1
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Jin L, Liu J, Zhang H, Zhu Y, Yang H, Wang J, Zhang L, Kuang C, Ji B, Zhang J, Liu X, Xu Y. Deep learning permits imaging of multiple structures with the same fluorophores. Biophys J 2024:S0006-3495(24)00593-9. [PMID: 39233442 DOI: 10.1016/j.bpj.2024.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 07/03/2024] [Accepted: 09/03/2024] [Indexed: 09/06/2024] Open
Abstract
Fluorescence microscopy, which employs fluorescent tags to label and observe cellular structures and their dynamics, is a powerful tool for life sciences. However, due to the spectral overlap between different dyes, a limited number of structures can be separately labeled and imaged for live-cell applications. In addition, the conventional sequential channel imaging procedure is quite time consuming, as it needs to switch either different lasers or filters. Here, we propose a novel double-structure network (DBSN) that consists of multiple connected models, which can extract six distinct subcellular structures from three raw images with only two separate fluorescent labels. DBSN combines the intensity-balance model to compensate for uneven fluorescent labels for different structures and the structure-separation model to extract multiple different structures with the same fluorescent labels. Therefore, DBSN breaks the bottleneck of the existing technologies and holds immense potential applications in the field of cell biology.
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Affiliation(s)
- Luhong Jin
- School of Information Science and Technology, Hangzhou Normal University, Hangzhou, China; Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Jingfang Liu
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Heng Zhang
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Yunqi Zhu
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Haixu Yang
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China; Binjiang Institute of Zhejiang University, Hangzhou, China
| | - Jianhang Wang
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China
| | - Luhao Zhang
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China; Binjiang Institute of Zhejiang University, Hangzhou, China
| | - Cuifang Kuang
- State Key Laboratory of Extreme Photonics and Instrumentation, Department of Optical Engineering, Zhejiang University, Hangzhou, China
| | - Baohua Ji
- Institute of Biomechanics and Applications, Department of Engineering Mechanics, Zhejiang University, Hangzhou, China
| | - Ju Zhang
- School of Information Science and Technology, Hangzhou Normal University, Hangzhou, China
| | - Xu Liu
- State Key Laboratory of Extreme Photonics and Instrumentation, Department of Optical Engineering, Zhejiang University, Hangzhou, China
| | - Yingke Xu
- Department of Biomedical Engineering, MOE Key Laboratory of Biomedical Engineering, State Key Laboratory of Modern Optical Instrumentation, Zhejiang Provincial Key Laboratory of Cardio-Cerebral Vascular Detection Technology and Medicinal Effectiveness Appraisal, Zhejiang University, Hangzhou, China; Binjiang Institute of Zhejiang University, Hangzhou, China; Department of Endocrinology, Children's Hospital of Zhejiang University School of Medicine, National Clinical Research Center for Children's Health, Hangzhou, China.
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2
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Shroff H, Testa I, Jug F, Manley S. Live-cell imaging powered by computation. Nat Rev Mol Cell Biol 2024; 25:443-463. [PMID: 38378991 DOI: 10.1038/s41580-024-00702-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/10/2024] [Indexed: 02/22/2024]
Abstract
The proliferation of microscopy methods for live-cell imaging offers many new possibilities for users but can also be challenging to navigate. The prevailing challenge in live-cell fluorescence microscopy is capturing intra-cellular dynamics while preserving cell viability. Computational methods can help to address this challenge and are now shifting the boundaries of what is possible to capture in living systems. In this Review, we discuss these computational methods focusing on artificial intelligence-based approaches that can be layered on top of commonly used existing microscopies as well as hybrid methods that integrate computation and microscope hardware. We specifically discuss how computational approaches can improve the signal-to-noise ratio, spatial resolution, temporal resolution and multi-colour capacity of live-cell imaging.
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Affiliation(s)
- Hari Shroff
- Janelia Research Campus, Howard Hughes Medical Institute (HHMI), Ashburn, VA, USA
| | - Ilaria Testa
- Department of Applied Physics and Science for Life Laboratory, KTH Royal Institute of Technology, Stockholm, Sweden
| | - Florian Jug
- Fondazione Human Technopole (HT), Milan, Italy
| | - Suliana Manley
- Institute of Physics, School of Basic Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland.
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3
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Kalisvaart D, Hung ST, Smith CS. Quantifying the minimum localization uncertainty of image scanning localization microscopy. BIOPHYSICAL REPORTS 2024; 4:100143. [PMID: 38380223 PMCID: PMC10878846 DOI: 10.1016/j.bpr.2024.100143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/09/2023] [Accepted: 01/09/2024] [Indexed: 02/22/2024]
Abstract
Modulation enhanced single-molecule localization microscopy (meSMLM), where emitters are sparsely activated with sequentially applied patterned illumination, increases the localization precision over single-molecule localization microscopy (SMLM). The precision improvement of modulation enhanced SMLM is derived from retrieving the position of an emitter relative to individual illumination patterns, which adds to existing point spread function information from SMLM. Here, we introduce SpinFlux: modulation enhanced localization for spinning disk confocal microscopy. SpinFlux uses a spinning disk with pinholes in its illumination and emission paths, to sequentially illuminate regions in the sample during each measurement. The resulting intensity-modulated emission signal is analyzed for each individual pattern to localize emitters with improved precision. We derive a statistical image formation model for SpinFlux and we quantify the theoretical minimum localization uncertainty in terms of the Cramér-Rao lower bound. Using the theoretical minimum uncertainty, we compare SpinFlux to localization on Fourier reweighted image scanning microscopy reconstructions. We find that localization on image scanning microscopy reconstructions with Fourier reweighting ideally results in a global precision improvement of 2.1 over SMLM. When SpinFlux is used for sequential illumination with three patterns around the emitter position, the localization precision improvement over SMLM is twofold when patterns are focused around the emitter position. If four donut-shaped illumination patterns are used for SpinFlux, the maximum local precision improvement over SMLM is increased to 3.5. Localization of image scanning microscopy reconstructions thus has the largest potential for global improvements of the localization precision, where SpinFlux is the method of choice for local refinements.
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Affiliation(s)
- Dylan Kalisvaart
- Delft Center for Systems and Control, Delft University of Technology, Delft, the Netherlands
| | - Shih-Te Hung
- Delft Center for Systems and Control, Delft University of Technology, Delft, the Netherlands
| | - Carlas S. Smith
- Delft Center for Systems and Control, Delft University of Technology, Delft, the Netherlands
- Department of Imaging Physics, Delft University of Technology, Delft, the Netherlands
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4
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Flaxer E, Bram L, Flaxer A, Roichman Y, Ebenstein Y. Programmable comprehensive controller for multi-color 3D confocal spinning-disk image scanning microscope. Ultramicroscopy 2024; 257:113888. [PMID: 38086290 DOI: 10.1016/j.ultramic.2023.113888] [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: 09/15/2023] [Revised: 11/12/2023] [Accepted: 11/23/2023] [Indexed: 01/05/2024]
Abstract
This paper introduces a compact, portable, and highly accurate triggering control system for a 3D confocal spinning-disk image scanning microscope (CSD-ISM). Building upon on our previously published research, we expanded the hardware of the controller and synchronized it with a sub-micron translator which scans the object in the z-direction. As well as expanding the hardware, the software also was extended from previously published work similarly as it is stated for hardware while allowing full control over the 3D movement. We showed a clear and smooth 3D image made up of a collection of 2D images at different heights.
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Affiliation(s)
- Eli Flaxer
- AFEKA - Tel-Aviv Academic College of Engineering, Tel-Aviv 69107, Israel; School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel.
| | - Lanna Bram
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Alona Flaxer
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Yael Roichman
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
| | - Yuval Ebenstein
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, Tel-Aviv 69978, Israel
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5
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Li H, Liu G, Zhong Q, Chen SC. Pixel-reassigned line-scanning microscopy for fast volumetric super-resolution imaging. OPTICS EXPRESS 2024; 32:2347-2355. [PMID: 38297767 DOI: 10.1364/oe.507217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 12/21/2023] [Indexed: 02/02/2024]
Abstract
Super-resolution microscopy has revolutionized the field of biophotonics by revealing detailed 3D biological structures. Nonetheless, the technique is still largely limited by the low throughput and hampered by increased background signals for dense or thick biological specimens. In this paper, we present a pixel-reassigned continuous line-scanning microscope for large-scale high-speed 3D super-resolution imaging, which achieves an imaging resolution of 0.41 µm in the lateral direction, i.e., a 2× resolution enhancement from the raw images. Specifically, the recorded line images are first reassigned to the line-excitation center at each scanning position to enhance the resolution. Next, a modified HiLo algorithm is applied to reduce the background signals. Parametric models have been developed to simulate the imaging results of randomly distributed fluorescent beads. Imaging experiments were designed and performed to verify the predicted performance on various biological samples, which demonstrated an imaging speed of 3400 pixels/ms on millimeter-scale specimens. These results confirm the pixel-reassigned line-scanning microscopy is a facile and powerful method to realize large-area super-resolution imaging on thick or dense biological samples.
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6
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Hung ST, Kalisvaart D, Smith C. Image scanning microscopy: a vectorial physical optics analysis. OPTICS EXPRESS 2024; 32:1524-1539. [PMID: 38297702 DOI: 10.1364/oe.500957] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 11/30/2023] [Indexed: 02/02/2024]
Abstract
Image scanning microscopy (ISM) achieves resolution beyond the diffraction limit by a factor of 2. However, prior ISM research predominantly employs scalar diffraction theory, neglecting critical physical effects such as polarization, aberrations, and Stokes shift. This paper presents a comprehensive vectorial ISM point spread function (PSF) model that accounts for these phenomena. By considering the effect of polarization in emission and excitation paths, as well as aberrations and Stokes shift, our model provides a more accurate representation of ISM. We analyze the differences between scalar and vectorial theories in ISM and investigate the impact of pinhole size and aberration strength on resolution. At a numerical aperture of 1.2, the full width half maximum (FWHM) discrepancy between scalar and vectorial ISM PSFs can reach 45 nm, representing a 30% deviation from the vectorial model. Additionally, we explore multiphoton excitation in ISM and observe increased FWHM for 2-photon and 3-photon excitation compared to 1-photon excitation. The FWHM of the 2-photon excitation ISM PSF increases by 20% and the FWHM of the 3-photon excitation ISM PSF increases by 28% compared to the 1-photon excitation ISM. In addition, we found that the optimal sweep factor for 2-photon ISM is 1.22, and the optimal sweep factor of 3-photon ISM is 1.12 instead of the 2 predicted by the one-photon scalar ISM theory. Our work improves the understanding of ISM and contributes to its advancement as a high-resolution imaging technique.
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7
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Paul TC, Hagen G. Improving optical sectioning with spinning disk structured illumination microscopy. OPTICS EXPRESS 2023; 31:38831-38839. [PMID: 38017977 DOI: 10.1364/oe.499277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Accepted: 10/04/2023] [Indexed: 11/30/2023]
Abstract
A new fluorescence microscopy technique for optical sectioning was investigated. This technique combined Spinning Disk microscopy (SD) with Structured Illumination Microscopy (SIM), resulting in more background removal than either method. Spinning Disk Structured Illumination Microscopy (SD-SIM) resulted in higher signal-to-background ratios. The method detected and quantified a dendritic spine neck that was impossible to detect with either SIM or SD alone.
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8
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Yoon K, Han K, Tadesse K, Mandracchia B, Jia S. Simultaneous Multicolor Multifocal Scanning Microscopy. ACS PHOTONICS 2023; 10:3035-3041. [PMID: 37743934 PMCID: PMC10515623 DOI: 10.1021/acsphotonics.3c00205] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Indexed: 09/26/2023]
Abstract
Super-resolution fluorescence microscopy has revolutionized cell biology over the past decade, enabling the visualization of subcellular complexity with unparalleled clarity and detail. However, the rapid development of image-scanning-based super-resolution systems still restrains convenient access to commonly used instruments such as epi-fluorescence microscopes. Here, we present multifocal scanning microscopy (MSM) for super-resolution imaging with simultaneous multicolor acquisition and minimal instrumental complexity. MSM implements a stationary, interposed multifocal multicolor excitation by exploiting the motion of the specimens, realizing super-resolution microscopy through a general epi-fluorescence platform without compromising the image-scanning mechanism or inducing complex instrument alignment. The system is demonstrated with various phantom and biological specimens, and the results present effective resolution doubling, optical sectioning, and contrast enhancement. We anticipate MSM, as a highly accessible and compatible super-resolution technique, to offer a promising methodological pathway for broad cell biological discoveries.
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Affiliation(s)
- Kyungduck Yoon
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
- George
W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Keyi Han
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Kidan Tadesse
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Biagio Mandracchia
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
| | - Shu Jia
- Wallace
H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, Georgia 30332, United States
- Parker
H. Petit Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
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9
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Sheppard CJR, Castello M, Tortarolo G, Zunino A, Slenders E, Bianchini P, Vicidomini G, Diaspro A. Image scanning microscopy with a doughnut beam: signal strength and integrated intensity. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2023; 40:1612-1619. [PMID: 37707118 DOI: 10.1364/josaa.495984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 07/11/2023] [Indexed: 09/15/2023]
Abstract
We discuss the effects of image scanning microscopy using doughnut beam illumination on the properties of signal strength and integrated intensity. Doughnut beam illumination can give better optical sectioning and background rejection than Airy disk illumination. The outer pixels of a detector array give a signal from defocused regions, so digital processing of these (e.g., by simple subtraction) can further improve optical sectioning and background rejection from a single in-focus scan.
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10
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Phillips TA, Caprettini V, Aggarwal N, Marcotti S, Tetley R, Mao Y, Shaw T, Chiappini C, Parsons M, Cox S. A method for reproducible high-resolution imaging of 3D cancer cell spheroids. J Microsc 2023; 291:30-42. [PMID: 36639864 PMCID: PMC10953429 DOI: 10.1111/jmi.13169] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Revised: 01/08/2023] [Accepted: 01/09/2023] [Indexed: 01/15/2023]
Abstract
Multicellular tumour cell spheroids embedded within three-dimensional (3D) hydrogels or extracellular matrices (ECM) are widely used as models to study cancer growth and invasion. Standard methods to embed spheroids in 3D matrices result in random placement in space which limits the use of inverted fluorescence microscopy techniques, and thus the resolution that can be achieved to image molecular detail within the intact spheroid. Here, we leverage UV photolithography to microfabricate PDMS (polydimethylsiloxane) stamps that allow for generation of high-content, reproducible well-like structures in multiple different imaging chambers. Addition of multicellular tumour spheroids into stamped collagen structures allows for precise positioning of spheroids in 3D space for reproducible high-/super-resolution imaging. Embedded spheroids can be imaged live or fixed and are amenable to immunostaining, allowing for greater flexibility of experimental approaches. We describe the use of these spheroid imaging chambers to analyse cell invasion, cell-ECM interaction, ECM alignment, force-dependent intracellular protein dynamics and extension of fine actin-based protrusions with a variety of commonly used inverted microscope platforms. This method enables reproducible, high-/super-resolution live imaging of multiple tumour spheroids, that can be potentially extended to visualise organoids and other more complex 3D in vitro systems.
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Affiliation(s)
- Thomas A. Phillips
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Valeria Caprettini
- Centre for Craniofacial & Regenerative BiologyKing's College LondonLondonUK
| | - Nandini Aggarwal
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
- Department of Inflammation BiologySchool of Immunology & Microbial SciencesKing's College LondonLondonUK
| | - Stefania Marcotti
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Rob Tetley
- Laboratory for Molecular Cell Biology and Institute for the Physics of Living SystemsUniversity College LondonLondonUK
| | - Yanlan Mao
- Laboratory for Molecular Cell Biology and Institute for the Physics of Living SystemsUniversity College LondonLondonUK
| | - Tanya Shaw
- Department of Inflammation BiologySchool of Immunology & Microbial SciencesKing's College LondonLondonUK
| | - Ciro Chiappini
- Centre for Craniofacial & Regenerative BiologyKing's College LondonLondonUK
| | - Maddy Parsons
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
| | - Susan Cox
- Randall Centre for Cell and Molecular BiophysicsKing's College LondonLondonUK
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11
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Flaxer E, Flaxer A, Sapir M, Bram L, Roichman Y, Ebenstein Y. Portable low-cost and highly accurate programmable triggering controller for confocal spinning disk image scanning microscope. Ultramicroscopy 2023; 249:113736. [PMID: 37031478 DOI: 10.1016/j.ultramic.2023.113736] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 03/27/2023] [Accepted: 04/03/2023] [Indexed: 04/08/2023]
Abstract
This work presents a very low-cost and highly accurate alternative way of implementing triggering control for a confocal spinning-disk image scanning microscope (CSD-ISM). Instead of using the previously reported hig-cost field programmable gate array (FPGA), that connects to a computer by an internal PCIe bus, we implemented the controller using a simple, low-cost real-time digital signal controller (DSC) development kit that connects to a computer via an external USB channel. The overall time resolution of the controller is better than 10 nanoseconds. The DSC programming is implemented using the free software included in the development kit and no additional commercial software is required. The operation of the CSD-ISM is performed by a 32-bit 150 MHz processor using the software environment Micro-Manager, a popular open-source platform for microscopy. Since software is used to calculate all the necessary times, the output signal is almost limitless.
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Affiliation(s)
- Eli Flaxer
- AFEKA - Tel-Aviv Academic College of Engineering, 69107 Tel-Aviv, Israel; School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel.
| | - Alona Flaxer
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Moran Sapir
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Lanna Bram
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Yael Roichman
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
| | - Yuval Ebenstein
- School of Chemistry, The Sackler Faculty of Exact Sciences, Tel-Aviv University, 69978 Tel-Aviv, Israel
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12
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Mo Y, Wang K, Li L, Xing S, Ye S, Wen J, Duan X, Luo Z, Gou W, Chen T, Zhang YH, Guo C, Fan J, Chen L. Quantitative structured illumination microscopy via a physical model-based background filtering algorithm reveals actin dynamics. Nat Commun 2023; 14:3089. [PMID: 37248215 DOI: 10.1038/s41467-023-38808-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Accepted: 05/12/2023] [Indexed: 05/31/2023] Open
Abstract
Despite the prevalence of superresolution (SR) microscopy, quantitative live-cell SR imaging that maintains the completeness of delicate structures and the linearity of fluorescence signals remains an uncharted territory. Structured illumination microscopy (SIM) is the ideal tool for live-cell SR imaging. However, it suffers from an out-of-focus background that leads to reconstruction artifacts. Previous post hoc background suppression methods are prone to human bias, fail at densely labeled structures, and are nonlinear. Here, we propose a physical model-based Background Filtering method for living cell SR imaging combined with the 2D-SIM reconstruction procedure (BF-SIM). BF-SIM helps preserve intricate and weak structures down to sub-70 nm resolution while maintaining signal linearity, which allows for the discovery of dynamic actin structures that, to the best of our knowledge, have not been previously monitored.
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Affiliation(s)
- Yanquan Mo
- State Key Laboratory of Membrane Biology, Center for Life Sciences, College of Future Technology, Peking University, Beijing, 100871, China
| | - Kunhao Wang
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Liuju Li
- State Key Laboratory of Membrane Biology, Center for Life Sciences, College of Future Technology, Peking University, Beijing, 100871, China
| | - Shijia Xing
- State Key Laboratory of Membrane Biology, Center for Life Sciences, College of Future Technology, Peking University, Beijing, 100871, China
| | - Shouhua Ye
- Guangzhou Computational Super-resolution Biotech Co., Ltd, Guangzhou, 510535, China
| | - Jiayuan Wen
- Guangzhou Computational Super-resolution Biotech Co., Ltd, Guangzhou, 510535, China
| | - Xinxin Duan
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Ziying Luo
- Guangzhou Computational Super-resolution Biotech Co., Ltd, Guangzhou, 510535, China
| | - Wen Gou
- Chongqing Key Laboratory of Image Cognition, College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China
| | - Tongsheng Chen
- Key Laboratory of Laser Life Science, Ministry of Education, College of Biophotonics, South China Normal University, Guangzhou, 510631, China
| | - Yu-Hui Zhang
- Britton Chance Center and MOE Key Laboratory for Biomedical Photonics, Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China
| | - Changliang Guo
- State Key Laboratory of Membrane Biology, Center for Life Sciences, College of Future Technology, Peking University, Beijing, 100871, China
| | - Junchao Fan
- Chongqing Key Laboratory of Image Cognition, College of Computer Science and Technology, Chongqing University of Posts and Telecommunications, Chongqing, 400065, China.
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Center for Life Sciences, College of Future Technology, Peking University, Beijing, 100871, China.
- PKU-IDG/McGovern Institute for Brain Research, Beijing, 100871, China.
- Beijing Academy of Artificial Intelligence, Beijing, 100871, China.
- National Biomedical Imaging Center, Beijing, 100871, China.
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13
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Deschamps J, Kieser C, Hoess P, Deguchi T, Ries J. MicroFPGA: An affordable FPGA platform for microscope control. HARDWAREX 2023; 13:e00407. [PMID: 36875260 PMCID: PMC9982678 DOI: 10.1016/j.ohx.2023.e00407] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Modern microscopy relies increasingly on microscope automation to improve throughput, ensure reproducibility or observe rare events. Automation requires computer control of the important elements of the microscope. Furthermore, optical elements that are usually fixed or manually movable can be placed on electronically-controllable elements. In most cases, a central electronics board is necessary to generate the control signals they require and to communicate with the computer. For such tasks, Arduino microcontrollers are widely used due to their low cost and programming entry barrier. However, they are limiting in their performance for applications that require high-speed or multiple parallel processes. Field programmable gate arrays (FPGA) are the perfect technology for high-speed microscope control, as they are capable of processing signals in parallel and with high temporal precision. While plummeting prices made the technology available to consumers, a major hurdle remaining is the complex languages used to configure them. In this work, we used an affordable FPGA, delivered with an open-source and friendly-to-use programming language, to create a versatile microscope control platform called MicroFPGA. It is capable of synchronously triggering cameras and multiple lasers following complex patterns, as well as generating various signals used to control microscope elements such as filter wheels, servomotor stages, flip-mirrors, laser power or acousto-optic modulators. MicroFPGA is open-source and we provide online Micro-Manager, Java, Python and LabVIEW libraries, together with blueprints and tutorials.
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Key Words
- (s) CMOS, (scientific) complementary metal–oxide–semiconductor
- ACB, analog conversion board
- AOM, acousto-optic modulator
- AOTF, acousto-optic tunable filter
- AOTF-CB, AOTF conversion board
- Automation
- BOM, bill of materials
- EMCCD, electron multiplying charge-coupled device
- Electronics
- FPGA
- FPGA, field-programmable gate array
- GND, ground
- HDL, hardware description language
- I/O, input/output
- Microscopy
- PWM, pulse-width modulation
- SCB, signal conversion board
- SDB, servo distribution board
- Synchronization
- TTL, transistor-transistor logic
- Triggering
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Affiliation(s)
- Joran Deschamps
- Computational Biology Center, Fondazione Human Technopole, Milan, Italy
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Christian Kieser
- Electronics Workshop, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Philipp Hoess
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Takahiro Deguchi
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
| | - Jonas Ries
- Cell Biology and Biophysics Unit, European Molecular Biology Laboratory, Heidelberg, Germany
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14
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Luo T, Yuan J, Chang J, Dai Y, Gong H, Luo Q, Yang X. Resolution and uniformity improvement of parallel confocal microscopy based on microlens arrays and a spatial light modulator. OPTICS EXPRESS 2023; 31:4537-4552. [PMID: 36785419 DOI: 10.1364/oe.478820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2022] [Accepted: 01/02/2023] [Indexed: 06/18/2023]
Abstract
In traditional fluorescence microscopy, it is hard to achieve a large uniform imaging field with high resolution. In this manuscript, we developed a confocal fluorescence microscope combining the microlens array with spatial light modulator to address this issue. In our system, a multi-spot array generated by a spatial light modulator passes through the microlens array to form an optical probe array. Then multi-spot adaptive pixel-reassignment method for image scanning microscopy (MAPR-ISM) will be introduced in this parallelized imaging to improve spatial resolution. To generate a uniform image, we employ an optimized double weighted Gerchberg-Saxton algorithm (ODWGS) using signal feedback from the camera. We have built a prototype system with a FOV of 3.5 mm × 3.5 mm illuminated by 2500 confocal points. The system provides a lateral resolution of ∼0.82 µm with ∼1.6 times resolution enhancement after ISM processing. And the nonuniformity across the whole imaging field is 3%. Experimental results of fluorescent beads, mouse brain slices and melanoma slices are presented to validate the applicability and effectiveness of our system.
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15
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He Y, Yao Y, He Y, Huang Z, Luo F, Zhang C, Qi D, Jia T, Wang Z, Sun Z, Yuan X, Zhang S. Surpassing the resolution limitation of structured illumination microscopy by an untrained neural network. BIOMEDICAL OPTICS EXPRESS 2023; 14:106-117. [PMID: 36698670 PMCID: PMC9842007 DOI: 10.1364/boe.479621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 12/01/2022] [Accepted: 12/01/2022] [Indexed: 06/17/2023]
Abstract
Structured illumination microscopy (SIM), as a flexible tool, has been widely applied to observing subcellular dynamics in live cells. It is noted, however, that SIM still encounters a problem with theoretical resolution limitation being only twice over wide-field microscopy, where imaging of finer biological structures and dynamics are significantly constrained. To surpass the resolution limitation of SIM, we developed an image postprocessing method to further improve the lateral resolution of SIM by an untrained neural network, i.e., deep resolution-enhanced SIM (DRE-SIM). DRE-SIM can further extend the spatial frequency components of SIM by employing the implicit priors based on the neural network without training datasets. The further super-resolution capability of DRE-SIM is verified by theoretical simulations as well as experimental measurements. Our experimental results show that DRE-SIM can achieve the resolution enhancement by a factor of about 1.4 compared with conventional SIM. Given the advantages of improving the lateral resolution while keeping the imaging speed, DRE-SIM will have a wide range of applications in biomedical imaging, especially when high-speed imaging mechanisms are integrated into the conventional SIM system.
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Affiliation(s)
- Yu He
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Contributed equally
| | - Yunhua Yao
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Contributed equally
| | - Yilin He
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhengqi Huang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Fan Luo
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, China
| | - Chonglei Zhang
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, China
| | - Dalong Qi
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Tianqing Jia
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Zhiyong Wang
- School of Mathematical Sciences, University of Electronic Science and Technology of China, Chengdu 611731, China
| | - Zhenrong Sun
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
| | - Xiaocong Yuan
- Nanophotonics Research Center, Shenzhen Key Laboratory of Micro-Scale Optical Information Technology, Institute of Microscale Optoelectronics, Shenzhen University, Shenzhen 518060, China
| | - Shian Zhang
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China
- Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan 030006, China
- Collaborative Innovation Center of Light Manipulations and Applications, Shandong Normal University, Jinan 250358, China
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16
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Su C, Gao Y, Zhou Y, Sun Y, Yan C, Yin H, Xiong B. AutoDeconJ: a GPU-accelerated ImageJ plugin for 3D light-field deconvolution with optimal iteration numbers predicting. Bioinformatics 2022; 39:6849514. [PMID: 36440906 PMCID: PMC9805591 DOI: 10.1093/bioinformatics/btac760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Revised: 10/25/2022] [Accepted: 11/24/2022] [Indexed: 11/30/2022] Open
Abstract
MOTIVATION Light-field microscopy (LFM) is a compact solution to high-speed 3D fluorescence imaging. Usually, we need to do 3D deconvolution to the captured raw data. Although there are deep neural network methods that can accelerate the reconstruction process, the model is not universally applicable for all system parameters. Here, we develop AutoDeconJ, a GPU-accelerated ImageJ plugin for 4.4× faster and more accurate deconvolution of LFM data. We further propose an image quality metric for the deconvolution process, aiding in automatically determining the optimal number of iterations with higher reconstruction accuracy and fewer artifacts. RESULTS Our proposed method outperforms state-of-the-art light-field deconvolution methods in reconstruction time and optimal iteration numbers prediction capability. It shows better universality of different light-field point spread function (PSF) parameters than the deep learning method. The fast, accurate and general reconstruction performance for different PSF parameters suggests its potential for mass 3D reconstruction of LFM data. AVAILABILITY AND IMPLEMENTATION The codes, the documentation and example data are available on an open source at: https://github.com/Onetism/AutoDeconJ.git. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Changqing Su
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai 264209, China,National Engineering Laboratory for Video Technology (NELVT), Peking University, Beijing 100871, China
| | - Yuhan Gao
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - You Zhou
- School of Electronic Science and Engineering, Nanjing University, Nanjing 210023, China
| | - Yaoqi Sun
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Chenggang Yan
- School of Mechanical, Electrical & Information Engineering, Shandong University, Weihai 264209, China,Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Haibing Yin
- Lishui Institute of Hangzhou Dianzi University, Hangzhou 323000, China
| | - Bo Xiong
- To whom correspondence should be addressed.
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17
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Proteomic mapping and optogenetic manipulation of membrane contact sites. Biochem J 2022; 479:1857-1875. [PMID: 36111979 PMCID: PMC9555801 DOI: 10.1042/bcj20220382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Revised: 08/31/2022] [Accepted: 09/01/2022] [Indexed: 11/17/2022]
Abstract
Membrane contact sites (MCSs) mediate crucial physiological processes in eukaryotic cells, including ion signaling, lipid metabolism, and autophagy. Dysregulation of MCSs is closely related to various diseases, such as type 2 diabetes mellitus (T2DM), neurodegenerative diseases, and cancers. Visualization, proteomic mapping and manipulation of MCSs may help the dissection of the physiology and pathology MCSs. Recent technical advances have enabled better understanding of the dynamics and functions of MCSs. Here we present a summary of currently known functions of MCSs, with a focus on optical approaches to visualize and manipulate MCSs, as well as proteomic mapping within MCSs.
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18
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Willig KI. In vivo super-resolution of the brain - How to visualize the hidden nanoplasticity? iScience 2022; 25:104961. [PMID: 36093060 PMCID: PMC9449647 DOI: 10.1016/j.isci.2022.104961] [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: 11/15/2022] Open
Abstract
Super-resolution fluorescence microscopy has entered most biological laboratories worldwide and its benefit is undisputable. Its application to brain imaging, for example in living mice, enables the study of sub-cellular structural plasticity and brain function directly in a living mammal. The demands of brain imaging on the different super-resolution microscopy techniques (STED, RESOLFT, SIM, ISM) and labeling strategies are discussed here as well as the challenges of the required cranial window preparation. Applications of super-resolution in the anesthetized mouse brain enlighten the stability and plasticity of synaptic nanostructures. These studies show the potential of in vivo super-resolution imaging and justify its application more widely in vivo to investigate the role of nanostructures in memory and learning.
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Affiliation(s)
- Katrin I Willig
- Group of Optical Nanoscopy in Neuroscience, Max Planck Institute for Multidisciplinary Sciences, City Campus, Göttingen, Germany
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19
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Kent RS, Briggs EM, Colon BL, Alvarez C, Silva Pereira S, De Niz M. Paving the Way: Contributions of Big Data to Apicomplexan and Kinetoplastid Research. Front Cell Infect Microbiol 2022; 12:900878. [PMID: 35734575 PMCID: PMC9207352 DOI: 10.3389/fcimb.2022.900878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/06/2022] [Indexed: 11/13/2022] Open
Abstract
In the age of big data an important question is how to ensure we make the most out of the resources we generate. In this review, we discuss the major methods used in Apicomplexan and Kinetoplastid research to produce big datasets and advance our understanding of Plasmodium, Toxoplasma, Cryptosporidium, Trypanosoma and Leishmania biology. We debate the benefits and limitations of the current technologies, and propose future advancements that may be key to improving our use of these techniques. Finally, we consider the difficulties the field faces when trying to make the most of the abundance of data that has already been, and will continue to be, generated.
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Affiliation(s)
- Robyn S. Kent
- Department of Microbiology and Molecular Genetics, University of Vermont, Burlington, VT, United States
| | - Emma M. Briggs
- Institute for Immunology and Infection Research, School of Biological Sciences, University Edinburgh, Edinburgh, United Kingdom
- Wellcome Centre for Integrative Parasitology, Institute of Infection, Immunity and Inflammation, University of Glasgow, Glasgow, United Kingdom
| | - Beatrice L. Colon
- Wellcome Centre for Anti-Infectives Research, Division of Biological Chemistry and Drug Discovery, School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Catalina Alvarez
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Sara Silva Pereira
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
| | - Mariana De Niz
- Instituto de Medicina Molecular João Lobo Antunes, Faculdade de Medicina da Universidade de Lisboa, Lisboa, Portugal
- Institut Pasteur, Paris, France
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20
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Wang H, Lachmann R, Marsikova B, Heintzmann R, Diederich B. UCsim2: two-dimensionally structured illumination microscopy using UC2. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20200148. [PMID: 35152763 DOI: 10.1098/rsta.2020.0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Accepted: 04/07/2021] [Indexed: 06/14/2023]
Abstract
State-of-the-art microscopy techniques enable the imaging of sub-diffraction barrier biological structures at the price of high costs or a lack of transparency. We try to reduce some of these barriers by presenting a super-resolution upgrade to our recently presented open-source optical toolbox UC2. Our new injection moulded parts allow larger builds with higher precision. The 4× lower manufacturing tolerance compared to three-dimensional printing makes assemblies more reproducible. By adding consumer-grade available open-source hardware such as digital mirror devices and laser projectors, we demonstrate a compact three-dimensional multimodal setup that combines image scanning microscopy and structured illumination microscopy. We demonstrate a gain in resolution and optical sectioning using the two different modes compared to the widefield limit by imaging Alexa Fluor ® 647- and Silicon Rhodamine-stained HeLa cells. We compare different objective lenses and by sharing the designs and manuals of our setup, we make super-resolution imaging available to everyone. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
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Affiliation(s)
- Haoran Wang
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Jena, Germany
| | - René Lachmann
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Barbora Marsikova
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Jena, Germany
- Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Benedict Diederich
- Leibniz Institute of Photonic Technology, Albert-Einstein-Straße 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Jena, Germany
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21
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Sparse deconvolution improves the resolution of live-cell super-resolution fluorescence microscopy. Nat Biotechnol 2022; 40:606-617. [PMID: 34782739 DOI: 10.1038/s41587-021-01092-2] [Citation(s) in RCA: 95] [Impact Index Per Article: 47.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 09/10/2021] [Indexed: 02/07/2023]
Abstract
A main determinant of the spatial resolution of live-cell super-resolution (SR) microscopes is the maximum photon flux that can be collected. To further increase the effective resolution for a given photon flux, we take advantage of a priori knowledge about the sparsity and continuity of biological structures to develop a deconvolution algorithm that increases the resolution of SR microscopes nearly twofold. Our method, sparse structured illumination microscopy (Sparse-SIM), achieves ~60-nm resolution at a frame rate of up to 564 Hz, allowing it to resolve intricate structures, including small vesicular fusion pores, ring-shaped nuclear pores formed by nucleoporins and relative movements of inner and outer mitochondrial membranes in live cells. Sparse deconvolution can also be used to increase the three-dimensional resolution of spinning-disc confocal-based SIM, even at low signal-to-noise ratios, which allows four-color, three-dimensional live-cell SR imaging at ~90-nm resolution. Overall, sparse deconvolution will be useful to increase the spatiotemporal resolution of live-cell fluorescence microscopy.
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22
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Zhang B, Sun X, Yang H, Guo C, Wu B, Tan J, Wang W. Simulation-driven learning: a deep learning approach for image scanning microscopy via physical imaging models. OPTICS EXPRESS 2022; 30:11848-11860. [PMID: 35473120 DOI: 10.1364/oe.450429] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 03/15/2022] [Indexed: 06/14/2023]
Abstract
Image reconstruction based on deep learning has become an effective tool in fluorescence microscopy. Most deep learning reconstruction methods ignore the mechanism of the imaging process where a large number of datasets are required. In addition, a lot of time is spent solving the aliasing problem from multi-scaled image pairs for data pre-processing. Here we demonstrate an improved generative adversarial network for image scanning microscopy (ISM) that can be trained by simulation data and has good generalization. Based on physical imaging models, this method can generate matching image pairs from simulation images and uses them as datasets for network training, without capturing a large number of real ISM images and avoiding image alignment preprocessing. Simulation and experimental results show that this simulation data-driven method improves the imaging quality of conventional microscopic images and reduces the cost of experiments. This method provides inspiration for optimizing network generalizability of the deep learning network.
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23
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Maltan L, Andova AM, Derler I. The Role of Lipids in CRAC Channel Function. Biomolecules 2022; 12:biom12030352. [PMID: 35327543 PMCID: PMC8944985 DOI: 10.3390/biom12030352] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/12/2022] [Accepted: 02/20/2022] [Indexed: 11/28/2022] Open
Abstract
The composition and dynamics of the lipid membrane define the physical properties of the bilayer and consequently affect the function of the incorporated membrane transporters, which also applies for the prominent Ca2+ release-activated Ca2+ ion channel (CRAC). This channel is activated by receptor-induced Ca2+ store depletion of the endoplasmic reticulum (ER) and consists of two transmembrane proteins, STIM1 and Orai1. STIM1 is anchored in the ER membrane and senses changes in the ER luminal Ca2+ concentration. Orai1 is the Ca2+-selective, pore-forming CRAC channel component located in the plasma membrane (PM). Ca2+ store-depletion of the ER triggers activation of STIM1 proteins, which subsequently leads to a conformational change and oligomerization of STIM1 and its coupling to as well as activation of Orai1 channels at the ER-PM contact sites. Although STIM1 and Orai1 are sufficient for CRAC channel activation, their efficient activation and deactivation is fine-tuned by a variety of lipids and lipid- and/or ER-PM junction-dependent accessory proteins. The underlying mechanisms for lipid-mediated CRAC channel modulation as well as the still open questions, are presented in this review.
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24
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Kratz J, Geisler C, Egner A. ISM-assisted tomographic STED microscopy. OPTICS EXPRESS 2022; 30:939-956. [PMID: 35209272 DOI: 10.1364/oe.445441] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 12/23/2021] [Indexed: 06/14/2023]
Abstract
Stimulated emission depletion (STED) microscopy theoretically provides unlimited resolution. However, in practice the achievable resolution in biological samples is essentially limited by photobleaching. One method which overcomes this problem is tomographic STED (tomoSTED) microscopy. In tomoSTED microscopy, one-dimensional depletion patterns facing in different directions are successively applied in order to acquire a highly-resolved image in two dimensions. In this context, the number of addressed directions depends on the desired angular homogeneity of the point spread function or the optical transfer function and thus on the resolution increase as compared to diffraction-limited imaging. At a reasonable angular homogeneity the light dose and thus bleaching can be reduced, as compared to conventional STED microscopy. Here, we propose and demonstrate for the first time, to our knowledge, that the number of required depletion pattern orientations can be reduced by combining tomoSTED microscopy with the concept of image scanning microscopy (ISM). With our realization of an ISM-tomoSTED microscope, we show that approximately a factor of 2 lower number of orientations are required to achieve the same resolution and image quality as in tomoSTED microscopy.
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25
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Saavedra G, Gimeno-Gómez A, Martínez-Corral M, Sola J, Sánchez-Ortiga E. Three-dimensional imaging through patterned type-1 microscopy. OPTICS EXPRESS 2022; 30:511-521. [PMID: 35201227 DOI: 10.1364/oe.443895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Accepted: 12/01/2021] [Indexed: 06/14/2023]
Abstract
We report a scanning non-confocal fluorescence microscopy scheme that provides images with optical sectioning and with a lateral resolution that surpasses by a factor of two the diffraction resolution limit. This technique is based on the type-1 microscopy concept combined with patterned illumination. The method does not require the application of phase-shifting or post-processing algorithms and provides artifact-free superresolved 3D images. We have validated the theory by means of experimental data.
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26
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Xiong B, Zhu T, Xiang Y, Li X, Yu J, Jiang Z, Niu Y, Jiang D, Zhang X, Fang L, Wu J, Dai Q. Mirror-enhanced scanning light-field microscopy for long-term high-speed 3D imaging with isotropic resolution. LIGHT, SCIENCE & APPLICATIONS 2021; 10:227. [PMID: 34737265 PMCID: PMC8568963 DOI: 10.1038/s41377-021-00665-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 10/05/2021] [Accepted: 10/18/2021] [Indexed: 05/05/2023]
Abstract
Various biological behaviors can only be observed in 3D at high speed over the long term with low phototoxicity. Light-field microscopy (LFM) provides an elegant compact solution to record 3D information in a tomographic manner simultaneously, which can facilitate high photon efficiency. However, LFM still suffers from the missing-cone problem, leading to degraded axial resolution and ringing effects after deconvolution. Here, we propose a mirror-enhanced scanning LFM (MiSLFM) to achieve long-term high-speed 3D imaging at super-resolved axial resolution with a single objective, by fully exploiting the extended depth of field of LFM with a tilted mirror placed below samples. To establish the unique capabilities of MiSLFM, we performed extensive experiments, we observed various organelle interactions and intercellular interactions in different types of photosensitive cells under extremely low light conditions. Moreover, we demonstrated that superior axial resolution facilitates more robust blood cell tracking in zebrafish larvae at high speed.
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Affiliation(s)
- Bo Xiong
- Department of Automation, Tsinghua University, Beijing, 100084, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China
| | - Tianyi Zhu
- Department of Automation, Tsinghua University, Beijing, 100084, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China
| | - Yuhan Xiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xiaopeng Li
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Jinqiang Yu
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Zheng Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yihan Niu
- Department of Automation, Tsinghua University, Beijing, 100084, China
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China
| | - Dong Jiang
- State Key Laboratory of Membrane Biology, Tsinghua University-Peking University Joint Centre for Life Sciences, Beijing Frontier Research Center for Biological Structure, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xu Zhang
- Beijing Institute of Collaborative Innovation, Beijing, 100094, China
| | - Lu Fang
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China.
- Department of Electronic Engineering, Tsinghua University, Beijing, 100084, China.
| | - Jiamin Wu
- Department of Automation, Tsinghua University, Beijing, 100084, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China.
| | - Qionghai Dai
- Department of Automation, Tsinghua University, Beijing, 100084, China.
- Institute for Brain and Cognitive Sciences, Tsinghua University, Beijing, 100084, China.
- Beijing Laboratory of Brain and Cognitive Intelligence, Beijing Municipal Education Commission, Beijing, 100084, China.
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27
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The Development of Microscopy for Super-Resolution: Confocal Microscopy, and Image Scanning Microscopy. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11198981] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Optical methods of super-resolution microscopy, such as confocal microscopy, structured illumination, nonlinear microscopy, and image scanning microscopy are reviewed. These methods avoid strong invasive interaction with a sample, allowing the observation of delicate biological samples. The meaning of resolution and the basic principles and different approaches to superresolution are discussed.
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28
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Sheppard CJR, Castello M, Tortarolo G, Slenders E, Deguchi T, Koho SV, Bianchini P, Vicidomini G, Diaspro A. Pixel reassignment in image scanning microscopy with a doughnut beam: example of maximum likelihood restoration. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2021; 38:1075-1084. [PMID: 34263763 DOI: 10.1364/josaa.426473] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/06/2021] [Indexed: 06/13/2023]
Abstract
In image scanning microscopy, the pinhole of a confocal microscope is replaced by a detector array. The point spread function for each detector element can be interpreted as the probability density function of the signal, the peak giving the most likely origin. This thus allows a form of maximum likelihood restoration, and compensation for aberrations, with similarities to adaptive optics. As an example of an aberration, we investigate theoretically and experimentally illumination with a vortex doughnut beam. After reassignment and summation over the detector array, the point spread function is compact, and the resolution and signal level higher than in a conventional microscope.
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Sheppard CJR. Structured illumination microscopy and image scanning microscopy: a review and comparison of imaging properties. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200154. [PMID: 33896206 DOI: 10.1098/rsta.2020.0154] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/10/2020] [Indexed: 05/19/2023]
Abstract
Structured illumination microscopy and image scanning microscopy are two microscopical tech- niques, rapidly increasing in practical application, that can result in improvement in transverse spatial resolution, and/or improvement in axial imaging performance. The history and principles of these techniques are reviewed, and the imaging properties of the two methods compared. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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MESH Headings
- Animals
- Humans
- Image Processing, Computer-Assisted/methods
- Image Processing, Computer-Assisted/statistics & numerical data
- Imaging, Three-Dimensional/methods
- Imaging, Three-Dimensional/statistics & numerical data
- Light
- Microscopy, Confocal/methods
- Microscopy, Confocal/statistics & numerical data
- Microscopy, Fluorescence/methods
- Microscopy, Fluorescence/statistics & numerical data
- Microscopy, Fluorescence, Multiphoton/methods
- Microscopy, Fluorescence, Multiphoton/statistics & numerical data
- Optical Phenomena
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Affiliation(s)
- Colin J R Sheppard
- Nanoscopy and NIC@IIT, Istituto Italiano di Tecnologia, Via Enrico Melen, 83 Edificio B, 16152 Genova, Italy
- Molecular Horizons, School of Chemistry and Molecular Biology, University of Wollongong, Wollongong 2522, New South Wales, Australia
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30
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Pilger C, Pospíšil J, Müller M, Ruoff M, Schütte M, Spiecker H, Huser T. Super-resolution fluorescence microscopy by line-scanning with an unmodified two-photon microscope. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200300. [PMID: 33896201 PMCID: PMC8072199 DOI: 10.1098/rsta.2020.0300] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Accepted: 12/20/2020] [Indexed: 05/19/2023]
Abstract
Fluorescence-based microscopy as one of the standard tools in biomedical research benefits more and more from super-resolution methods, which offer enhanced spatial resolution allowing insights into new biological processes. A typical drawback of using these methods is the need for new, complex optical set-ups. This becomes even more significant when using two-photon fluorescence excitation, which offers deep tissue imaging and excellent z-sectioning. We show that the generation of striped-illumination patterns in two-photon laser scanning microscopy can readily be exploited for achieving optical super-resolution and contrast enhancement using open-source image reconstruction software. The special appeal of this approach is that even in the case of a commercial two-photon laser scanning microscope no optomechanical modifications are required to achieve this modality. Modifying the scanning software with a custom-written macro to address the scanning mirrors in combination with rapid intensity switching by an electro-optic modulator is sufficient to accomplish the acquisition of two-photon striped-illumination patterns on an sCMOS camera. We demonstrate and analyse the resulting resolution improvement by applying different recently published image resolution evaluation procedures to the reconstructed filtered widefield and super-resolved images. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Christian Pilger
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Jakub Pospíšil
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
- Department of Radioelectronics, Faculty of Electrical Engineering, Czech Technical University in Prague, Technická 2, 166 27 Prague 6, Czech Republic
| | - Marcel Müller
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
| | - Martin Ruoff
- LaVision BioTec GmbH, Astastraße 14, 33617 Bielefeld, Germany
| | - Martin Schütte
- LaVision BioTec GmbH, Astastraße 14, 33617 Bielefeld, Germany
| | | | - Thomas Huser
- Biomolecular Photonics, Department of Physics, University of Bielefeld, Bielefeld, Germany
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31
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Siegel N, Brooker G. Single shot holographic super-resolution microscopy. OPTICS EXPRESS 2021; 29:15953-15968. [PMID: 34154169 DOI: 10.1364/oe.424175] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 04/29/2021] [Indexed: 06/13/2023]
Abstract
An exceptionally simple and versatile advance in super-resolution microscopy has been created by adding a new birefringent FINCH holographic lens system including an inexpensive uncooled CMOS camera to a standard microscope. Resolution, after only a single image capture, is equivalent to or better than other more complex popular methods such as SIM, Airyscan and a number of image scanning microscopy methods that boost resolution about two-fold. This new FINCH implementation uniquely works for any objective power and NA and is solid state, fast, and calibration-free. In addition to being as easy to operate and maintain as a standard fluorescence microscope, it can uniquely create super-resolved images with any type or wavelength of light including fluorescence, bioluminescence or reflected light because its principle depends only on emitted light from objects and requires no prior training or knowledge about the sample being imaged. This microscope technique increases the utility and availability of super-resolution microscopy for any user in any research lab.
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32
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Imaging of spine synapses using super-resolution microscopy. Anat Sci Int 2021; 96:343-358. [PMID: 33459976 DOI: 10.1007/s12565-021-00603-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/04/2021] [Indexed: 12/17/2022]
Abstract
Neuronal circuits in the neocortex and hippocampus are essential for higher brain functions such as motor learning and spatial memory. In the mammalian forebrain, most excitatory synapses of pyramidal neurons are formed on spines, which are tiny protrusions extending from the dendritic shaft. The spine contains specialized molecular machinery that regulates synaptic transmission and plasticity. Spine size correlates with the efficacy of synaptic transmission, and spine morphology affects signal transduction at the post-synaptic compartment. Plasticity-related changes in the structural and molecular organization of spine synapses are thought to underlie the cellular basis of learning and memory. Recent advances in super-resolution microscopy have revealed the molecular mechanisms of the nanoscale synaptic structures regulating synaptic transmission and plasticity in living neurons, which are difficult to investigate using electron microscopy alone. In this review, we summarize recent advances in super-resolution imaging of spine synapses and discuss the implications of nanoscale structures in the regulation of synaptic function, learning, and memory.
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33
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Yang Z, Samanta S, Yan W, Yu B, Qu J. Super-resolution Microscopy for Biological Imaging. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 3233:23-43. [PMID: 34053021 DOI: 10.1007/978-981-15-7627-0_2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Studying the ultra-fine structures and functions of the subcellular organelles and exploring the dynamic biological events in depth are the key issues in contemporary biological research. Fluorescence bio-imaging has been used to study cell biology for decades. However, the structures and functions of the subcellular organelles which fall under the diffraction limit are still not explored fully at a nanoscale level. Several super-resolution microscopy (SRM) techniques have been devised over the years which can be utilized to overcome diffraction limit. These techniques have opened a new window in biological research. However, SRM methods are highly vulnerable to the lack of appropriate fluorophores and other sophisticated technical considerations. Therefore, this chapter briefly summarizes the basic principles of various SRM methods which have been frequently utilized in biological imaging. The chapter not only gives an overview of the technical advantages and drawbacks about using different SRM techniques for bio-imaging applications but also briefly articulates the nitty-gritties of selecting a proper fluorescent probe for a specific SRM experiment with biological samples.
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Affiliation(s)
- Zhigang Yang
- Center for Biomedical Phonics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Soham Samanta
- Center for Biomedical Phonics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Wei Yan
- Center for Biomedical Phonics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Bin Yu
- Center for Biomedical Phonics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China
| | - Junle Qu
- Center for Biomedical Phonics, College of Physics and Optoelectronic Engineering, Shenzhen University, Shenzhen, China.
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34
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Zhang C, Zhang W, Yu B, Danying L, Qu J. Enhanced multifocal structured illumination microscopy with desired optical sectioning capability and lateral resolution improvement. OPTICS EXPRESS 2020; 28:37946-37957. [PMID: 33379618 DOI: 10.1364/oe.412489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Multifocal structured illumination microscopy (MSIM) can rapidly retrieve 3D structures of thick samples by using multi-spot excitation and detection. Although numerous super-resolution (SR) and optical sectioning (OS) methods have been introduced in this field, the existing OS-SR method in MSIM still has the difficulty in rejecting deep defocused light, which may lead to strong background signal in the retrieved results. To this end, an enhanced OS-SR method is proposed to simultaneously achieve the desired OS capability and significant resolution improvement in MSIM. The enhanced OS-SR image is obtained by combining the standard deviation image with the conventional OS-SR image in the frequency domain. The validity of the proposed method is demonstrated by simulation and experimental results.
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35
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Doubling the resolution of a confocal spinning-disk microscope using image scanning microscopy. Nat Protoc 2020; 16:164-181. [PMID: 33247283 DOI: 10.1038/s41596-020-00408-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 09/07/2020] [Indexed: 11/09/2022]
Abstract
Fluorescence microscopy has become an indispensable tool for cell biology. Recently, super-resolution methods have been developed to overcome the diffraction limit of light and have shown living cells in unprecedented detail. Often, these methods come at a high cost and with complexity in terms of instrumentation and sample preparation, thus calling for the development of low-cost, more accessible methods. We previously developed image scanning microscopy (ISM), which uses structured illumination to double the resolution and quadruple the contrast of a confocal microscope. Implementing this technique into a confocal spinning-disk (CSD) microscope allows recording ISM images with up to ~1 frame per second, making it ideal for imaging dynamic biological processes. Here we present a step-by-step protocol describing how to convert any existing commercial CSD microscope into a CSD-ISM, with only moderate changes to the hardware and at low cost. Operation of the CSD-ISM is realized with a field programmable gate array using the software environment Micro-Manager, a popular open-source platform for microscopy. The provided software ( https://projects.gwdg.de/projects/csdism-2020 ) takes care of all algorithmic complexities and numerical workload of the CSD-ISM, including hardware synchronization and image reconstruction. The hardware modifications described here result in a theoretical maximum increase in resolution of √2 ≈ 1.41, which can be further improved by deconvolution to obtain a theoretical maximum twofold increase. An existing CSD setup can be upgraded in ~3 d by anyone with basic knowledge in optics, electronics and microscopy software.
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36
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Sheppard CJR, Castello M, Tortarolo G, Slenders E, Deguchi T, Koho SV, Vicidomini G, Diaspro A. Image scanning microscopy with multiphoton excitation or Bessel beam illumination. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2020; 37:1639-1649. [PMID: 33104611 DOI: 10.1364/josaa.402048] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Accepted: 09/02/2020] [Indexed: 06/11/2023]
Abstract
Image scanning microscopy is a technique of confocal microscopy in which the confocal pinhole is replaced by a detector array, and the image is reconstructed most straightforwardly by pixel reassignment. In the fluorescence mode, the detector array collects most of the fluorescent light, so the signal-to-noise ratio is much improved compared with confocal microscopy with a small pinhole, while the resolution is improved compared with conventional fluorescence microscopy. Here we consider two cases in which the illumination and detection point spread functions are dissimilar: illumination with a Bessel beam and multiphoton microscopy. It has been shown previously that for Bessel beam illumination in image scanning microscopy with a large array, the imaging performance is degraded. On the other hand, it is also known that the resolution of confocal microscopy is improved by Bessel beam illumination. Here we analyze image scanning microscopy with Bessel beam illumination together with a small array and show that an improvement in transverse resolution (width of the point spread function) by a factor of 1.78 compared with a conventional fluorescence microscope can be obtained. We also examine the behavior of image scanning microscopy in two- or three-photon fluorescence and for two-photon excitation also with Bessel beam illumination. The combination of the optical sectioning effect of image scanning microscopy with multiphoton microscopy reduces background from the sample surface, which can increase penetration depth. For a detector array size of two Airy units, the resolution of two-photon image scanning microscopy is a factor 1.85 better and the peak of the point spread function 2.84 times higher than in nonconfocal two-photon fluorescence. The resolution of three-photon image scanning microscopy is a factor 2.10 better, and the peak of the point spread function is 3.77 times higher than in nonconfocal three-photon fluorescence. The resolution of two-photon image scanning microscopy with Bessel beam illumination is a factor 2.13 better than in standard two-photon fluorescence. Axial resolution and optical sectioning in two-photon or three-photon fluorescence are also improved by using the image scanning modality.
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37
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Mahecic D, Gambarotto D, Douglass KM, Fortun D, Banterle N, Ibrahim KA, Le Guennec M, Gönczy P, Hamel V, Guichard P, Manley S. Homogeneous multifocal excitation for high-throughput super-resolution imaging. Nat Methods 2020; 17:726-733. [PMID: 32572233 DOI: 10.1038/s41592-020-0859-z] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Accepted: 05/13/2020] [Indexed: 12/13/2022]
Abstract
Super-resolution microscopies have become an established tool in biological research. However, imaging throughput remains a main bottleneck in acquiring large datasets required for quantitative biology. Here we describe multifocal flat illumination for field-independent imaging (mfFIFI). By integrating mfFIFI into an instant structured illumination microscope (iSIM), we extend the field of view (FOV) to >100 × 100 µm2 while maintaining high-speed, multicolor, volumetric imaging at double the diffraction-limited resolution. We further extend the effective FOV by stitching adjacent images for fast live-cell super-resolution imaging of dozens of cells. Finally, we combine our flat-fielded iSIM with ultrastructure expansion microscopy to collect three-dimensional (3D) images of hundreds of centrioles in human cells, or thousands of purified Chlamydomonas reinhardtii centrioles, per hour at an effective resolution of ~35 nm. Classification and particle averaging of these large datasets enables 3D mapping of posttranslational modifications of centriolar microtubules, revealing differences in their coverage and positioning.
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Affiliation(s)
- Dora Mahecic
- Laboratory for Experimental Biophysics, Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. .,Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland.
| | - Davide Gambarotto
- Department of Cell Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Kyle M Douglass
- Laboratory for Experimental Biophysics, Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Denis Fortun
- ICube UMR 7357, CNRS, University of Strasbourg, Illkirch, France
| | - Niccoló Banterle
- Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Khalid A Ibrahim
- Laboratory for Experimental Biophysics, Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Maeva Le Guennec
- Department of Cell Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Pierre Gönczy
- Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland.,Swiss Institute for Experimental Cancer Research, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland
| | - Virginie Hamel
- Department of Cell Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Paul Guichard
- Department of Cell Biology, Sciences III, University of Geneva, Geneva, Switzerland
| | - Suliana Manley
- Laboratory for Experimental Biophysics, Institute of Physics, Swiss Federal Institute of Technology Lausanne (EPFL), Lausanne, Switzerland. .,Swiss National Centre for Competence in Research (NCCR) in Chemical Biology, University of Geneva, Geneva, Switzerland.
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38
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Koho SV, Slenders E, Tortarolo G, Castello M, Buttafava M, Villa F, Tcarenkova E, Ameloot M, Bianchini P, Sheppard CJR, Diaspro A, Tosi A, Vicidomini G. Two-photon image-scanning microscopy with SPAD array and blind image reconstruction. BIOMEDICAL OPTICS EXPRESS 2020; 11:2905-2924. [PMID: 32637232 DOI: 10.1101/563288] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 05/25/2023]
Abstract
Two-photon excitation (2PE) laser scanning microscopy is the imaging modality of choice when one desires to work with thick biological samples. However, its spatial resolution is poor, below confocal laser scanning microscopy. Here, we propose a straightforward implementation of 2PE image scanning microscopy (2PE-ISM) that, by leveraging our recently introduced single-photon avalanche diode (SPAD) array detector and a novel blind image reconstruction method, is shown to enhance the effective resolution, as well as the overall image quality of 2PE microscopy. With our adaptive pixel reassignment procedure ∼1.6 times resolution increase is maintained deep into thick semi-transparent samples. The integration of Fourier ring correlation based semi-blind deconvolution is shown to further enhance the effective resolution by a factor of ∼2 - and automatic background correction is shown to boost the image quality especially in noisy images. Most importantly, our 2PE-ISM implementation requires no calibration measurements or other input from the user, which is an important aspect in terms of day-to-day usability of the technique.
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Affiliation(s)
- Sami V Koho
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- University of Turku, Department of Cell Biology and Anatomy, Institute of Biomedicine and Medicity Research Laboratories, Laboratory of Biophysics, Turku, Finland
- These authors contributed equally to this work
| | - Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Hasselt University, Biomedical Research Institute (BIOMED), Diepenbeek, Belgium
- These authors contributed equally to this work
| | - Giorgio Tortarolo
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Informatiche, Bioingegneria, Robotica e Ingegneria dei Sistemi, University of Genoa, Italy
| | - Marco Castello
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mauro Buttafava
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Federica Villa
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Elena Tcarenkova
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- University of Turku, Department of Cell Biology and Anatomy, Institute of Biomedicine and Medicity Research Laboratories, Laboratory of Biophysics, Turku, Finland
| | - Marcel Ameloot
- Hasselt University, Biomedical Research Institute (BIOMED), Diepenbeek, Belgium
| | | | | | - Alberto Diaspro
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Fisica, University of Genoa, Genoa, Italy
| | - Alberto Tosi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
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39
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Koho SV, Slenders E, Tortarolo G, Castello M, Buttafava M, Villa F, Tcarenkova E, Ameloot M, Bianchini P, Sheppard CJR, Diaspro A, Tosi A, Vicidomini G. Two-photon image-scanning microscopy with SPAD array and blind image reconstruction. BIOMEDICAL OPTICS EXPRESS 2020; 11:2905-2924. [PMID: 32637232 PMCID: PMC7316014 DOI: 10.1364/boe.374398] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 05/07/2023]
Abstract
Two-photon excitation (2PE) laser scanning microscopy is the imaging modality of choice when one desires to work with thick biological samples. However, its spatial resolution is poor, below confocal laser scanning microscopy. Here, we propose a straightforward implementation of 2PE image scanning microscopy (2PE-ISM) that, by leveraging our recently introduced single-photon avalanche diode (SPAD) array detector and a novel blind image reconstruction method, is shown to enhance the effective resolution, as well as the overall image quality of 2PE microscopy. With our adaptive pixel reassignment procedure ∼1.6 times resolution increase is maintained deep into thick semi-transparent samples. The integration of Fourier ring correlation based semi-blind deconvolution is shown to further enhance the effective resolution by a factor of ∼2 - and automatic background correction is shown to boost the image quality especially in noisy images. Most importantly, our 2PE-ISM implementation requires no calibration measurements or other input from the user, which is an important aspect in terms of day-to-day usability of the technique.
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Affiliation(s)
- Sami V. Koho
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- University of Turku, Department of Cell Biology and Anatomy, Institute of Biomedicine and Medicity Research Laboratories, Laboratory of Biophysics, Turku, Finland
- These authors contributed equally to this work
| | - Eli Slenders
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Hasselt University, Biomedical Research Institute (BIOMED), Diepenbeek, Belgium
- These authors contributed equally to this work
| | - Giorgio Tortarolo
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Informatiche, Bioingegneria, Robotica e Ingegneria dei Sistemi, University of Genoa, Italy
| | - Marco Castello
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
| | - Mauro Buttafava
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Federica Villa
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Elena Tcarenkova
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- University of Turku, Department of Cell Biology and Anatomy, Institute of Biomedicine and Medicity Research Laboratories, Laboratory of Biophysics, Turku, Finland
| | - Marcel Ameloot
- Hasselt University, Biomedical Research Institute (BIOMED), Diepenbeek, Belgium
| | | | | | - Alberto Diaspro
- Nanoscopy, Istituto Italiano di Tecnologia, Genoa, Italy
- Dipartimento di Fisica, University of Genoa, Genoa, Italy
| | - Alberto Tosi
- Dipartimento di Elettronica, Informazione e Bioingegneria, Politecnico di Milano, Milan, Italy
| | - Giuseppe Vicidomini
- Molecular Microscopy and Spectroscopy, Istituto Italiano di Tecnologia, Genoa, Italy
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40
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Huang X, Jiang C, Yu L, Yang A. Current and Emerging Approaches for Studying Inter-Organelle Membrane Contact Sites. Front Cell Dev Biol 2020; 8:195. [PMID: 32292782 PMCID: PMC7118198 DOI: 10.3389/fcell.2020.00195] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/09/2020] [Indexed: 12/24/2022] Open
Abstract
Inter-organelle membrane contact sites (MCSs) are classically defined as areas of close proximity between heterologous membranes and established by specific proteins (termed tethers). The interest on MCSs has rapidly increased in the last years, since MCSs play a crucial role in the transfer of cellular components between different organelles and have been involved in important cellular functions such as apoptosis, organelle division and biogenesis, and cell growth. Recently, an unprecedented depth and breadth in insights into the details of MCSs have been uncovered. On one hand, extensive MCSs (organelles interactome) are revealed by comprehensive analysis of organelle network with high temporal-spatial resolution at the system level. On the other hand, more and more tethers involving in MCSs are identified and further works are focusing on addressing the role of these tethers in regulating the function of MCSs at the molecular level. These enormous progresses largely depend on the powerful approaches, including several different types of microscopies and various biochemical techniques. These approaches have greatly accelerated recent advances in MCSs at the system and molecular level. In this review, we summarize the current and emerging approaches for studying MCSs, such as various microscopies, proximity-driven fluorescent signal generation and proximity-dependent biotinylation. In addition, we highlight the advantages and disadvantages of the techniques to provide a general guidance for the study of MCSs.
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Affiliation(s)
- Xue Huang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Chen Jiang
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Lihua Yu
- School of Life Sciences, Chongqing University, Chongqing, China
| | - Aimin Yang
- School of Life Sciences, Chongqing University, Chongqing, China
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41
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Sheppard CJR, Castello M, Tortarolo G, Deguchi T, Koho SV, Vicidomini G, Diaspro A. Pixel reassignment in image scanning microscopy: a re-evaluation. JOURNAL OF THE OPTICAL SOCIETY OF AMERICA. A, OPTICS, IMAGE SCIENCE, AND VISION 2020; 37:154-162. [PMID: 32118893 DOI: 10.1364/josaa.37.000154] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Accepted: 11/29/2019] [Indexed: 05/23/2023]
Abstract
Image scanning microscopy is a technique based on confocal microscopy, in which the confocal pinhole is replaced by a detector array, and the resulting image is reconstructed, usually by the process of pixel reassignment. The detector array collects most of the fluorescent light, so the signal-to-noise ratio is much improved compared with confocal microscopy with a small pinhole, while the resolution is improved compared with conventional (wide-field) microscopy. In previous studies, it has usually been assumed that pixels should be reassigned by a constant factor, to a point midway between the illumination and detection spots. Here it is shown that the peak intensity of the effective point spread function (PSF) can be further increased by 4% by a new choice of the pixel reassignment factor. For an array of two Airy units, the peak of the effective PSF is 1.90 times that of a conventional microscope, and the transverse resolution is 1.53 times better. It is confirmed that image scanning microscopy gives optical sectioning strength identical to that of a confocal microscope with a pinhole equal to the size of the detector array. However, it is shown that image scanning microscopy exhibits axial resolution superior to a confocal microscope with a pinhole the same size as the detector array. For a two-Airy-unit array, the axial resolution is 1.34 times better than in a conventional microscope for the standard reassignment factor, and 1.28 times better for the new reassignment factor. The axial resolution of a confocal microscope with a two-Airy-unit pinhole is only 1.04 times better than conventional microscopy. We also examine the signal-to-noise ratio of a point object in a uniform background (called the detectability), and show that it is 1.6 times higher than in a confocal microscope.
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42
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Super-resolution provided by the arbitrarily strong superlinearity of the blackbody radiation. Nat Commun 2019; 10:5761. [PMID: 31848354 PMCID: PMC6917796 DOI: 10.1038/s41467-019-13780-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 11/27/2019] [Indexed: 11/11/2022] Open
Abstract
Blackbody radiation is a fundamental phenomenon in nature, and its explanation by Planck marks a cornerstone in the history of Physics. In this theoretical work, we show that the spectral radiance given by Planck’s law is strongly superlinear with temperature, with an arbitrarily large local exponent for decreasing wavelengths. From that scaling analysis, we propose a new concept of super-resolved detection and imaging: if a focused beam of energy is scanned over an object that absorbs and linearly converts that energy into heat, a highly nonlinear thermal radiation response is generated, and its point spread function can be made arbitrarily smaller than the excitation beam focus. Based on a few practical scenarios, we propose to extend the notion of super-resolution beyond its current niche in microscopy to various kinds of excitation beams, a wide range of spatial scales, and a broader diversity of target objects. Here, the authors propose a new principle to achieve super-resolution for a wide class of targets. If an object is heated up by a beam, electromagnetic or acoustic, they show that the super-linearity of the induced thermal radiation leads to an arbitrarily high spatial compression factor relative to diffraction-limited beam profile.
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Abstract
Fluorescence microscopy has long been a valuable tool for biological and medical imaging. Control of optical parameters such as the amplitude, phase, polarization and propagation angle of light gives fluorescence imaging great capabilities ranging from super-resolution imaging to long-term real-time observation of living organisms. In this review, we discuss current fluorescence imaging techniques in terms of the use of tailored or structured light for the sample illumination and fluorescence detection, providing a clear overview of their working principles and capabilities.
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Affiliation(s)
- Jialei Tang
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Jinhan Ren
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
- These authors contributed equally to this work
| | - Kyu Young Han
- CREOL, The College of Optics and Photonics, University of Central Florida, Orlando, Florida, USA
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Chen Y, Liu S, Zhang C, Zhang Z, Kuang C, Hao X, Liu XU. Image scanning difference microscopy. J Microsc 2019; 276:98-106. [PMID: 31691969 DOI: 10.1111/jmi.12840] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 09/14/2019] [Accepted: 10/31/2019] [Indexed: 11/30/2022]
Abstract
Here, we propose a novel imaging method, which is called image scanning difference microscopy (ISDM), for superresolution imaging. In ISDM, we implement a detector array composed of 19 avalanche photodiodes (APD) rather than single-point detector in standard confocal microscopy for reconstructing superresolved images with higher signal-to-noise ratio (SNR). Combining with our former proposed fluorescence emission difference (FED) method, we have achieved a lateral resolution of 111 nm (∼λ/6) without the damage of image quality, the highest FED resolution to the best of our knowledge. With its simple setup and remarkable performance, we believe that ISDM can become a versatile observation tool in biology and other fundamental studies. LAY DESCRIPTION: Fluorescence emission difference (FED) microscopy is a really simple and generalisable superresolved fluorescence microscopy method based on PSF engineering and difference algorithm recently. Compared to stimulated-emission-depletion fluorescence microscopy (STED), FED don't need complicated system or precise alignment and polarisation, available for wide variety of dyes and has low photobleaching and phototoxicity for living cells. However, the distortion caused by negative value is one of the biggest obstacles to the further development of FED. In light of this, we propose a novel superresolution imaging method based on the FED method with parallel detection system, which is called image scanning difference microscopy (ISDM). Our method has achieved a significant breakthrough in FED, increasing the resolution further while reducing artefacts generated by negative values, which cannot be accomplished through combining other methods. In addition, ISDM does not require complex setup and optical alignment, long time imaging and imposing no constraint on dyes. Importantly, we realised a transverse resolution of ∼λ/6 (triple diffraction limit) with single wavelength, single incident path and low light intensity, which has never been achieved in any other far-field superresolution microscopy.
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Affiliation(s)
- Yuchen Chen
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Shaocong Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Chengfeng Zhang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Zhimin Zhang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - Cuifang Kuang
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Ningbo Research Institute, Zhejiang University, Ningbo, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
| | - Xiang Hao
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China
| | - X U Liu
- State Key Laboratory of Modern Optical Instrumentation, College of Optical Science and Engineering, Zhejiang University, Hangzhou, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, China
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Oketani R, Suda H, Uegaki K, Kubo T, Matsuda T, Yamanaka M, Arai Y, Smith NI, Nagai T, Fujita K. Visible-wavelength two-photon excitation microscopy with multifocus scanning for volumetric live-cell imaging. JOURNAL OF BIOMEDICAL OPTICS 2019; 25:1-5. [PMID: 31691550 PMCID: PMC7008499 DOI: 10.1117/1.jbo.25.1.014502] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Accepted: 06/03/2019] [Indexed: 05/05/2023]
Abstract
Two-photon excitation microscopy is one of the key techniques used to observe three-dimensional (3-D) structures in biological samples. We utilized a visible-wavelength laser beam for two-photon excitation in a multifocus confocal scanning system to improve the spatial resolution and image contrast in 3-D live-cell imaging. Experimental and numerical analyses revealed that the axial resolution has improved for a wide range of pinhole sizes used for confocal detection. We observed the 3-D movements of the Golgi bodies in living HeLa cells with an imaging speed of 2 s per volume. We also confirmed that the time-lapse observation up to 8 min did not cause significant cell damage in two-photon excitation experiments using wavelengths in the visible light range. These results demonstrate that multifocus, two-photon excitation microscopy with the use of a visible wavelength can constitute a simple technique for 3-D visualization of living cells with high spatial resolution and image contrast.
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Affiliation(s)
- Ryosuke Oketani
- Osaka University, Department of Applied Physics, Suita, Osaka, Japan
| | - Haruka Suda
- Osaka University, Department of Applied Physics, Suita, Osaka, Japan
| | - Kumiko Uegaki
- Osaka University, Department of Applied Physics, Suita, Osaka, Japan
| | - Toshiki Kubo
- Osaka University, Department of Applied Physics, Suita, Osaka, Japan
- AIST-Osaka University, Advanced Photonics and Biosensing Open Innovation Laboratory, Suita, Osaka, Japan
| | - Tomoki Matsuda
- Osaka University, Institute of Scientific and Industrial Research, Ibaraki, Osaka, Japan
| | - Masahito Yamanaka
- Osaka University, Department of Applied Physics, Suita, Osaka, Japan
| | - Yoshiyuki Arai
- Osaka University, Institute of Scientific and Industrial Research, Ibaraki, Osaka, Japan
| | - Nicholas I. Smith
- Osaka University, Immunology Frontier Research Center, Suita, Osaka, Japan
| | - Takeharu Nagai
- Osaka University, Institute of Scientific and Industrial Research, Ibaraki, Osaka, Japan
- Osaka University, Institute for Open and Transdisciplinary Research Initiatives, Transdimensional Life Imaging Division, Suita, Osaka, Japan
| | - Katsumasa Fujita
- Osaka University, Department of Applied Physics, Suita, Osaka, Japan
- AIST-Osaka University, Advanced Photonics and Biosensing Open Innovation Laboratory, Suita, Osaka, Japan
- Osaka University, Institute for Open and Transdisciplinary Research Initiatives, Transdimensional Life Imaging Division, Suita, Osaka, Japan
- Address all correspondence to Katsumasa Fujita, E-mail:
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Video-rate multi-color structured illumination microscopy with simultaneous real-time reconstruction. Nat Commun 2019; 10:4315. [PMID: 31541134 PMCID: PMC6754501 DOI: 10.1038/s41467-019-12165-x] [Citation(s) in RCA: 67] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/21/2019] [Indexed: 12/14/2022] Open
Abstract
Super-resolved structured illumination microscopy (SR-SIM) is among the fastest fluorescence microscopy techniques capable of surpassing the optical diffraction limit. Current custom-build instruments are able to deliver two-fold resolution enhancement with high acquisition speed. SR-SIM is usually a two-step process, with raw-data acquisition and subsequent, time-consuming post-processing for image reconstruction. In contrast, wide-field and (multi-spot) confocal techniques produce high-resolution images instantly. Such immediacy is also possible with SR-SIM, by tight integration of a video-rate capable SIM with fast reconstruction software. Here we present instant SR-SIM by VIGOR (Video-rate Immediate GPU-accelerated Open-Source Reconstruction). We demonstrate multi-color SR-SIM at video frame-rates, with less than 250 ms delay between measurement and reconstructed image display. This is achieved by modifying and extending high-speed SR-SIM image acquisition with a new, GPU-enhanced, network-enabled image-reconstruction software. We demonstrate high-speed surveying of biological samples in multiple colors and live imaging of moving mitochondria as an example of intracellular dynamics. Sequential acquisition and image reconstruction in super-resolved structured illumination microscopy (SR-SIM) is time-consuming. Here the authors optimise both acquisition and reconstruction software to achieve multicolour SR-SIM at video frame-rates with reconstructed images displaying with only milliseconds delay during the experiment.
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Image scanning microscopy. Curr Opin Chem Biol 2019; 51:74-83. [DOI: 10.1016/j.cbpa.2019.05.011] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/01/2019] [Accepted: 05/13/2019] [Indexed: 12/27/2022]
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48
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Mahecic D, Testa I, Griffié J, Manley S. Strategies for increasing the throughput of super-resolution microscopies. Curr Opin Chem Biol 2019; 51:84-91. [DOI: 10.1016/j.cbpa.2019.05.012] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/30/2019] [Accepted: 05/13/2019] [Indexed: 11/29/2022]
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49
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Xia A, Yang S, Zhang R, Ni L, Xing X, Jin F. Imaging the Separation Distance between the Attached Bacterial Cells and the Surface with a Total Internal Reflection Dark-Field Microscope. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2019; 35:8860-8866. [PMID: 31194567 DOI: 10.1021/acs.langmuir.9b01378] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The attachment of bacterial cells to a surface is implicated in the formation of biofilms. Although the surface-related behaviors in this process, such as single cell motility and surface sensing, have been investigated intensively, the precise information of separation distance between the attached cells and the surface has remained unclear. Here, we set a prism-based total internal reflection dark-field microscope (p-TIRDFM) combined with the microfluidic method to image the separation distance of single attached cells. We directly observed that bacterial cells attached to the surface with one nearest touchpoint, and it gradually changed to two touchpoints, respectively, for the two offspring with the cell division. We first monitored the fluctuation of the relative distance on nanometer scale when cells twitch on a surface and further established the relationship between the twitching velocity and the separation distance. The results indicated that the moving cells are a considerable distance apart from the surface and the separation distance fluctuated more widely than immobile cells.
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50
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Jing J, Liu G, Huang Y, Zhou Y. A molecular toolbox for interrogation of membrane contact sites. J Physiol 2019; 598:1725-1739. [PMID: 31119749 PMCID: PMC7098838 DOI: 10.1113/jp277761] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 04/17/2019] [Indexed: 01/04/2023] Open
Abstract
Membrane contact sites (MCSs) are specialized subcellular compartments formed by closely apposed membranes from two organelles. The intermembrane gap is separated by a distance ranging from 10 to 35 nm. MCSs are typically maintained through dynamic protein–protein and protein–lipid interactions. These intermembrane contact sites constitute important intracellular signalling hotspots to mediate a plethora of cellular processes, including calcium homeostasis, lipid metabolism, membrane biogenesis and organelle remodelling. In recent years, a series of genetically encoded probes and chemogenetic or optogenetic actuators have been invented to aid the visualization and interrogation of MCSs in both fixed and living cells. These molecular tools have greatly accelerated the pace of mechanistic dissection of membrane contact sites at the molecular level. In this review, we present an overview on the latest progress in this endeavour, and provide a general guide to the selection of methods and molecular tools for probing interorganellar membrane contact sites.
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Affiliation(s)
- Ji Jing
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Gan Liu
- Cockrell School of Engineering, University of Texas, Austin, TX, 78712, USA
| | - Yun Huang
- Center for Epigenetics and Disease Prevention, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
| | - Yubin Zhou
- Center for Translational Cancer Research, Institute of Biosciences and Technology, College of Medicine, Texas A&M University, Houston, TX, 77030, USA
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