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Manton JD. Answering some questions about structured illumination microscopy. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2022; 380:20210109. [PMID: 35152757 PMCID: PMC8841787 DOI: 10.1098/rsta.2021.0109] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Structured illumination microscopy (SIM) provides images of fluorescent objects at an enhanced resolution greater than that of conventional epifluorescence wide-field microscopy. Initially demonstrated in 1999 to enhance the lateral resolution twofold, it has since been extended to enhance axial resolution twofold (2008), applied to live-cell imaging (2009) and combined with myriad other techniques, including interferometric detection (2008), confocal microscopy (2010) and light sheet illumination (2012). Despite these impressive developments, SIM remains, perhaps, the most poorly understood 'super-resolution' method. In this article, we provide answers to the 13 questions regarding SIM proposed by Prakash et al. along with answers to a further three questions. After providing a general overview of the technique and its developments, we explain why SIM as normally used is still diffraction-limited. We then highlight the necessity for a non-polynomial, and not just nonlinear, response to the illuminating light in order to make SIM a true, diffraction-unlimited, super-resolution technique. In addition, we present a derivation of a real-space SIM reconstruction approach that can be used to process conventional SIM and image scanning microscopy (ISM) data and extended to process data with quasi-arbitrary illumination patterns. Finally, we provide a simple bibliometric analysis of SIM development over the past two decades and provide a short outlook on potential future work. This article is part of the Theo Murphy meeting issue 'Super-resolution structured illumination microscopy (part 2)'.
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Affiliation(s)
- James D. Manton
- MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
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2
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Bermond K, Wobbe C, Tarau IS, Heintzmann R, Hillenkamp J, Curcio CA, Sloan KR, Ach T. Autofluorescent Granules of the Human Retinal Pigment Epithelium: Phenotypes, Intracellular Distribution, and Age-Related Topography. Invest Ophthalmol Vis Sci 2020; 61:35. [PMID: 32433758 PMCID: PMC7405767 DOI: 10.1167/iovs.61.5.35] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Purpose The human retinal pigment epithelium (RPE) accumulates granules significant for autofluorescence imaging. Knowledge of intracellular accumulation and distribution is limited. Using high-resolution microscopy techniques, we determined the total number of granules per cell, intracellular distribution, and changes related to retinal topography and age. Methods RPE cells from the fovea, perifovea, and near-periphery of 15 human RPE flat mounts were imaged using structured illumination microscopy (SIM) and confocal fluorescence microscopy in young (≤51 years, n = 8) and older (>80 years, n = 7) donors. Using custom FIJI plugins, granules were marked with computer assistance, classified based on morphological and autofluorescence properties, and analyzed with regard to intracellular distribution, total number per cell, and granule density. Results A total of 193,096 granules in 450 RPE cell bodies were analyzed. Based on autofluorescence properties, size, and composition, the RPE granules exhibited nine different phenotypes (lipofuscin, two; melanolipofuscin, five; melanosomes, two), distinguishable by SIM. Overall, lipofuscin (low at the fovea but increases with eccentricity and age) and melanolipofuscin (equally distributed at all three locations with no age-related changes) were the major granule types. Melanosomes were under-represented due to suboptimal visualization of apical processes in flat mounts. Conclusions Low lipofuscin and high melanolipofuscin content within foveal RPE cell bodies and abundant lipofuscin at the perifovea suggest a different genesis, plausibly related to the population of overlying photoreceptors (fovea, cones only; perifovea, highest rod density). This systematic analysis provides further insight into RPE cell and granule physiology and links granule load to cell autofluorescence, providing a subcellular basis for the interpretation of clinical fundus autofluorescence.
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Ströhl F, Opstad IS, Tinguely JC, Dullo FT, Mela I, Osterrieth JWM, Ahluwalia BS, Kaminski CF. Super-condenser enables labelfree nanoscopy. OPTICS EXPRESS 2019; 27:25280-25292. [PMID: 31510402 PMCID: PMC6825610 DOI: 10.1364/oe.27.025280] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 06/23/2019] [Accepted: 06/26/2019] [Indexed: 05/16/2023]
Abstract
Labelfree nanoscopy encompasses optical imaging with resolution in the 100 nm range using visible wavelengths. Here, we present a labelfree nanoscopy method that combines coherent imaging techniques with waveguide microscopy to realize a super-condenser featuring maximally inclined coherent darkfield illumination with artificially stretched wave vectors due to large refractive indices of the employed Si3N4 waveguide material. We produce the required coherent plane wave illumination for Fourier ptychography over imaging areas 400 μm2 in size via adiabatically tapered single-mode waveguides and tackle the overlap constraints of the Fourier ptychography phase retrieval algorithm two-fold: firstly, the directionality of the illumination wave vector is changed sequentially via a multiplexed input structure of the waveguide chip layout and secondly, the wave vector modulus is shortend via step-wise increases of the illumination light wavelength over the visible spectrum. We test the method in simulations and in experiments and provide details on the underlying image formation theory as well as the reconstruction algorithm. While the generated Fourier ptychography reconstructions are found to be prone to image artefacts, an alternative coherent imaging method, rotating coherent scattering microscopy (ROCS), is found to be more robust against artefacts but with less achievable resolution.
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Affiliation(s)
- Florian Ströhl
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037 Tromsø,
Norway
- Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, United Kingdom
| | - Ida S. Opstad
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037 Tromsø,
Norway
| | - Jean-Claude Tinguely
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037 Tromsø,
Norway
| | - Firehun T. Dullo
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037 Tromsø,
Norway
| | - Ioanna Mela
- Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, United Kingdom
| | - Johannes W. M. Osterrieth
- Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, United Kingdom
| | - Balpreet S. Ahluwalia
- Department of Physics and Technology, UiT The Arctic University of Norway, NO-9037 Tromsø,
Norway
| | - Clemens F. Kaminski
- Department of Chemical Engineering and Biotechnology, University of Cambridge, CB3 0AS Cambridge, United Kingdom
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Schlüter A, Rossberger S, Dannehl D, Janssen JM, Vorwald S, Hanne J, Schultz C, Mauceri D, Engelhardt M. Dynamic Regulation of Synaptopodin and the Axon Initial Segment in Retinal Ganglion Cells During Postnatal Development. Front Cell Neurosci 2019; 13:318. [PMID: 31417359 PMCID: PMC6682679 DOI: 10.3389/fncel.2019.00318] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Accepted: 06/28/2019] [Indexed: 12/14/2022] Open
Abstract
A key component allowing a neuron to function properly within its dynamic environment is the axon initial segment (AIS), the site of action potential generation. In visual cortex, AIS of pyramidal neurons undergo periods of activity-dependent structural plasticity during development. However, it remains unknown how AIS morphology is organized during development for downstream cells in the visual pathway (retinal ganglion cells; RGCs) and whether AIS retain the ability to dynamically adjust to changes in network state. Here, we investigated the maturation of AIS in RGCs during mouse retinal development, and tested putative activity-dependent mechanisms by applying visual deprivation with a focus on the AIS-specific cisternal organelle (CO), a presumed Ca2+-store. Whole-mount retinae from wildtype and Thy1-GFP transgenic mice were processed for multi-channel immunofluorescence using antibodies against AIS scaffolding proteins ankyrin-G, βIV-spectrin and the CO marker synaptopodin (synpo). Confocal microscopy in combination with morphometrical analysis of AIS length and position as well as synpo cluster size was performed. Data indicated that a subset of RGC AIS contains synpo clusters and that these show significant dynamic regulation in size during development as well as after visual deprivation. Using super resolution microscopy, we addressed the subcellular localization of synpo in RGC axons. Similar to cortical neurons, RGCs show a periodic distribution of AIS scaffolding proteins. A previously reported scaffold-deficient nanodomain correlating with synpo localization is not evident in all RGC AIS. In summary, our work demonstrates a dynamic regulation of both the AIS and synpo in RGCs during retinal development and after visual deprivation, providing first evidence that the AIS and CO in RGCs can undergo structural plasticity in response to changes in network activity.
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Affiliation(s)
- Annabelle Schlüter
- Institute of Neuroanatomy, Center for Biomedical Research and Medical Technology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany.,Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Sabrina Rossberger
- Kirchhoff-Institute for Physics, Applied Optics, Heidelberg University, Heidelberg Germany
| | - Dominik Dannehl
- Institute of Neuroanatomy, Center for Biomedical Research and Medical Technology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Jan Maximilian Janssen
- Institute of Neuroanatomy, Center for Biomedical Research and Medical Technology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Silke Vorwald
- Institute of Neuroanatomy, Center for Biomedical Research and Medical Technology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | | | - Christian Schultz
- Institute of Neuroanatomy, Center for Biomedical Research and Medical Technology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
| | - Daniela Mauceri
- Department of Neurobiology, Interdisciplinary Center for Neurosciences, Heidelberg University, Heidelberg, Germany
| | - Maren Engelhardt
- Institute of Neuroanatomy, Center for Biomedical Research and Medical Technology, Medical Faculty Mannheim, Heidelberg University, Mannheim, Germany
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Affiliation(s)
- 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, 07745 Jena, Germany
| | - Thomas Huser
- Biomolecular
Photonics, Department of Physics, University of Bielefeld, Universitätsstraße
25, 33615 Bielefeld, Germany
- Department
of Internal Medicine and NSF Center for Biophotonics, University of California, Davis, Sacramento, California 95817, United States
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Analytical Model of the Optical Vortex Scanning Microscope with a Simple Phase Object. PHOTONICS 2017. [DOI: 10.3390/photonics4020038] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Cremer C, Szczurek A, Schock F, Gourram A, Birk U. Super-resolution microscopy approaches to nuclear nanostructure imaging. Methods 2017; 123:11-32. [PMID: 28390838 DOI: 10.1016/j.ymeth.2017.03.019] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 03/23/2017] [Indexed: 12/14/2022] Open
Abstract
The human genome has been decoded, but we are still far from understanding the regulation of all gene activities. A largely unexplained role in these regulatory mechanisms is played by the spatial organization of the genome in the cell nucleus which has far-reaching functional consequences for gene regulation. Until recently, it appeared to be impossible to study this problem on the nanoscale by light microscopy. However, novel developments in optical imaging technology have radically surpassed the limited resolution of conventional far-field fluorescence microscopy (ca. 200nm). After a brief review of available super-resolution microscopy (SRM) methods, we focus on a specific SRM approach to study nuclear genome structure at the single cell/single molecule level, Spectral Precision Distance/Position Determination Microscopy (SPDM). SPDM, a variant of localization microscopy, makes use of conventional fluorescent proteins or single standard organic fluorophores in combination with standard (or only slightly modified) specimen preparation conditions; in its actual realization mode, the same laser frequency can be used for both photoswitching and fluorescence read out. Presently, the SPDM method allows us to image nuclear genome organization in individual cells down to few tens of nanometer (nm) of structural resolution, and to perform quantitative analyses of individual small chromatin domains; of the nanoscale distribution of histones, chromatin remodeling proteins, and transcription, splicing and repair related factors. As a biomedical research application, using dual-color SPDM, it became possible to monitor in mouse cardiomyocyte cells quantitatively the effects of ischemia conditions on the chromatin nanostructure (DNA). These novel "molecular optics" approaches open an avenue to study the nuclear landscape directly in individual cells down to the single molecule level and thus to test models of functional genome architecture at unprecedented resolution.
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Affiliation(s)
- Christoph Cremer
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany. http://www.optics.imb-mainz.de
| | - Aleksander Szczurek
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Florian Schock
- Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
| | - Amine Gourram
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany
| | - Udo Birk
- Superresolution Microscopy, Institute of Molecular Biology (IMB), Mainz, Germany; Department of Physics, University of Mainz (JGU), Mainz, Germany; Institute for Pharmacy and Molecular Biotechnology (IPMB), and Kirchhoff Institute for Physics (KIP), University of Heidelberg, Heidelberg, Germany
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Lopez Perez R, Best G, Nicolay NH, Greubel C, Rossberger S, Reindl J, Dollinger G, Weber KJ, Cremer C, Huber PE. Superresolution light microscopy shows nanostructure of carbon ion radiation-induced DNA double-strand break repair foci. FASEB J 2016; 30:2767-76. [PMID: 27166088 DOI: 10.1096/fj.201500106r] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2015] [Accepted: 04/12/2016] [Indexed: 12/13/2022]
Abstract
Carbon ion radiation is a promising new form of radiotherapy for cancer, but the central question about the biologic effects of charged particle radiation is yet incompletely understood. Key to this question is the understanding of the interaction of ions with DNA in the cell's nucleus. Induction and repair of DNA lesions including double-strand breaks (DSBs) are decisive for the cell. Several DSB repair markers have been used to investigate these processes microscopically, but the limited resolution of conventional microscopy is insufficient to provide structural insights. We have applied superresolution microscopy to overcome these limitations and analyze the fine structure of DSB repair foci. We found that the conventionally detected foci of the widely used DSB marker γH2AX (Ø 700-1000 nm) were composed of elongated subfoci with a size of ∼100 nm consisting of even smaller subfocus elements (Ø 40-60 nm). The structural organization of the subfoci suggests that they could represent the local chromatin structure of elementary DSB repair units at the DSB damage sites. Subfocus clusters may indicate induction of densely spaced DSBs, which are thought to be associated with the high biologic effectiveness of carbon ions. Superresolution microscopy might emerge as a powerful tool to improve our knowledge of interactions of ionizing radiation with cells.-Lopez Perez, R., Best, G., Nicolay, N. H., Greubel, C., Rossberger, S., Reindl, J., Dollinger, G., Weber, K.-J., Cremer, C., Huber, P. E. Superresolution light microscopy shows nanostructure of carbon ion radiation-induced DNA double-strand break repair foci.
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Affiliation(s)
- Ramon Lopez Perez
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany;
| | - Gerrit Best
- Department of Ophthalmology, Heidelberg University Hospital, Heidelberg, Germany; Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Nils H Nicolay
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Greubel
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany; and
| | - Sabrina Rossberger
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany
| | - Judith Reindl
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany; and
| | - Günther Dollinger
- Institut für Angewandte Physik und Messtechnik, Universität der Bundeswehr München, Neubiberg, Germany; and
| | - Klaus-Josef Weber
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Christoph Cremer
- Kirchhoff-Institute for Physics, Heidelberg University, Heidelberg, Germany; Superresolution Microscopy of Functional Nuclear Nanostructure, Institute of Molecular Biology, Mainz, Germany
| | - Peter E Huber
- Clinical Cooperation Unit and Molecular Radiation Oncology, German Cancer Research Center, Heidelberg University Hospital, Heidelberg, Germany; Department of Radiation Oncology, Heidelberg University Hospital, Heidelberg, Germany;
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Płocinniczak Ł, Popiołek-Masajada A, Masajada J, Szatkowski M. Analytical model of the optical vortex microscope. APPLIED OPTICS 2016; 55:B20-B27. [PMID: 27140125 DOI: 10.1364/ao.55.000b20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Accepted: 12/18/2015] [Indexed: 06/05/2023]
Abstract
This paper presents an analytical model of the optical vortex scanning microscope. In this microscope the Gaussian beam with an embedded optical vortex is focused into the sample plane. Additionally, the optical vortex can be moved inside the beam, which allows fine scanning of the sample. We provide an analytical solution of the whole path of the beam in the system (within paraxial approximation)-from the vortex lens to the observation plane situated on the CCD camera. The calculations are performed step by step from one optical element to the next. We show that at each step, the expression for light complex amplitude has the same form with only four coefficients modified. We also derive a simple expression for the vortex trajectory of small vortex displacements.
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Kirmes I, Szczurek A, Prakash K, Charapitsa I, Heiser C, Musheev M, Schock F, Fornalczyk K, Ma D, Birk U, Cremer C, Reid G. A transient ischemic environment induces reversible compaction of chromatin. Genome Biol 2015; 16:246. [PMID: 26541514 PMCID: PMC4635527 DOI: 10.1186/s13059-015-0802-2] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2015] [Accepted: 10/09/2015] [Indexed: 11/10/2022] Open
Abstract
Background Cells detect and adapt to hypoxic and nutritional stress through immediate transcriptional, translational and metabolic responses. The environmental effects of ischemia on chromatin nanostructure were investigated using single molecule localization microscopy of DNA binding dyes and of acetylated histones, by the sensitivity of chromatin to digestion with DNAseI, and by fluorescence recovery after photobleaching (FRAP) of core and linker histones. Results Short-term oxygen and nutrient deprivation of the cardiomyocyte cell line HL-1 induces a previously undescribed chromatin architecture, consisting of large, chromatin-sparse voids interspersed between DNA-dense hollow helicoid structures 40–700 nm in dimension. The chromatin compaction is reversible, and upon restitution of normoxia and nutrients, chromatin transiently adopts a more open structure than in untreated cells. The compacted state of chromatin reduces transcription, while the open chromatin structure induced upon recovery provokes a transitory increase in transcription. Digestion of chromatin with DNAseI confirms that oxygen and nutrient deprivation induces compaction of chromatin. Chromatin compaction is associated with depletion of ATP and redistribution of the polyamine pool into the nucleus. FRAP demonstrates that core histones are not displaced from compacted chromatin; however, the mobility of linker histone H1 is considerably reduced, to an extent that far exceeds the difference in histone H1 mobility between heterochromatin and euchromatin. Conclusions These studies exemplify the dynamic capacity of chromatin architecture to physically respond to environmental conditions, directly link cellular energy status to chromatin compaction and provide insight into the effect ischemia has on the nuclear architecture of cells. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0802-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ina Kirmes
- Institute for Molecular Biology, 55128, Mainz, Germany
| | | | - Kirti Prakash
- Institute for Molecular Biology, 55128, Mainz, Germany.,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany
| | | | | | | | | | - Karolina Fornalczyk
- Institute for Molecular Biology, 55128, Mainz, Germany.,Department of Molecular Biophysics, University of Łódź, Łódź, Poland
| | - Dongyu Ma
- Institute for Molecular Biology, 55128, Mainz, Germany.,Centre for Biomedicine and Medical Technology Mannheim (CBTM), University of Heidelberg, 68167, Mannheim, Germany
| | - Udo Birk
- Institute for Molecular Biology, 55128, Mainz, Germany
| | - Christoph Cremer
- Institute for Molecular Biology, 55128, Mainz, Germany. .,Institute of Pharmacy and Molecular Biotechnology, University of Heidelberg, 69120, Heidelberg, Germany.
| | - George Reid
- Institute for Molecular Biology, 55128, Mainz, Germany.
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Lu-Walther HW, Kielhorn M, Förster R, Jost A, Wicker K, Heintzmann R. fastSIM: a practical implementation of fast structured illumination microscopy. Methods Appl Fluoresc 2015; 3:014001. [DOI: 10.1088/2050-6120/3/1/014001] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Gao L. QSIM: quantitative structured illumination microscopy image processing in ImageJ. Biomed Eng Online 2015; 14:4. [PMID: 25588495 PMCID: PMC4360942 DOI: 10.1186/1475-925x-14-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2014] [Accepted: 01/07/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Structured illumination microscopy has been extensively used in biological imaging due to its low cost and easy implementation. However, the lack of quantitative imaging capability limits its application in absolute irradiance measurements. METHOD We have developed a quantitative structured illumination microscopy image processing algorithm (QSIM) as a plugin for the widely used ImageJ software. QSIM can work with the raw images acquired by a traditional structured illumination microscope and can quantitatively measure photon numbers, with noise estimates for both wide-field images and sectioned images. RESULTS AND CONCLUSION We demonstrated the quantitative image processing capability of QSIM by imaging a mouse kidney section in 3D. The results show that QSIM can transform structured illumination microscopy from qualitative to quantitative, which is essential for demanding fluorescence imaging applications.
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Affiliation(s)
- Liang Gao
- Department of Biomedical Engineering, Washington University, St, Louis, MO 63139, USA.
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13
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Dan D, Yao B, Lei M. Structured illumination microscopy for super-resolution and optical sectioning. ACTA ACUST UNITED AC 2014. [DOI: 10.1007/s11434-014-0181-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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14
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Brunstein M, Wicker K, Hérault K, Heintzmann R, Oheim M. Full-field dual-color 100-nm super-resolution imaging reveals organization and dynamics of mitochondrial and ER networks. OPTICS EXPRESS 2013; 21:26162-73. [PMID: 24216840 DOI: 10.1364/oe.21.026162] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Most structured illumination microscopes use a physical or synthetic grating that is projected into the sample plane to generate a periodic illumination pattern. Albeit simple and cost-effective, this arrangement hampers fast or multi-color acquisition, which is a critical requirement for time-lapse imaging of cellular and sub-cellular dynamics. In this study, we designed and implemented an interferometric approach allowing large-field, fast, dual-color imaging at an isotropic 100-nm resolution based on a sub-diffraction fringe pattern generated by the interference of two colliding evanescent waves. Our all-mirror-based system generates illumination pat-terns of arbitrary orientation and period, limited only by the illumination aperture (NA = 1.45), the response time of a fast, piezo-driven tip-tilt mirror (10 ms) and the available fluorescence signal. At low µW laser powers suitable for long-period observation of life cells and with a camera exposure time of 20 ms, our system permits the acquisition of super-resolved 50 µm by 50 µm images at 3.3 Hz. The possibility it offers for rapidly adjusting the pattern between images is particularly advantageous for experiments that require multi-scale and multi-color information. We demonstrate the performance of our instrument by imaging mitochondrial dynamics in cultured cortical astrocytes. As an illustration of dual-color excitation dual-color detection, we also resolve interaction sites between near-membrane mitochondria and the endoplasmic reticulum. Our TIRF-SIM microscope provides a versatile, compact and cost-effective arrangement for super-resolution imaging, allowing the investigation of co-localization and dynamic interactions between organelles--important questions in both cell biology and neurophysiology.
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Wicker K. Non-iterative determination of pattern phase in structured illumination microscopy using auto-correlations in Fourier space. OPTICS EXPRESS 2013; 21:24692-701. [PMID: 24150313 DOI: 10.1364/oe.21.024692] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
The artefact-free reconstruction of structured illumination microscopy images requires precise knowledge of the pattern phases in the raw images. If this parameter cannot be controlled precisely enough in an experimental setup, the phases have to be determined a posteriori from the acquired data. While an iterative optimisation based on cross-correlations between individual Fourier images yields accurate results, it is rather time-consuming. Here I present a fast non-iterative technique which determines each pattern phase from an auto-correlation of the respective Fourier image. In addition to improving the speed of the reconstruction, simulations show that this method is also more robust, yielding errors of typically less than λ/500 under realistic signal-to-noise levels.
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Wicker K, Mandula O, Best G, Fiolka R, Heintzmann R. Phase optimisation for structured illumination microscopy. OPTICS EXPRESS 2013; 21:2032-49. [PMID: 23389185 DOI: 10.1364/oe.21.002032] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Structured illumination microscopy can achieve super-resolution in fluorescence imaging. The sample is illuminated with periodic light patterns, and a series of images are acquired for different pattern positions, also called phases. From these a super-resolution image can be computed. However, for an artefact-free reconstruction it is important that the pattern phases be known with very high precision. If the necessary precision cannot be guaranteed experimentally, the phase information has to be retrieved a posteriori from the acquired data. We present a fast and robust algorithm that iteratively determines these phases with a precision of typically below λ/100. Our method, which is based on cross-correlations, allows optimisation of pattern phase even when the pattern itself is too fine for detection, in which case most other methods inevitably fail. We analyse the performance of this method using simulated data from a synthetic 2D sample as well as experimental single-slice data from a 3D sample and compare it with another previously published approach.
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Affiliation(s)
- Kai Wicker
- Institute of Physical Chemistry, Abbe Center of Photonics, Friedrich-Schiller-University Jena, Jena, Germany.
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Bhattacharya D, Singh VR, Zhi C, So PTC, Matsudaira P, Barbastathis G. Three dimensional HiLo-based structured illumination for a digital scanned laser sheet microscopy (DSLM) in thick tissue imaging. OPTICS EXPRESS 2012; 20:27337-47. [PMID: 23262684 PMCID: PMC3601593 DOI: 10.1364/oe.20.027337] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Laser sheet based microscopy has become widely accepted as an effective active illumination method for real time three-dimensional (3D) imaging of biological tissue samples. The light sheet geometry, where the camera is oriented perpendicular to the sheet itself, provides an effective method of eliminating some of the scattered light and minimizing the sample exposure to radiation. However, residual background noise still remains, limiting the contrast and visibility of potentially interesting features in the samples. In this article, we investigate additional structuring of the illumination for improved background rejection, and propose a new technique, "3D HiLo" where we combine two HiLo images processed from orthogonal directions to improve the condition of the 3D reconstruction. We present a comparative study of conventional structured illumination based demodulation methods, namely 3Phase and HiLo with a newly implemented 3D HiLo approach and demonstrate that the latter yields superior signal-to-background ratio in both lateral and axial dimensions, while simultaneously suppressing image processing artifacts.
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Hagen N, Gao L, Tkaczyk TS. Quantitative sectioning and noise analysis for structured illumination microscopy. OPTICS EXPRESS 2012; 20:403-13. [PMID: 22274364 PMCID: PMC3336372 DOI: 10.1364/oe.20.000403] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Structured illumination (SI) has long been regarded as a nonquantitative technique for obtaining sectioned microscopic images. Its lack of quantitative results has restricted the use of SI sectioning to qualitative imaging experiments, and has also limited researchers' ability to compare SI against competing sectioning methods such as confocal microscopy. We show how to modify the standard SI sectioning algorithm to make the technique quantitative, and provide formulas for calculating the noise in the sectioned images. The results indicate that, for an illumination source providing the same spatially-integrated photon flux at the object plane, and for the same effective slice thicknesses, SI sectioning can provide higher SNR images than confocal microscopy for an equivalent setup when the modulation contrast exceeds about 0.09.
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Affiliation(s)
- Nathan Hagen
- Department of Bioengineering, Rice University, Houston, Texas 77005,
USA
| | - Liang Gao
- Department of Bioengineering, Rice University, Houston, Texas 77005,
USA
| | - Tomasz S. Tkaczyk
- Department of Bioengineering, Rice University, Houston, Texas 77005,
USA
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