA
| | - Vatsal Agarwal
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Jerry Yang
- Department of Biology, University of Maryland, College Park, MD 20742, USA
| | - Colenso M. Speer
- Department of Biology, University of Maryland, College Park, MD 20742, USA
- Brain and Behavior Institute, University of Maryland, College Park, MD 20742, USA
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10
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Enhanced super-resolution microscopy by extreme value based emitter recovery. Sci Rep 2021; 11:20417. [PMID: 34650088 PMCID: PMC8517018 DOI: 10.1038/s41598-021-00066-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 10/05/2021] [Indexed: 11/09/2022] Open
Abstract
Super-resolution localization microscopy allows visualization of biological structure at nanoscale resolution. However, the presence of heterogeneous background can degrade the nanoscale resolution by tens of nanometers and introduce significant image artifacts. Here we investigate and validate an efficient approach, referred to as extreme value-based emitter recovery (EVER), to accurately recover the distorted fluorescent emitters from heterogeneous background. Through numerical simulation and biological experiments, we validated the accuracy of EVER in improving the fidelity of the reconstructed super-resolution image for a wide variety of imaging characteristics. EVER requires no manual adjustment of parameters and has been implemented as an easy-to-use ImageJ plugin that can immediately enhance the quality of reconstructed super-resolution images. This method is validated as an efficient way for robust nanoscale imaging of samples with heterogeneous background fluorescence, such as thicker tissue and cells.
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11
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Opstad IS, Hansen DH, Acuña S, Ströhl F, Priyadarshi A, Tinguely JC, Dullo FT, Dalmo RA, Seternes T, Ahluwalia BS, Agarwal K. Fluorescence fluctuation-based super-resolution microscopy using multimodal waveguided illumination. OPTICS EXPRESS 2021; 29:23368-23380. [PMID: 34614603 DOI: 10.1364/oe.423809] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Photonic chip-based total internal reflection fluorescence microscopy (c-TIRFM) is an emerging technology enabling a large TIRF excitation area decoupled from the detection objective. Additionally, due to the inherent multimodal nature of wide waveguides, it is a convenient platform for introducing temporal fluctuations in the illumination pattern. The fluorescence fluctuation-based nanoscopy technique multiple signal classification algorithm (MUSICAL) does not assume stochastic independence of the emitter emission and can therefore exploit fluctuations arising from other sources, as such multimodal illumination patterns. In this work, we demonstrate and verify the utilization of fluctuations in the illumination for super-resolution imaging using MUSICAL on actin in salmon keratocytes. The resolution improvement was measured to be 2.2-3.6-fold compared to the corresponding conventional images.
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12
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Adam N, Beattie TL, Riabowol K. Fluorescence microscopy methods for examining telomeres during cell aging. Ageing Res Rev 2021; 68:101320. [PMID: 33744488 DOI: 10.1016/j.arr.2021.101320] [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: 12/01/2020] [Revised: 02/24/2021] [Accepted: 03/08/2021] [Indexed: 10/21/2022]
Abstract
Telomeres are protective structures, composed of nucleic acids and a complex protein mixture, located at the end of the chromosomes. They play an important role in preventing genomic instability and ensuring cell health. Defects in telomere integrity result in cell dysfunction and the development of diseases, including neurodegenerative disorders, cancer and premature aging syndromes, among others. Loss of telomere integrity during normal cell aging also initiates DNA damage signals that culminate in the senescence phenotype. Fluorescence microscopy has allowed researchers to study the dynamics, shape, localization, and co-distribution of telomeres with proteins of interest. The microscopy tools to investigate these structures have evolved, making it possible to understand in greater detail the molecular mechanisms affecting telomeres that contribute to cell aging and the development of age-related diseases. Using human fibroblasts as an example, we will highlight several characteristics of telomeres that can be investigated using three different microscopy systems, including wide-field microscopy, and the two super-resolution techniques called 3D Structured Illumination Microscopy (3D-SIM) and direct Stochastic Optical Reconstruction Microscopy (dSTORM). In this review, we will also discuss their limitations and highlight their importance in answering telomere-related scientific questions.
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13
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Arista-Romero M, Pujals S, Albertazzi L. Towards a Quantitative Single Particle Characterization by Super Resolution Microscopy: From Virus Structures to Antivirals Design. Front Bioeng Biotechnol 2021; 9:647874. [PMID: 33842446 PMCID: PMC8033170 DOI: 10.3389/fbioe.2021.647874] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Accepted: 03/08/2021] [Indexed: 12/15/2022] Open
Abstract
In the last year the COVID19 pandemic clearly illustrated the potential threat that viruses pose to our society. The characterization of viral structures and the identification of key proteins involved in each step of the cycle of infection are crucial to develop treatments. However, the small size of viruses, invisible under conventional fluorescence microscopy, make it difficult to study the organization of protein clusters within the viral particle. The applications of super-resolution microscopy have skyrocketed in the last years, converting this group into one of the leading techniques to characterize viruses and study the viral infection in cells, breaking the diffraction limit by achieving resolutions up to 10 nm using conventional probes such as fluorescent dyes and proteins. There are several super-resolution methods available and the selection of the right one it is crucial to study in detail all the steps involved in the viral infection, quantifying and creating models of infection for relevant viruses such as HIV-1, Influenza, herpesvirus or SARS-CoV-1. Here we review the use of super-resolution microscopy (SRM) to study all steps involved in the viral infection and antiviral design. In light of the threat of new viruses, these studies could inspire future assays to unveil the viral mechanism of emerging viruses and further develop successful antivirals against them.
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Affiliation(s)
- Maria Arista-Romero
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Silvia Pujals
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Electronics and Biomedical Engineering, Faculty of Physics, Universitat de Barcelona, Barcelona, Spain
| | - Lorenzo Albertazzi
- Nanoscopy for Nanomedicine Group, Institute for Bioengineering of Catalonia (IBEC), The Barcelona Institute of Science and Technology, Barcelona, Spain
- Department of Biomedical Engineering, Institute for Complex Molecular Systems (ICMS), Eindhoven University of Technology, Eindhoven, Netherlands
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14
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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: 285] [Impact Index Per Article: 95.0] [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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;
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15
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Franch N, Canals J, Moro V, Vilá A, Romano-Rodríguez A, Prades JD, Gülink J, Bezshlyakh D, Waag A, Kluczyk-Korch K, Auf der Maur M, di Carlo A, Diéguez Á. Nano illumination microscopy: a technique based on scanning with an array of individually addressable nanoLEDs. OPTICS EXPRESS 2020; 28:19044-19057. [PMID: 32672190 DOI: 10.1364/oe.391497] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2020] [Accepted: 04/29/2020] [Indexed: 06/11/2023]
Abstract
In lensless microscopy, spatial resolution is usually provided by the pixel density of current digital cameras, which are reaching a hard-to-surpass pixel size / resolution limit over 1 µm. As an alternative, the dependence of the resolving power can be moved from the detector to the light sources, offering a new kind of lensless microscopy setups. The use of continuously scaled-down Light-Emitting Diode (LED) arrays to scan the sample allows resolutions on order of the LED size, giving rise to compact and low-cost microscopes without mechanical scanners or optical accessories. In this paper, we present the operation principle of this new approach to lensless microscopy, with simulations that demonstrate the possibility to use it for super-resolution, as well as a first prototype. This proof-of-concept setup integrates an 8 × 8 array of LEDs, each 5 × 5 μm2 pixel size and 10 μm pitch, and an optical detector. We characterize the system using Electron-Beam Lithography (EBL) pattern. Our prototype validates the imaging principle and opens the way to improve resolution by further miniaturizing the light sources.
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16
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Troy K, Liu Y, Hainer SJ. PathSTORM: a road to early cancer detection. Mol Cell Oncol 2020; 7:1776086. [PMID: 32944634 PMCID: PMC7469673 DOI: 10.1080/23723556.2020.1776086] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Disruption of chromatin structure could enable early carcinogenesis by facilitating malignant transformation. Using stochastic optical reconstruction microscopy optimized for pathological tissue (PathSTORM), we uncovered a gradual decompaction of higher-order chromatin folding through progressive stages of carcinogenesis. We demonstrated potential detection of pre-cancerous genomic architecture not easily discernible by conventional pathology.
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Affiliation(s)
- Kris Troy
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Sarah J Hainer
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, USA
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17
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Clowsley AH, Kaufhold WT, Lutz T, Meletiou A, Di Michele L, Soeller C. Detecting Nanoscale Distribution of Protein Pairs by Proximity-Dependent Super-resolution Microscopy. J Am Chem Soc 2020; 142:12069-12078. [DOI: 10.1021/jacs.9b03418] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Alexander H. Clowsley
- Living Systems Institute & Biomedical Physics, University of Exeter, Exeter EX4 4QD, U.K
| | - William T. Kaufhold
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London SW7 2AZ, U.K
| | - Tobias Lutz
- Living Systems Institute & Biomedical Physics, University of Exeter, Exeter EX4 4QD, U.K
| | - Anna Meletiou
- Living Systems Institute & Biomedical Physics, University of Exeter, Exeter EX4 4QD, U.K
| | - Lorenzo Di Michele
- Cavendish Laboratory, University of Cambridge, Cambridge CB3 0HE, U.K
- Department of Chemistry, Molecular Sciences Research Hub, Imperial College London, London SW7 2AZ, U.K
| | - Christian Soeller
- Living Systems Institute & Biomedical Physics, University of Exeter, Exeter EX4 4QD, U.K
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18
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Ma H, Liu Y. Super-resolution localization microscopy: Toward high throughput, high quality, and low cost. APL PHOTONICS 2020; 5:060902. [PMID: 34350342 PMCID: PMC8330581 DOI: 10.1063/5.0011731] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
After nearly 15 years since its initial debut, super-resolution localization microscopy that surpasses the diffraction-limited resolution barrier of optical microscopy has rapidly gotten out of the ivory tower and entered a new phase to address various challenging biomedical questions. Recent advances in this technology greatly increased the imaging throughput, improved the imaging quality, simplified the sample preparation, and reduced the system cost, making this technology suitable for routine biomedical research. We will provide our perspective on the recent technical advances and their implications in serving the community of biomedical research.
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Affiliation(s)
- Hongqiang Ma
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, Pennsylvania 15213, USA
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19
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Fast and accurate sCMOS noise correction for fluorescence microscopy. Nat Commun 2020; 11:94. [PMID: 31901080 PMCID: PMC6941997 DOI: 10.1038/s41467-019-13841-8] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 11/29/2019] [Indexed: 12/12/2022] Open
Abstract
The rapid development of scientific CMOS (sCMOS) technology has greatly advanced optical microscopy for biomedical research with superior sensitivity, resolution, field-of-view, and frame rates. However, for sCMOS sensors, the parallel charge-voltage conversion and different responsivity at each pixel induces extra readout and pattern noise compared to charge-coupled devices (CCD) and electron-multiplying CCD (EM-CCD) sensors. This can produce artifacts, deteriorate imaging capability, and hinder quantification of fluorescent signals, thereby compromising strategies to reduce photo-damage to live samples. Here, we propose a content-adaptive algorithm for the automatic correction of sCMOS-related noise (ACsN) for fluorescence microscopy. ACsN combines camera physics and layered sparse filtering to significantly reduce the most relevant noise sources in a sCMOS sensor while preserving the fine details of the signal. The method improves the camera performance, enabling fast, low-light and quantitative optical microscopy with video-rate denoising for a broad range of imaging conditions and modalities. Scientific complementary metal-oxide semiconductor (sCMOS) cameras have advanced the imaging field, but they often suffer from additional noise compared to CCD sensors. Here the authors present a content-adaptive algorithm for the automatic correction of sCMOS-related noise for fluorescence microscopy.
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20
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Kabir MM, Rajput HS, Kelkar VA, Salazar Coariti AC, Toussaint KC. Demonstration of flat-top beam illumination in widefield multiphoton microscopy. JOURNAL OF BIOMEDICAL OPTICS 2019; 25:1-8. [PMID: 31729201 PMCID: PMC7008505 DOI: 10.1117/1.jbo.25.1.014503] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Accepted: 10/24/2019] [Indexed: 06/10/2023]
Abstract
Multiphoton microscopy provides a suitable technique for imaging biological tissues with submicrometer resolution. Usually a Gaussian beam (GB) is used for illumination, leading to a reduced power efficiency in the multiphoton response and vignetting for a square-shaped imaging area. A flat-top beam (FTB) provides a uniform spatial intensity distribution that equalizes the probability of a multiphoton effect across the imaging area. We employ a customized widefield multiphoton microscope to compare the performance of a square-shaped FTB illumination with that based on using a GB, for both two-photon fluorescence (TPF) and second-harmonic generation (SHG) imaging. The variation in signal-to-noise ratio across TPF images of fluorescent dyes spans ∼5.6 dB for the GB and ∼1.2 dB for the FTB illumination, respectively. For the GB modality, TPF images of mouse colon and Convallaria root, and SHG images of chicken tendon and human breast biopsy tissue showcase ∼20 % area that are not imaged due to either insufficient or lack of illumination. For quantitative analysis that depends on the illuminated area, this effect can potentially lead to inaccuracies. This work emphasizes the applicability of FTB illumination to multiphoton applications.
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Affiliation(s)
- Mohammad M. Kabir
- University of Illinois at Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
- Laboratory for Photonics Research of Bio/Nano Environments (PROBE Lab), Urbana, Illinois and Providence, Rhode Island, United States
| | - Hemangg S. Rajput
- Laboratory for Photonics Research of Bio/Nano Environments (PROBE Lab), Urbana, Illinois and Providence, Rhode Island, United States
- University of Illinois at Urbana-Champaign, Department of Mechanical Science and Engineering, Urbana, Illinois, United States
| | - Varun A. Kelkar
- University of Illinois at Urbana-Champaign, Department of Electrical and Computer Engineering, Urbana, Illinois, United States
- Laboratory for Photonics Research of Bio/Nano Environments (PROBE Lab), Urbana, Illinois and Providence, Rhode Island, United States
| | - Adriana C. Salazar Coariti
- Laboratory for Photonics Research of Bio/Nano Environments (PROBE Lab), Urbana, Illinois and Providence, Rhode Island, United States
| | - Kimani C. Toussaint
- Laboratory for Photonics Research of Bio/Nano Environments (PROBE Lab), Urbana, Illinois and Providence, Rhode Island, United States
- Brown University, School of Engineering, Providence, Rhode Island, United States
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21
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Colville MJ, Park S, Zipfel WR, Paszek MJ. High-speed device synchronization in optical microscopy with an open-source hardware control platform. Sci Rep 2019; 9:12188. [PMID: 31434941 PMCID: PMC6704125 DOI: 10.1038/s41598-019-48455-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2019] [Accepted: 07/31/2019] [Indexed: 12/27/2022] Open
Abstract
Azimuthal beam scanning eliminates the uneven excitation field arising from laser interference in through-objective total internal reflection fluorescence (TIRF) microscopy. The same principle can be applied to scanning angle interference microscopy (SAIM), where precision control of the scanned laser beam presents unique technical challenges for the builders of custom azimuthal scanning microscopes. Accurate synchronization between the instrument computer, beam scanning system and excitation source is required to collect high quality data and minimize sample damage in SAIM acquisitions. Drawing inspiration from open-source prototyping systems, like the Arduino microcontroller boards, we developed a new instrument control platform to be affordable, easily programmed, and broadly useful, but with integrated, precision analog circuitry and optimized firmware routines tailored to advanced microscopy. We show how the integration of waveform generation, multiplexed analog outputs, and native hardware triggers into a single central hub provides a versatile platform for performing fast circle-scanning acquisitions, including azimuthal scanning SAIM and multiangle TIRF. We also demonstrate how the low communication latency of our hardware platform can reduce image intensity and reconstruction artifacts arising from synchronization errors produced by software control. Our complete platform, including hardware design, firmware, API, and software, is available online for community-based development and collaboration.
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Affiliation(s)
| | - Sangwoo Park
- Field of Biophysics, Cornell University, Ithaca, NY, 14853, USA
| | - Warren R Zipfel
- Field of Biophysics, Cornell University, Ithaca, NY, 14853, USA.,Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.,Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, 14853, USA
| | - Matthew J Paszek
- Field of Biophysics, Cornell University, Ithaca, NY, 14853, USA. .,Robert Frederick Smith School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Field of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA. .,Kavli Institute at Cornell for Nanoscale Science, Ithaca, NY, 14853, USA.
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22
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Martens KJA, van Beljouw SPB, van der Els S, Vink JNA, Baas S, Vogelaar GA, Brouns SJJ, van Baarlen P, Kleerebezem M, Hohlbein J. Visualisation of dCas9 target search in vivo using an open-microscopy framework. Nat Commun 2019; 10:3552. [PMID: 31391532 PMCID: PMC6685946 DOI: 10.1038/s41467-019-11514-0] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Accepted: 07/19/2019] [Indexed: 02/07/2023] Open
Abstract
CRISPR-Cas9 is widely used in genomic editing, but the kinetics of target search and its relation to the cellular concentration of Cas9 have remained elusive. Effective target search requires constant screening of the protospacer adjacent motif (PAM) and a 30 ms upper limit for screening was recently found. To further quantify the rapid switching between DNA-bound and freely-diffusing states of dCas9, we developed an open-microscopy framework, the miCube, and introduce Monte-Carlo diffusion distribution analysis (MC-DDA). Our analysis reveals that dCas9 is screening PAMs 40% of the time in Gram-positive Lactoccous lactis, averaging 17 ± 4 ms per binding event. Using heterogeneous dCas9 expression, we determine the number of cellular target-containing plasmids and derive the copy number dependent Cas9 cleavage. Furthermore, we show that dCas9 is not irreversibly bound to target sites but can still interfere with plasmid replication. Taken together, our quantitative data facilitates further optimization of the CRISPR-Cas toolbox.
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Affiliation(s)
- Koen J A Martens
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
- Laboratory of Bionanotechnology, Wageningen University and Research, Bornse Weilanden 9, 6708 WG, Wageningen, The Netherlands
| | - Sam P B van Beljouw
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Simon van der Els
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
- NIZO food research, Kernhemseweg 2, 6718 ZB, Ede, The Netherlands
| | - Jochem N A Vink
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Sander Baas
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - George A Vogelaar
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands
| | - Stan J J Brouns
- Kavli Institute of Nanoscience, Department of Bionanoscience, Delft University of Technology, Van der Maasweg 9, 2629 HZ, Delft, The Netherlands
| | - Peter van Baarlen
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Michiel Kleerebezem
- Host-Microbe Interactomics Group, Animal Sciences, Wageningen University and Research, De Elst 1, 6708 WD, Wageningen, The Netherlands
| | - Johannes Hohlbein
- Laboratory of Biophysics, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
- Microspectroscopy Research Facility, Wageningen University and Research, Stippeneng 4, 6708 WE, Wageningen, The Netherlands.
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23
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Varga D, Majoros H, Ujfaludi Z, Erdélyi M, Pankotai T. Quantification of DNA damage induced repair focus formation via super-resolution dSTORM localization microscopy. NANOSCALE 2019; 11:14226-14236. [PMID: 31317161 DOI: 10.1039/c9nr03696b] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
In eukaryotic cells, each process, in which DNA is involved, should take place in the context of a chromatin structure. DNA double-strand breaks (DSBs) are one of the most deleterious lesions often leading to chromosomal rearrangement. In response to environmental stresses, cells have developed repair mechanisms to eliminate the DSBs. Upon DSB induction, several factors play roles in chromatin relaxation by catalysing the appropriate histone posttranslational modification (PTM) steps, therefore promoting the access of the repair factors to the DSBs. Among these PTMs, the phosphorylation of the histone variant H2AX at its Ser139 residue (also known as γH2AX) could be observed at the break sites. The structure of a DNA double-strand break induced repair focus has to be organized during the repair as it contributes to the accessibility of specific repair proteins to the damaged site. Our aim was to develop a quantitative approach to analyse the morphology of single repair foci by super-resolution dSTORM microscopy to gain insight into chromatin organization in DNA repair. We have established a specific dSTORM measurement process by developing a new analytical algorithm for gaining quantitative information about chromatin morphology and repair foci topology at an individual γH2AX enriched repair focus. Using this method we quantified single repair foci to show the distribution of γH2AX. The image of individual γH2AX referred to as the Single target Molecule response scatter Plot (SMPlot) was obtained by using high lateral resolution dSTORM images. Determination of the average localization numbers in an SMPlot was one of the key steps of quantitative dSTORM. A repair focus is made up of nanofoci. Such a substructure of repair foci can only be resolved and detected with super-resolution microscopy. Determination of the number of γH2AXs in the nanofoci was another key step of quantitative dSTORM. Additionally, based on our new analysis method, we were able to show the number of nucleosomes in each nanofocus that could allow us to define the possible chromatin structure and the nucleosome density around the break sites. This method is one of the first demonstrations of a single-cell based quantitative measurement of a discrete repair focus, which could provide new opportunities to categorize the spatial organization of nanofoci by parametric determination of topological similarity.
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Affiliation(s)
- Dániel Varga
- University of Szeged, Department of Optics and Quantum Electronics, Hungary.
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24
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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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25
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Liu Y, Xu J. High-resolution microscopy for imaging cancer pathobiology. CURRENT PATHOBIOLOGY REPORTS 2019; 7:85-96. [PMID: 32953251 PMCID: PMC7500261 DOI: 10.1007/s40139-019-00201-w] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
PURPOSE OF REVIEW Light microscopy plays an essential role in clinical diagnosis and understanding the pathogenesis of cancer. Conventional bright-field microscope is used to visualize abnormality in tissue architecture and nuclear morphology, but often suffers from many limitations. This review focuses on the potential of new imaging techniques to improve basic and clinical research in pathobiology. RECENT FINDINGS Light microscopy has significantly expanded its ability in resolution, imaging volume, speed and contrast. It now allows 3D high-resolution volumetric imaging of tissue architecture from large tissue and molecular structures at nanometer resolution. SUMMARY Pathologists and researchers now have access to various imaging tools to study cancer pathobiology in both breadth and depth. Although clinical adoption of a new technique is slow, the new imaging tools will provide significant new insights and open new avenues for improving early cancer detection, personalized risk assessment and identifying the best treatment strategies.
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Affiliation(s)
- Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
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26
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Xu J, Liu Y. A guide to visualizing the spatial epigenome with super-resolution microscopy. FEBS J 2019; 286:3095-3109. [PMID: 31127980 DOI: 10.1111/febs.14938] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2018] [Revised: 03/24/2019] [Accepted: 05/23/2019] [Indexed: 12/28/2022]
Abstract
Genomic DNA in eukaryotic cells is tightly compacted with histone proteins into nucleosomes, which are further packaged into the higher-order chromatin structure. The physical structuring of chromatin is highly dynamic and regulated by a large number of epigenetic modifications in response to various environmental exposures, both in normal development and pathological processes such as aging and cancer. Higher-order chromatin structure has been indirectly inferred by conventional bulk biochemical assays on cell populations, which do not allow direct visualization of the spatial information of epigenomics (referred to as spatial epigenomics). With recent advances in super-resolution microscopy, the higher-order chromatin structure can now be visualized in vivo at an unprecedent resolution. This opens up new opportunities to study physical compaction of 3D chromatin structure in single cells, maintaining a well-preserved spatial context of tissue microenvironment. This review discusses the recent application of super-resolution fluorescence microscopy to investigate the higher-order chromatin structure of different epigenomic states. We also envision the synergistic integration of super-resolution microscopy and high-throughput genomic technologies for the analysis of spatial epigenomics to fully understand the genome function in normal biological processes and diseases.
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Affiliation(s)
- Jianquan Xu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
| | - Yang Liu
- Biomedical Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA, USA
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27
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Ma H, Xu J, Liu Y. WindSTORM: Robust online image processing for high-throughput nanoscopy. SCIENCE ADVANCES 2019; 5:eaaw0683. [PMID: 31032419 PMCID: PMC6486217 DOI: 10.1126/sciadv.aaw0683] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 03/07/2019] [Indexed: 05/03/2023]
Abstract
High-throughput nanoscopy becomes increasingly important for unraveling complex biological processes from a large heterogeneous cell population at a nanoscale resolution. High-density emitter localization combined with a large field of view and fast imaging frame rate is commonly used to achieve a high imaging throughput, but the image processing speed and the presence of heterogeneous background in the dense emitter scenario remain a bottleneck. Here, we present a simple non-iterative approach, referred to as WindSTORM, to achieve high-speed high-density emitter localization with robust performance for various image characteristics. We demonstrate that WindSTORM improves the computation speed by two orders of magnitude on CPU and three orders of magnitude upon GPU acceleration to realize online image processing, without compromising localization accuracy. Further, WindSTORM is highly robust to maximize the localization accuracy and minimize the image artifacts in the presence of nonuniform background. WindSTORM paves the way for next generation high-throughput nanoscopy.
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Affiliation(s)
- Hongqiang Ma
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Jianquan Xu
- Biomedical and Optical Imaging Laboratory, Departments of Medicine and Bioengineering, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Yang Liu
- Corresponding author. (H.M.); (Y.L.)
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28
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Abstract
Understanding the cellular basis of human health and disease requires the spatial resolution of microscopy and the molecular-level details provided by spectroscopy. This review highlights imaging methods at the intersection of microscopy and spectroscopy with applications in cell biology. Imaging methods are divided into three broad categories: fluorescence microscopy, label-free approaches, and imaging tools that can be applied to multiple imaging modalities. Just as these imaging methods allow researchers to address new biological questions, progress in biological sciences will drive the development of new imaging methods. We highlight four topics in cell biology that illustrate the need for new imaging tools: nanoparticle-cell interactions, intracellular redox chemistry, neuroscience, and the increasing use of spheroids and organoids. Overall, our goal is to provide a brief overview of individual imaging methods and highlight recent advances in the use of microscopy for cell biology.
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Affiliation(s)
- Joshua D Morris
- School of Science and Technology, Georgia Gwinnett College, Lawrenceville, Georgia 30043, USA
| | - Christine K Payne
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA;
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29
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MUNRO I, GARCÍA E, YAN M, GULDBRAND S, KUMAR S, KWAKWA K, DUNSBY C, NEIL M, FRENCH P. Accelerating single molecule localization microscopy through parallel processing on a high-performance computing cluster. J Microsc 2019; 273:148-160. [PMID: 30508256 PMCID: PMC6378585 DOI: 10.1111/jmi.12772] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2018] [Revised: 11/14/2018] [Accepted: 11/18/2018] [Indexed: 12/25/2022]
Abstract
Super-resolved microscopy techniques have revolutionized the ability to study biological structures below the diffraction limit. Single molecule localization microscopy (SMLM) techniques are widely used because they are relatively straightforward to implement and can be realized at relatively low cost, e.g. compared to laser scanning microscopy techniques. However, while the data analysis can be readily undertaken using open source or other software tools, large SMLM data volumes and the complexity of the algorithms used often lead to long image data processing times that can hinder the iterative optimization of experiments. There is increasing interest in high throughput SMLM, but its further development and application is inhibited by the data processing challenges. We present here a widely applicable approach to accelerating SMLM data processing via a parallelized implementation of ThunderSTORM on a high-performance computing (HPC) cluster and quantify the speed advantage for a four-node cluster (with 24 cores and 128 GB RAM per node) compared to a high specification (28 cores, 128 GB RAM, SSD-enabled) desktop workstation. This data processing speed can be readily scaled by accessing more HPC resources. Our approach is not specific to ThunderSTORM and can be adapted for a wide range of SMLM software. LAY DESCRIPTION: Optical microscopy is now able to provide images with a resolution far beyond the diffraction limit thanks to relatively new super-resolved microscopy (SRM) techniques, which have revolutionized the ability to study biological structures. One approach to SRM is to randomly switch on and off the emission of fluorescent molecules in an otherwise conventional fluorescence microscope. If only a sparse subset of the fluorescent molecules labelling a sample can be switched on at a time, then each emitter will be, on average, spaced further apart than the diffraction-limited resolution of the conventional microscope and the separate bright spots in the image corresponding to each emitter can be localised to high precision by finding the centre of each feature using a computer program. Thus, a precise map of the emitter positions can be recorded by sequentially mapping the localisation of different subsets of emitters as they are switched on and others switched off. Typically, this approach, described as single molecule localisation microscopy (SMLM), results in large image data sets that can take many minutes to hours to process, depending on the size of the field of view and whether the SMLM analysis employs a computationally-intensive iterative algorithm. Such a slow workflow makes it difficult to optimise experiments and to analyse large numbers of samples. Faster SMLM experiments would be generally useful and automated high throughput SMLM studies of arrays of samples, such as cells, could be applied to drug discovery and other applications. However, the time required to process the resulting data would be prohibitive on a normal computer. To address this, we have developed a method to run standard SMLM data analysis software tools in parallel on a high-performance computing cluster (HPC). This can be used to accelerate the analysis of individual SMLM experiments or it can be scaled to analyse high throughput SMLM data by extending it to run on an arbitrary number of HPC processors in parallel. In this paper we outline the design of our parallelised SMLM software for HPC and quantify the speed advantage when implementing it on four HPC nodes compared to a powerful desktop computer.
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Affiliation(s)
- I. MUNRO
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
| | - E. GARCÍA
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
| | - M. YAN
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
- Northwest Institute of Nuclear TechnologyXi'anShaanxiP.R. China
| | - S. GULDBRAND
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
| | - S. KUMAR
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
- The Francis Crick InstituteLondonU.K.
| | - K. KWAKWA
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
| | - C. DUNSBY
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
- Centre for PathologyImperial College LondonLondonU.K.
| | - M.A.A. NEIL
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
| | - P.M.W. FRENCH
- Photonics GroupPhysics Department, Imperial College LondonLondonU.K.
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cellSTORM-Cost-effective super-resolution on a cellphone using dSTORM. PLoS One 2019; 14:e0209827. [PMID: 30625170 PMCID: PMC6326471 DOI: 10.1371/journal.pone.0209827] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/12/2018] [Indexed: 01/12/2023] Open
Abstract
High optical resolution in microscopy usually goes along with costly hardware components, such as lenses, mechanical setups and cameras. Several studies proved that Single Molecular Localization Microscopy can be made affordable, relying on off-the-shelf optical components and industry grade CMOS cameras. Recent technological advantages have yielded consumer-grade camera devices with surprisingly good performance. The camera sensors of smartphones have benefited of this development. Combined with computing power smartphones provide a fantastic opportunity for “imaging on a budget”. Here we show that a consumer cellphone is capable of optical super-resolution imaging by (direct) Stochastic Optical Reconstruction Microscopy (dSTORM), achieving optical resolution better than 80 nm. In addition to the use of standard reconstruction algorithms, we used a trained image-to-image generative adversarial network (GAN) to reconstruct video sequences under conditions where traditional algorithms provide sub-optimal localization performance directly on the smartphone. We believe that “cellSTORM” paves the way to make super-resolution microscopy not only affordable but available due to the ubiquity of cellphone cameras.
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31
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Schermelleh L, Ferrand A, Huser T, Eggeling C, Sauer M, Biehlmaier O, Drummen GPC. Super-resolution microscopy demystified. Nat Cell Biol 2019; 21:72-84. [PMID: 30602772 DOI: 10.1038/s41556-018-0251-8] [Citation(s) in RCA: 540] [Impact Index Per Article: 108.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2018] [Accepted: 11/12/2018] [Indexed: 02/08/2023]
Abstract
Super-resolution microscopy (SRM) bypasses the diffraction limit, a physical barrier that restricts the optical resolution to roughly 250 nm and was previously thought to be impenetrable. SRM techniques allow the visualization of subcellular organization with unprecedented detail, but also confront biologists with the challenge of selecting the best-suited approach for their particular research question. Here, we provide guidance on how to use SRM techniques advantageously for investigating cellular structures and dynamics to promote new discoveries.
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Affiliation(s)
- Lothar Schermelleh
- Micron Oxford Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford, UK.
| | - Alexia Ferrand
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Christian Eggeling
- MRC Human Immunology Unit and Wolfson Imaging Centre Oxford, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Institute for Applied Optics, Friedrich-Schiller-University Jena & Leibniz Institute of Photonic Technology, Jena, Germany
| | - Markus Sauer
- Department of Biotechnology & Biophysics, Biocenter, Julius Maximilian University of Würzburg, Würzburg, Germany
| | - Oliver Biehlmaier
- Imaging Core Facility, Biozentrum, University of Basel, Basel, Switzerland
| | - Gregor P C Drummen
- Advanced Bio-Imaging Program, Bio&Nano Solutions‒LAB3BIO, Bielefeld, Germany.
- ICON-Europe.org, Exxilon Scientific Events, Steinhagen, Germany.
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32
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Gibbs DR, Kaur A, Megalathan A, Sapkota K, Dhakal S. Build Your Own Microscope: Step-By-Step Guide for Building a Prism-Based TIRF Microscope. Methods Protoc 2018; 1:mps1040040. [PMID: 31164580 PMCID: PMC6481079 DOI: 10.3390/mps1040040] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2018] [Revised: 10/31/2018] [Accepted: 10/31/2018] [Indexed: 01/09/2023] Open
Abstract
Prism-based total internal reflection fluorescence (pTIRF) microscopy is one of the most widely used techniques for the single molecule analysis of a vast range of samples including biomolecules, nanostructures, and cells, to name a few. It allows for excitation of surface bound molecules/particles/quantum dots via evanescent field of a confined region of space, which is beneficial not only for single molecule detection but also for analysis of single molecule dynamics and for acquiring kinetics data. However, there is neither a commercial microscope available for purchase nor a detailed guide dedicated for building this microscope. Thus far, pTIRF microscopes are custom-built with the use of a commercially available inverted microscope, which requires high level of expertise in selecting and handling sophisticated instrument-parts. To directly address this technology gap, here we describe a step-by-step guide on how to build and characterize a pTIRF microscope for in vitro single-molecule imaging, nanostructure analysis and other life sciences research.
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Affiliation(s)
- Dalton R Gibbs
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anisa Kaur
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Anoja Megalathan
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Kumar Sapkota
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
| | - Soma Dhakal
- Department of Chemistry, Virginia Commonwealth University, 1001 West Main Street, Richmond, VA 23284, USA.
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Nanometer-scale Multiplexed Super-Resolution Imaging with an Economic 3D-DNA-PAINT Microscope. Chemphyschem 2018; 19:3024-3034. [DOI: 10.1002/cphc.201800630] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Indexed: 01/08/2023]
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Intrinsic refractive index matched 3D dSTORM with two objectives: Comparison of detection techniques. Sci Rep 2018; 8:13343. [PMID: 30190491 PMCID: PMC6127109 DOI: 10.1038/s41598-018-31595-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 07/23/2018] [Indexed: 01/21/2023] Open
Abstract
We have built a setup for 3D single molecule localisation microscopy (SMLM) where a very high resolution is achieved by, firstly, the use of two objectives instead of one and, secondly, minimizing optical aberrations by refractive index matching with a glycerol-water mixture as immersion medium in conjunction with glycerol-immersion objectives. Multiple optical paths of the microscope allow to switch between astigmatic and interferometric localisation along the optical axis, thus enabling a direct comparison of the performance of these localisation methods.
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Flat-Field Super-Resolution Localization Microscopy with a Low-Cost Refractive Beam-Shaping Element. Sci Rep 2018; 8:5630. [PMID: 29618762 PMCID: PMC5884788 DOI: 10.1038/s41598-018-24052-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/14/2018] [Indexed: 11/08/2022] Open
Abstract
Super-resolution single-molecule localization microscopy, often referred to as PALM/STORM, works by ensuring that fewer than one fluorophore in a diffraction-limited volume is emitting at any one time, allowing the observer to infer that the emitter is located at the center of the point-spread function. This requires careful control over the incident light intensity in order to control the rate at which fluorophores are switched on; if too many fluorophores are activated, their point-spread functions overlap, which impedes efficient localization. If too few are activated, the imaging time is impractically long. There is therefore considerable recent interest in constructing so-called 'top-hat' illumination profiles that provide a uniform illumination over the whole field of view. We present the use of a single commercially-available low-cost refractive beamshaping element that can be retrofitted to almost any existing microscope; the illumination profile created by this element demonstrates a marked improvement in the power efficiency of dSTORM microscopy, as well as a significant reduction in the propensity for reconstruction artifacts, compared to conventional Gaussian illumination.
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36
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Babcock HP. Multiplane and Spectrally-Resolved Single Molecule Localization Microscopy with Industrial Grade CMOS cameras. Sci Rep 2018; 8:1726. [PMID: 29379074 PMCID: PMC5789017 DOI: 10.1038/s41598-018-19981-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2017] [Accepted: 01/04/2018] [Indexed: 01/04/2023] Open
Abstract
This work explores the use of industrial grade CMOS cameras for single molecule localization microscopy (SMLM). We show that industrial grade CMOS cameras approach the performance of scientific grade CMOS cameras at a fraction of the cost. This makes it more economically feasible to construct high-performance imaging systems with multiple cameras that are capable of a diversity of applications. In particular we demonstrate the use of industrial CMOS cameras for biplane, multiplane and spectrally resolved SMLM. We also provide open-source software for simultaneous control of multiple CMOS cameras and for the reduction of the movies that are acquired to super-resolution images.
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Affiliation(s)
- Hazen P Babcock
- Center for Advanced Imaging, Harvard University, Cambridge, MA, 02138, USA.
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37
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Characterization of an industry-grade CMOS camera well suited for single molecule localization microscopy - high performance super-resolution at low cost. Sci Rep 2017; 7:14425. [PMID: 29089524 PMCID: PMC5663701 DOI: 10.1038/s41598-017-14762-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/12/2017] [Indexed: 01/27/2023] Open
Abstract
Many commercial as well as custom-built fluorescence microscopes use scientific-grade cameras that represent a substantial share of the instrument's cost. This holds particularly true for super-resolution localization microscopy where high demands are placed especially on the detector with respect to sensitivity, noise, and also image acquisition speed. Here, we present and carefully characterize an industry-grade CMOS camera as a cost-efficient alternative to commonly used scientific cameras. Direct experimental comparison of these two detector types shows widely similar performance for imaging by single molecule localization microscopy (SMLM). Furthermore, high image acquisition speeds are demonstrated for the CMOS detector by ultra-fast SMLM imaging.
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