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Zhao W, Huang X, Yang J, Qu L, Qiu G, Zhao Y, Wang X, Su D, Ding X, Mao H, Jiu Y, Hu Y, Tan J, Zhao S, Pan L, Chen L, Li H. Quantitatively mapping local quality of super-resolution microscopy by rolling Fourier ring correlation. LIGHT, SCIENCE & APPLICATIONS 2023; 12:298. [PMID: 38097537 PMCID: PMC10721804 DOI: 10.1038/s41377-023-01321-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 10/18/2023] [Accepted: 10/31/2023] [Indexed: 12/17/2023]
Abstract
In fluorescence microscopy, computational algorithms have been developed to suppress noise, enhance contrast, and even enable super-resolution (SR). However, the local quality of the images may vary on multiple scales, and these differences can lead to misconceptions. Current mapping methods fail to finely estimate the local quality, challenging to associate the SR scale content. Here, we develop a rolling Fourier ring correlation (rFRC) method to evaluate the reconstruction uncertainties down to SR scale. To visually pinpoint regions with low reliability, a filtered rFRC is combined with a modified resolution-scaled error map (RSM), offering a comprehensive and concise map for further examination. We demonstrate their performances on various SR imaging modalities, and the resulting quantitative maps enable better SR images integrated from different reconstructions. Overall, we expect that our framework can become a routinely used tool for biologists in assessing their image datasets in general and inspire further advances in the rapidly developing field of computational imaging.
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Affiliation(s)
- Weisong Zhao
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
- Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China
| | - Xiaoshuai Huang
- Biomedical Engineering Department, International Cancer Institute, Peking University Cancer Hospital and Institute, Health Science Center, Peking University, Beijing, China
| | - Jianyu Yang
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China
| | - Liying Qu
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Guohua Qiu
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China
| | - Yue Zhao
- Department of Control Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Xinwei Wang
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Deer Su
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Xumin Ding
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China
| | - Heng Mao
- School of Mathematical Sciences, Peking University, Beijing, China
| | - Yaming Jiu
- Unit of Cell Biology and Imaging Study of Pathogen Host Interaction, The Center for Microbes, Development and Health, Key Laboratory of Molecular Virology and Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Ying Hu
- School of Life Science and Technology, Harbin Institute of Technology, Harbin, China
| | - Jiubin Tan
- Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China
| | - Shiqun Zhao
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China.
| | - Leiting Pan
- The Key Laboratory of Weak-Light Nonlinear Photonics of Education Ministry, School of Physics and TEDA Institute of Applied Physics, Frontiers Science Center for Cell Responses, Nankai University, Tianjin, China.
| | - Liangyi Chen
- State Key Laboratory of Membrane Biology, Beijing Key Laboratory of Cardiometabolic Molecular Medicine, Institute of Molecular Medicine, National Biomedical Imaging Center, School of Future Technology, Peking University, Beijing, China.
- PKU-IDG/McGovern Institute for Brain Research, Beijing, China.
- Beijing Academy of Artificial Intelligence, Beijing, China.
| | - Haoyu Li
- Innovation Photonics and Imaging Center, School of Instrumentation Science and Engineering, Harbin Institute of Technology, Harbin, China.
- Key Laboratory of Ultra-Precision Intelligent Instrumentation of Ministry of Industry and Information Technology, Harbin Institute of Technology, Harbin, China.
- Frontiers Science Center for Matter Behave in Space Environment, Harbin Institute of Technology, Harbin, China.
- Key Laboratory of Micro-Systems and Micro-Structures Manufacturing of Ministry of Education, Harbin Institute of Technology, Harbin, China.
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Prakash K, Diederich B, Heintzmann R, Schermelleh L. Super-resolution microscopy: a brief history and new avenues. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20210110. [PMID: 35152764 PMCID: PMC8841785 DOI: 10.1098/rsta.2021.0110] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 01/18/2022] [Indexed: 05/03/2023]
Abstract
Super-resolution microscopy (SRM) is a fast-developing field that encompasses fluorescence imaging techniques with the capability to resolve objects below the classical diffraction limit of optical resolution. Acknowledged with the Nobel prize in 2014, numerous SRM methods have meanwhile evolved and are being widely applied in biomedical research, all with specific strengths and shortcomings. While some techniques are capable of nanometre-scale molecular resolution, others are geared towards volumetric three-dimensional multi-colour or fast live-cell imaging. In this editorial review, we pick on the latest trends in the field. We start with a brief historical overview of both conceptual and commercial developments. Next, we highlight important parameters for imaging successfully with a particular super-resolution modality. Finally, we discuss the importance of reproducibility and quality control and the significance of open-source tools in microscopy. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
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Affiliation(s)
- Kirti Prakash
- Integrated Pathology Unit, Centre for Molecular Pathology, The Royal Marsden Trust and Institute of Cancer Research, Sutton SM2 5NG, UK
| | - Benedict Diederich
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
| | - Rainer Heintzmann
- Leibniz Institute for Photonic Technology, Albert-Einstein-Strasse 9, 07745 Jena, Germany
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich-Schiller-University, Helmholtzweg 4, 07743 Jena, Germany
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Schock F, Best G, Celik N, Heintzmann R, Dithmar S, Cremer C. Structured illumination ophthalmoscope: super-resolution microscopy on the living human eye. PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY A: MATHEMATICAL, PHYSICAL AND ENGINEERING SCIENCES 2022; 380:20210151. [PMID: 0 DOI: 10.1098/rsta.2021.0151] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 01/15/2022] [Indexed: 05/19/2023]
Abstract
In this paper, we present the prototype of an ophthalmoscope that uses structured illumination microscopy (SIM) to enable super-resolved imaging of the human retina, and give first insights into clinical application possibilities. The SIM technique was applied to build a prototype that uses the lens of the human eye as an objective to ‘super-resolve’ the retina of a living human. In our multidisciplinary collaboration, we have adapted this well-established technique in ophthalmology and successfully imaged a human retina using significantly lower light intensity than a state-of-the-art ophthalmoscope. Here, we focus on the technical implementation and highlight future perspectives of this method. A more application-oriented note for physicians on the diagnostic and disease-preventive value of this method, as well as the medical results of the clinical study carried out, will be published in a report addressed to an appropriate specialist audience.
This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 2)’.
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Affiliation(s)
- Florian Schock
- Institute of Physics, Johannes Gutenberg University Mainz, Mainz, Germany
- Kirchhoff-Institute for Physics, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
| | - Gerrit Best
- Kirchhoff-Institute for Physics, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany
| | - Nil Celik
- Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany
| | - Rainer Heintzmann
- Institute of Physical Chemistry and Abbe Center of Photonics, Friedrich Schiller University, Jena, Germany
- Leibniz Institute of Photonic Technology, Jena, Germany
| | - Stefan Dithmar
- Department of Ophthalmology, HELIOS-HSK, Wiesbaden, Germany
- Department of Ophthalmology, University of Heidelberg, Heidelberg, Germany
| | - Christoph Cremer
- Institute of Physics, Johannes Gutenberg University Mainz, Mainz, Germany
- Kirchhoff-Institute for Physics, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Institute of Pharmacy and Molecular Biotechnology, Ruprecht-Karls-University Heidelberg, Heidelberg, Germany
- Max Planck Institute for Polymer Research, Mainz, Germany
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Prakash K, Diederich B, Reichelt S, Heintzmann R, Schermelleh L. Super-resolution structured illumination microscopy: past, present and future. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2021; 379:20200143. [PMID: 33896205 PMCID: PMC8366908 DOI: 10.1098/rsta.2020.0143] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Structured illumination microscopy (SIM) has emerged as an essential technique for three-dimensional (3D) and live-cell super-resolution imaging. However, to date, there has not been a dedicated workshop or journal issue covering the various aspects of SIM, from bespoke hardware and software development and the use of commercial instruments to biological applications. This special issue aims to recap recent developments as well as outline future trends. In addition to SIM, we cover related topics such as complementary super-resolution microscopy techniques, computational imaging, visualization and image processing methods. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 1)'.
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Affiliation(s)
- Kirti Prakash
- National Physical Laboratory, TW11 0LW Teddington, UK
- Department of Paediatrics, Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
| | - 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, Helmholtzweg 4, Jena, Germany
| | - Stefanie Reichelt
- CRUK Cambridge Research Institute, Robinson Way, Cambridge CB2 0RE, UK
| | - 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, Helmholtzweg 4, Jena, Germany
- Faculty of Physics and Astronomy, Friedrich-Schiller-University, Jena, Germany
| | - Lothar Schermelleh
- Micron Advanced Bioimaging Unit, Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK
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