The Experts below are selected from a list of 360 Experts worldwide ranked by ideXlab platform
Rainer Heintzmann - One of the best experts on this subject based on the ideXlab platform.
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super resolution Structured Illumination Microscopy past present and future
Philosophical Transactions of the Royal Society A, 2021Co-Authors: Benedict Diederich, Kirti Prakash, Stefanie Reichelt, Rainer Heintzmann, Lothar SchermellehAbstract: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 wo...
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video rate multi color Structured Illumination Microscopy with simultaneous real time reconstruction
Nature Communications, 2019Co-Authors: Andreas Markwirth, Rainer Heintzmann, Thomas R Huser, Marcel Muller, Viola Monkemoller, Wolfgang Hubner, Mario LachettaAbstract: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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successful optimization of reconstruction parameters in Structured Illumination Microscopy a practical guide
Optics Communications, 2019Co-Authors: Christian Karras, Rainer Heintzmann, Ronny Forster, Maria Smedh, Hendrik Deschout, Julia FernandezrodriguezAbstract:Abstract The impact of the different reconstruction parameters in super-resolution Structured Illumination Microscopy (SIM) on image artifacts is carefully analyzed. These parameters comprise the Wiener filter parameter, an apodization function, zero-frequency suppression and modifications of the optical transfer function. A detailed investigation of the reconstructed image spectrum is concluded to be suitable for identifying artifacts. For this purpose, two samples, an artificial test slide and a more realistic biological system, were used to characterize the artifact classes and their correlation with the image spectra as well as the reconstruction parameters. In addition, a guideline for efficient parameter optimization is suggested and the implementation of the parameters in selected up-to-date processing packages (proprietary and open-source) is depicted.
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signal noise and resolution in linear and nonlinear Structured Illumination Microscopy
Journal of Microscopy, 2019Co-Authors: E A Ingerman, Rainer Heintzmann, Mats G L Gustafsson, R A LondonAbstract:Structured-Illumination Microscopy allows widefield fluorescence imaging with resolution beyond the classical diffraction limit. Its linear form extends resolution by a factor of two, and its nonlinear form by an in-principle infinite factor, the effective resolution in practice being determined by noise. In this paper, we analyse the noise properties and achievable resolution of linear and nonlinear 1D and 2D patterned SIM from a frequency-space perspective. We develop an analytical theory for a general case of linear or nonlinear fluorescent imaging, and verify the analytical calculations with numerical simulation for a special case where nonlinearity is produced by photoswitching of fluorescent labels. We compare the performance of two alternative implementations, using either two-dimensional (2D) Illumination patterns or sequentially rotated one-dimensional (ID) patterns. We show that 1D patterns are advantageous in the linear case, and that in the nonlinear case 2D patterns provide a slight signal-to-noise advantage under idealised conditions, but perform worse than 1D patterns in the presence of nonswitchable fluorescent background. LAY DESCRIPTION: Structured-Illumination Microscopy (SIM) is a high-resolution light Microscopy technique that allows imaging of fluorescence at a resolution about twice the classical diffraction limit. There are various ways that the Illumination can be Structured, but it is not obvious how the choice of Illumination pattern affects the final image quality, especially in view of the noise. We present a detailed performance analysis considering two Illumination techniques: sequential Illumination with line-gratings that are shifted and rotated during image acquisition and two-dimensional (2D) Illumination structures requiring only shift operations. Our analysis is based on analytical theory, supported by simulations of images considering noise. We also extend our analysis to a nonlinear variant of SIM, with which enhanced resolution can be achieved, limited only by noise. This includes nonlinear SIM based on the light-induced switching of the fluorescent molecules between a bright and a dark state. We find sequential Illumination with line-gratings to be advantageous in ordinary (linear) SIM, whereas 2D patterns provides a slight signal-to-noise advantage under idealised conditions in nonlinear SIM if there is no nonswitching background.
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successful optimization of reconstruction parameters in Structured Illumination Microscopy a practical guide
bioRxiv, 2018Co-Authors: Christian Karras, Ronny Forster, Maria Smedh, Hendrik Deschout, Julia Fernandezrodriguez, Rainer HeintzmannAbstract:The impact of the different reconstruction parameters in super-resolution Structured Illumination Microscopy (SIM) onto artifacts is carefully analyzed. They comprise the Wiener filter parameter, an apodization function, zero-frequency suppression and modifications of the optical transfer function. A detailed investigation of the reconstructed image spectrum is concluded to be suitable for identifying artifacts. For this purpose, two samples, an artificial test slide and a more realistic biological system, were used to characterize the artifact classes and their correlation with the image spectra as well as the reconstruction parameters. In addition, a guideline for efficient parameter optimization is suggested and the implementation of the parameters in selected up-to-date processing packages (proprietary and open-source) is depicted.
Zhaowei Liu - One of the best experts on this subject based on the ideXlab platform.
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localized plasmonic Structured Illumination Microscopy with gaps in spatial frequencies
Optics Letters, 2019Co-Authors: Anna Bezryadina, Junxiang Zhao, Yang Xia, Yeon Ui Lee, Xiang Zhang, Zhaowei LiuAbstract:Localized plasmonic Structured Illumination Microscopy (LPSIM) is a super-resolution fluorescent Microscopy method to image samples at a high speed with a wide field of view and low phototoxicity. Here we propose a methodology to extend the resolution capability of LPSIM by shifting spatial frequencies farther away from the diffraction-limited cutoff frequency with a plasmonic nano-array. We analyze the performance and accuracy of image reconstruction by using simulations of standard Structured Illumination Microscopy (SIM) and blind-LPSIM. LPSIM experiments were also performed by using various LPSIM substrates and different microscope objectives. The experiments and simulations show that by shifting spatial frequencies farther away, resolution improvement can be extended up to 5 times beyond the diffraction limit with minimal deformation and artifacts in the reconstructed image.
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high spatiotemporal resolution imaging with localized plasmonic Structured Illumination Microscopy
ACS Nano, 2018Co-Authors: Anna Bezryadina, Junxiang Zhao, Yang Xia, Xiang Zhang, Zhaowei LiuAbstract:Localized plasmonic Structured Illumination Microscopy (LPSIM) provides multicolor wide-field super-resolution imaging with low phototoxicity and high-speed capability. LPSIM utilizes a nanoscale plasmonic antenna array to provide a series of tunable Illumination patterns beyond the traditional diffraction limit, allowing for enhanced resolving powers down to a few tens of nanometers. Here, we demonstrate wide-field LPSIM with 50 nm spatial resolution at video rate speed by imaging microtubule dynamics with low Illumination power intensity. The design of the LPSIM system makes it suitable for imaging surface effects of cells and tissues with regular sample preparation protocols. LPSIM can be extended to much higher resolution, representing an excellent technology for live-cell imaging of protein dynamics and interactions.
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localized plasmonic Structured Illumination Microscopy with an optically trapped microlens
Nanoscale, 2017Co-Authors: Anna Bezryadina, Joseph Ponsetto, Eric Huang, Junxiang Zhao, Alefia Kothambawala, Joseph Wang, Zhaowei LiuAbstract:Localized plasmonic Structured Illumination Microscopy (LPSIM) is a recently developed super resolution technique that demonstrates immense potential via arrays of localized plasmonic antennas. Microlens Microscopy represents another distinct approach for improving resolution by introducing a spherical lens with a large refractive index to boost the effective numerical aperture of the imaging system. In this paper, we bridge together the LPSIM and optically trapped spherical microlenses, for the first time, to demonstrate a new super resolution technique for surface imaging. By trapping and moving polystyrene and TiO2 microspheres with optical tweezers on top of a LPSIM substrate, the new imaging system has achieved a higher NA and improved resolution.
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experimental demonstration of localized plasmonic Structured Illumination Microscopy
ACS Nano, 2017Co-Authors: Joseph Ponsetto, Feifei Wei, Hao Shen, Eric Huang, Anna Bezryadina, Keisuke Onishi, Lorenzo Ferrari, Yimin Zou, Zhaowei LiuAbstract:Super-resolution imaging methods such as Structured Illumination Microscopy and others have offered various compromises between resolution, imaging speed, and biocompatibility. Here we experimentally demonstrate a physical mechanism for super-resolution that offers advantages over existing technologies. Using finely Structured, resonant, and controllable near-field excitation from localized surface plasmons in a planar nanoantenna array, we achieve wide-field surface imaging with resolution down to 75 nm while maintaining reasonable speed and compatibility with biological specimens.
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wide field super resolution surface imaging through plasmonic Structured Illumination Microscopy
Nano Letters, 2014Co-Authors: Feifei Wei, Hao Shen, Weiwei Wan, Joseph Ponsetto, Eric Huang, Zhaowei LiuAbstract:We experimentally demonstrate a wide field surface plasmon (SP) assisted super-resolution imaging technique, plasmonic Structured Illumination Microscopy (PSIM), by combining tunable SP interference (SPI) with Structured Illumination Microscopy (SIM). By replacing the laser interference fringes in conventional SIM with SPI patterns, PSIM exhibits greatly enhanced resolving power thanks to the unique properties of SP waves. This PSIM technique is a wide field, surface super-resolution imaging technique with potential applications in the field of high-speed biomedical imaging.
Lothar Schermelleh - One of the best experts on this subject based on the ideXlab platform.
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super resolution Structured Illumination Microscopy past present and future
Philosophical Transactions of the Royal Society A, 2021Co-Authors: Benedict Diederich, Kirti Prakash, Stefanie Reichelt, Rainer Heintzmann, Lothar SchermellehAbstract: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 wo...
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quantitative 3d Structured Illumination Microscopy of nuclear structures
Nature Protocols, 2017Co-Authors: Felix Kraus, Heinrich Leonhardt, Justin Demmerle, Ezequiel Miron, Tsotne Chitiashvili, Alexei Budco, Quentin Alle, Atsushi Matsuda, Lothar SchermellehAbstract:3D Structured Illumination Microscopy (3D-SIM) is the super-resolution technique of choice for multicolor volumetric imaging. Here we provide a validated sample preparation protocol for labeling nuclei of cultured mammalian cells, image acquisition and registration practices, and downstream image analysis of nuclear structures and epigenetic marks. Using immunostaining and replication labeling combined with image segmentation, centroid mapping and nearest-neighbor analyses in open-source environments, 3D maps of nuclear structures are analyzed in individual cells and normalized to fluorescence standards on the nanometer scale. This protocol fills an unmet need for the application of 3D-SIM to the technically challenging nuclear environment, and subsequent quantitative analysis of 3D nuclear structures and epigenetic modifications. In addition, it establishes practical guidelines and open-source solutions using ImageJ/Fiji and the TANGO plugin for high-quality and routinely comparable data generation in immunostaining experiments that apply across model systems. From sample preparation through image analysis, the protocol can be executed within one week.
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simcheck a toolbox for successful super resolution Structured Illumination Microscopy
Scientific Reports, 2015Co-Authors: Graeme Ball, Justin Demmerle, Rainer Kaufmann, Ilan Davis, Ian M Dobbie, Lothar SchermellehAbstract:Three-dimensional Structured Illumination Microscopy (3D-SIM) is a versatile and accessible method for super-resolution fluorescence imaging, but generating high-quality data is challenging, particularly for non-specialist users. We present SIMcheck, a suite of ImageJ plugins enabling users to identify and avoid common problems with 3D-SIM data, and assess resolution and data quality through objective control parameters. Additionally, SIMcheck provides advanced calibration tools and utilities for common image processing tasks. This open-source software is applicable to all commercial and custom platforms, and will promote routine application of super-resolution SIM imaging in cell biology.
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3d Structured Illumination Microscopy provides novel insight into architecture of human centrosomes
Biology Open, 2012Co-Authors: Katharina F Sonnen, Lothar Schermelleh, Heinrich Leonhardt, Erich A. NiggAbstract:Centrioles are essential for the formation of cilia and flagella. They also form the core of the centrosome, which organizes microtubule arrays important for cell shape, polarity, motility and division. Here, we have used super-resolution 3D-Structured Illumination Microscopy to analyse the spatial relationship of 18 centriole and pericentriolar matrix (PCM) components of human centrosomes at different cell cycle stages. During mitosis, PCM proteins formed extended networks with interspersed γ-Tubulin. During interphase, most proteins were arranged at specific distances from the walls of centrioles, resulting in ring staining, often with discernible density masses. Through use of site-specific antibodies, we found the C-terminus of Cep152 to be closer to centrioles than the N-terminus, illustrating the power of 3D-SIM to study protein disposition. Appendage proteins showed rings with multiple density masses, and the number of these masses was strongly reduced during mitosis. At the proximal end of centrioles, Sas-6 formed a dot at the site of daughter centriole assembly, consistent with its role in cartwheel formation. Plk4 and STIL co-localized with Sas-6, but Cep135 was associated mostly with mother centrioles. Remarkably, Plk4 formed a dot on the surface of the mother centriole before Sas-6 staining became detectable, indicating that Plk4 constitutes an early marker for the site of nascent centriole formation. Our study provides novel insights into the architecture of human centrosomes and illustrates the power of super-resolution Microscopy in revealing the relative localization of centriole and PCM proteins in unprecedented detail.
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the potential of 3d fish and super resolution Structured Illumination Microscopy for studies of 3d nuclear architecture
BioEssays, 2012Co-Authors: Yolanda Markaki, Lothar Schermelleh, Thomas Cremer, Daniel Smeets, Susanne Fiedler, Volker Schmid, Marion CremerAbstract:Three-dimensional Structured Illumination Microscopy (3D-SIM) has opened up new possibilities to study nuclear architecture at the ultrastructural level down to the ~100 nm range. We present first results and assess the potential using 3D-SIM in combination with 3D fluorescence in situ hybridization (3D-FISH) for the topographical analysis of defined nuclear targets. Our study also deals with the concern that artifacts produced by FISH may counteract the gain in resolution. We address the topography of DAPI-stained DNA in nuclei before and after 3D-FISH, nuclear pores and the lamina, chromosome territories, chromatin domains, and individual gene loci. We also look at the replication patterns of chromocenters and the topographical relationship of Xist-RNA within the inactive X-territory. These examples demonstrate that an appropriately adapted 3D-FISH/3D-SIM approach preserves key characteristics of the nuclear ultrastructure and that the gain in information obtained by 3D-SIM yields new insights into the functional nuclear organization.
Clemens F. Kaminski - One of the best experts on this subject based on the ideXlab platform.
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Concepts for Structured Illumination Microscopy with extended axial resolution through mirrored Illumination.
Biomedical optics express, 2020Co-Authors: James D. Manton, Florian Strohl, Reto Fiolka, Clemens F. Kaminski, Eric J. ReesAbstract:Wide-field fluorescence Microscopy, while much faster than confocal Microscopy, suffers from a lack of optical sectioning and poor axial resolution. 3D Structured Illumination Microscopy (SIM) has been demonstrated to provide optical sectioning and to double the resolution limit both laterally and axially, but even with this the axial resolution is still worse than the lateral resolution of unmodified wide-field Microscopy. Interferometric schemes using two high numerical aperture objectives, such as 4Pi confocal and I5M Microscopy, have improved the axial resolution beyond that of the lateral, but at the cost of a significantly more complex optical setup. Here, we theoretically and numerically investigate a simpler dual-objective scheme which we propose can be easily added to an existing 3D-SIM microscope, providing lateral and axial resolutions in excess of 125 nm with conventional fluorophores and without the need for interferometric detection.
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Concepts for Structured Illumination Microscopy with extended axial resolution through mirrored Illumination
2019Co-Authors: James D. Manton, Florian Strohl, Reto Fiolka, Clemens F. Kaminski, Eric J. ReesAbstract:Wide-field fluorescence Microscopy, while much faster than confocal Microscopy, suffers from a lack of optical sectioning and poor axial resolution. 3D Structured Illumination Microscopy (SIM) has been demonstrated to provide optical sectioning and to double the resolution limit both laterally and axially, but even with this the axial resolution is still worse than the lateral resolution of unmodified wide-field Microscopy. Interferometric schemes using two high numerical aperture objectives, such as 4Pi confocal and I5M Microscopy, have improved the axial resolution beyond that of the lateral, but at the cost of a significantly more complex optical setup. Here, we investigate a simpler dual-objective scheme which we propose can be easily added to an existing 3D-SIM microscope, providing lateral and axial resolutions in excess of 125 nm with conventional fluorophores and without the need for interferometric detection.
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Structured Illumination Microscopy combined with machine learning enables the high throughput analysis and classification of virus structure
bioRxiv, 2018Co-Authors: Romain F Laine, Gemma Goodfellow, Laurence J Young, Jon Travers, Danielle Carroll, Oliver Dibben, Helen Bright, Clemens F. KaminskiAbstract:Optical super-resolution Microscopy techniques enable high molecular specificity with high spatial resolution and constitute a set of powerful tools in the investigation of the structure of supramolecular assemblies such as viruses. Here, we report on a new methodology which combines Structured Illumination Microscopy (SIM) with machine learning algorithms to image and classify the structure of large populations of biopharmaceutical viruses with high resolution. The method offers information on virus morphology that can ultimately be linked with functional performance. We demonstrate the approach on viruses produced for oncolytic viriotherapy (Newcastle Disease Virus) and vaccine development (Influenza). This unique tool enables the rapid assessment of the quality of viral production with high throughput obviating the need for traditional batch testing methods which are complex and time consuming. We show that our method also works on non-purified samples from pooled harvest fluids directly from the production line.
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frontiers in Structured Illumination Microscopy
Optica, 2016Co-Authors: Florian Strohl, Clemens F. KaminskiAbstract:At the start of this millennium, the principles of Structured Illumination Microscopy (SIM) had been established and the concept of resolution doubling demonstrated experimentally in two dimensions. Breathtaking advances have since taken place, making SIM one of the most powerful and versatile superresolution methods available today, routinely used in the study of biochemical processes in laboratories around the world. In theory there is no inherent limit to the resolution obtainable with certain modalities of SIM, and new variants have the potential to operate at even higher speeds and sensitivity than currently realized. In this review, we focus on the very latest innovations in SIM theory and practice, which are set to continue the revolution of this method into the future. Examples include confocal implementations of the SIM principle, which can be used in combination with two-photon excitation and adaptive optics. We present recent applications of such approaches in the life sciences, which illustrate their potential to revolutionize intravital research, by providing the ability to watch life at the molecular scale, at high speeds, and deep within living organisms. A different variant makes use of standing plasmonic waves or localized surface plasmons to confer performance enhancements to 2D SIM modalities. Research on these latter techniques is in its infancy but already shows great potential for their development into powerful in vitro probes for chemical processes at solid/liquid interfaces. Physical concepts are reviewed in detail, and future directions are presented along which the field might fruitfully develop, holding promise for new discoveries on the molecular scale.
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a joint richardson lucy deconvolution algorithm for the reconstruction of multifocal Structured Illumination Microscopy data
Conference on Lasers and Electro-Optics, 2015Co-Authors: Florian Strohl, Clemens F. KaminskiAbstract:We demonstrate the reconstruction of multifocal Structured Illumination Microscopy images using a joint Richardson-Lucy deconvolution algorithm, named jRL-MSIM, which is based on an underlying widefield image-formation model and particularly well suited for noise corrupted data.
Marcel Muller - One of the best experts on this subject based on the ideXlab platform.
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video rate multi color Structured Illumination Microscopy with simultaneous real time reconstruction
Nature Communications, 2019Co-Authors: Andreas Markwirth, Rainer Heintzmann, Thomas R Huser, Marcel Muller, Viola Monkemoller, Wolfgang Hubner, Mario LachettaAbstract: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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multifocus Structured Illumination Microscopy for fast volumetric super resolution imaging
Biomedical Optics Express, 2017Co-Authors: Sara Abrahamsson, Marcel Muller, Hans Blom, Ana Agostinho, Daniel C Jans, Aurelie Jost, Linnea Nilsson, Kristoffer Bernhem, Talley J Lambert, Rainer HeintzmannAbstract:We here report for the first time the synergistic implementation of Structured Illumination Microscopy (SIM) and multifocus Microscopy (MFM). This imaging modality is designed to alleviate the problem of insufficient volumetric acquisition speed in super-resolution biological imaging. SIM is a wide-field super-resolution technique that allows imaging with visible light beyond the classical diffraction limit. Employing multifocus diffractive optics we obtain simultaneous wide-field 3D imaging capability in the SIM acquisition sequence, improving volumetric acquisition speed by an order of magnitude. Imaging performance is demonstrated on biological specimens.
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strategic and practical guidelines for successful Structured Illumination Microscopy
Nature Protocols, 2017Co-Authors: Justin Demmerle, Marcel Muller, Graeme Ball, Ian M Dobbie, Ezequiel Miron, Atsushi Matsuda, Cassandravictoria Innocent, Alison J North, Yolanda MarkakiAbstract:Linear 2D- or 3D-Structured Illumination Microscopy (SIM or3D-SIM, respectively) enables multicolor volumetric imaging of fixed and live specimens with subdiffraction resolution in all spatial dimensions. However, the reliance of SIM on algorithmic post-processing renders it particularly sensitive to artifacts that may reduce resolution, compromise data and its interpretations, and drain resources in terms of money and time spent. Here we present a protocol that allows users to generate high-quality SIM data while accounting and correcting for common artifacts. The protocol details preparation of calibration bead slides designed for SIM-based experiments, the acquisition of calibration data, the documentation of typically encountered SIM artifacts and corrective measures that should be taken to reduce them. It also includes a conceptual overview and checklist for experimental design and calibration decisions, and is applicable to any commercially available or custom platform. This protocol, plus accompanying guidelines, allows researchers from students to imaging professionals to create an optimal SIM imaging environment regardless of specimen type or structure of interest. The calibration sample preparation and system calibration protocol can be executed within 1-2 d.
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open source image reconstruction of super resolution Structured Illumination Microscopy data in imagej
Nature Communications, 2016Co-Authors: Marcel Muller, Thomas R Huser, Viola Monkemoller, Simon Hennig, Wolfgang HubnerAbstract:Super-resolved Structured Illumination Microscopy (SR-SIM) is an important tool for fluorescence Microscopy. SR-SIM microscopes perform multiple image acquisitions with varying Illumination patterns, and reconstruct them to a super-resolved image. In its most frequent, linear implementation, SR-SIM doubles the spatial resolution. The reconstruction is performed numerically on the acquired wide-field image data, and thus relies on a software implementation of specific SR-SIM image reconstruction algorithms. We present fairSIM, an easy-to-use plugin that provides SR-SIM reconstructions for a wide range of SR-SIM platforms directly within ImageJ. For research groups developing their own implementations of super-resolution Structured Illumination Microscopy, fairSIM takes away the hurdle of generating yet another implementation of the reconstruction algorithm. For users of commercial microscopes, it offers an additional, in-depth analysis option for their data independent of specific operating systems. As a modular, open-source solution, fairSIM can easily be adapted, automated and extended as the field of SR-SIM progresses.
