scholarly journals Moments reconstruction and local dynamic range compression of high order Superresolution Optical Fluctuation Imaging

2018 ◽  
Author(s):  
Xiyu Yi ◽  
Sungho Son ◽  
Ryoko Ando ◽  
Atsushi Miyawaki ◽  
Shimon Weiss
Keyword(s):  
Dynamic Range ◽  
Imaging Techniques ◽  
Resolution Enhancement ◽  
Super Resolution ◽  
High Order ◽  
Live Cells ◽  
Local Dynamic ◽  
Actin Stress Fiber ◽  
Dynamic Range Compression ◽  
Even Order

Abstract:Super-resolution Optical Fluctuation Imaging (SOFI) offers a simple and affordable alternative to other super-resolution (SR) imaging techniques. The theoretical resolution enhancement of SOFI scales linearly with the cumulants’ order, while imaging conditions are less phototoxic to living samples as compared to other SR methods. High order SOFI could, therefore, be a method of choice for dynamic live cell imaging. However, due to cusp-artifacts and to dynamic range expansion of pixel intensities, this promise has not been materialized as of yet. Here we investigated and compared high order moments vs. high order cumulants SOFI reconstructions. We demonstrate that even-order moments reconstructions are intrinsically free of cusp artifacts, allowing for a subsequent deconvolution operation to be performed, hence enhancing the resolution even further. High order moments reconstructions performance was examined for various (simulated) conditions and applied to (experimental) imaging of QD labeled microtubules in fixed cells, and actin stress fiber dynamics in live cells.

scholarly journals Cusp-artifacts in high order Superresolution Optical Fluctuation Imaging

2019 ◽  
Author(s):  
Xiyu Yi ◽  
Shimon Weiss
Keyword(s):  
Dynamic Range ◽  
Imaging Techniques ◽  
Photophysical Properties ◽  
Super Resolution ◽  
High Order ◽  
Fluorescence Probes ◽  
Structured Illumination ◽  
Odd Order ◽  
Even Order ◽  
High Order Cumulants

AbstractSuperresolution Optical Fluctuation Imaging (SOFI) offers a simple and affordable alternative to the more sophisticated (and expensive) super-resolution imaging techniques such as STED, PALM, STORM, structured illumination, and other derivative methods. In SOFI, the calculation of high order cumulants provides higher resolution but drastically expands the dynamic range of the resulting image. In this study, we have identified another type of artifact for high order SOFI cumulants, dubbed as ‘cusp artifacts.’ A series of realistic simulations are performed to study the cusp artifacts under the influences of various factors, including the blinking statistics, the spatial distribution of photophysical properties of the sample, the total number of frames processed per dataset, photobleaching, and noise. Experiments, simulations, and theory all show that high order cumulants and odd-order moments could suffer from cusp artifacts. These cusp artifacts also degrade the fidelity of bSOFI that has been proposed to solve the dynamic range expansion of image pixel intensities. Alternatively, cusp-artifacts could be altogether eliminated by utilizing even-order moments constructed directly or from cumulants for image reconstruction. Together with dynamic range compression, these approaches yield improved SOFI images. Our study provides new insight into the nature of high order SOFI images, outlines guidelines for developing and screening SOFI-optimized fluorescence probes, and suggests improved strategies for SOFI data acquisition.

scholarly journals Moments reconstruction and local dynamic range compression of high order superresolution optical fluctuation imaging

2019 ◽  
Vol 10 (5) ◽  
pp. 2430 ◽  
Author(s):  
Xiyu Yi ◽  
Sungho Son ◽  
Ryoko Ando ◽  
Atsushi Miyawaki ◽  
Shimon Weiss
Keyword(s):  
Dynamic Range ◽  
High Order ◽  
Local Dynamic ◽  
Dynamic Range Compression

scholarly journals 3D super-resolved imaging in live cells using sub-diffractive plasmonic localization of hybrid nanopillar arrays

Nanophotonics ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 2847-2859
Author(s):  
Soojung Kim ◽  
Hyerin Song ◽  
Heesang Ahn ◽  
Seung Won Jun ◽  
Seungchul Kim ◽  
...  
Keyword(s):  
Signal To Noise Ratio ◽  
Imaging Techniques ◽  
Optical Loss ◽  
Super Resolution ◽  
Living Cells ◽  
Live Cells ◽  
Complex Biological System ◽  
Observation Volume ◽  
Resolution Imaging ◽  
Nanopillar Arrays

AbstractAnalysing dynamics of a single biomolecule using high-resolution imaging techniques has been had significant attentions to understand complex biological system. Among the many approaches, vertical nanopillar arrays in contact with the inside of cells have been reported as a one of useful imaging applications since an observation volume can be confined down to few-tens nanometre theoretically. However, the nanopillars experimentally are not able to obtain super-resolution imaging because their evanescent waves generate a high optical loss and a low signal-to-noise ratio. Also, conventional nanopillars have a limitation to yield 3D information because they do not concern field localization in z-axis. Here, we developed novel hybrid nanopillar arrays (HNPs) that consist of SiO2 nanopillars terminated with gold nanodisks, allowing extreme light localization. The electromagnetic field profiles of HNPs are obtained through simulations and imaging resolution of cell membrane and biomolecules in living cells are tested using one-photon and 3D multiphoton fluorescence microscopy, respectively. Consequently, HNPs present approximately 25 times enhanced intensity compared to controls and obtained an axial and lateral resolution of 110 and 210 nm of the intensities of fluorophores conjugated with biomolecules transported in living cells. These structures can be a great platform to analyse complex intracellular environment.

An overview of structured illumination microscopy: recent advances and perspectives

2021 ◽  
Author(s):  
Krishnendu Samanta ◽  
Joby Joseph
Keyword(s):  
Spatial Frequency ◽  
Basic Principle ◽  
Imaging Techniques ◽  
Resolution Enhancement ◽  
Super Resolution ◽  
Diffraction Limit ◽  
Structured Illumination ◽  
Post Processing ◽  
Structured Illumination Microscopy ◽  
Near Future

Abstract Structured illumination microscopy (SIM) is one of the most significant widefield super-resolution optical imaging techniques. The conventional SIM utilizes a sinusoidal structured pattern to excite the fluorescent sample; which eventually down-modulates higher spatial frequency sample information within the diffraction-limited passband of the microscopy system and provides around two-fold resolution enhancement over diffraction limit after suitable computational post-processing. Here we provide an overview of the basic principle, image reconstruction, technical development of the SIM technique. Nonetheless, in order to push the SIM resolution further towards the extreme nanoscale dimensions, several different approaches are launched apart from the conventional SIM. Among the various SIM methods, some of the important techniques e.g. TIRF, non-linear, plasmonic, speckle SIM etc. are discussed elaborately. Moreover, we highlight different implementations of SIM in various other imaging modalities to enhance their imaging performances with augmented capabilities. Finally, some future outlooks are mentioned which might develop fruitfully and pave the way for new discoveries in near future.

scholarly journals Engineering of a fluorescent chemogenetic reporter with tunable color for advanced live-cell imaging

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Hela Benaissa ◽  
Karim Ounoughi ◽  
Isabelle Aujard ◽  
Evelyne Fischer ◽  
Rosette Goïame ◽  
...  
Keyword(s):  
Spectral Properties ◽  
Rational Design ◽  
Imaging Techniques ◽  
Resonance Energy Transfer ◽  
Resonance Energy ◽  
Super Resolution ◽  
Visible Spectrum ◽  
Live Cells ◽  
Fluorescent Reporters ◽  
Entire Visible Spectrum

AbstractBiocompatible fluorescent reporters with spectral properties spanning the entire visible spectrum are indispensable tools for imaging the biochemistry of living cells and organisms in real time. Here, we report the engineering of a fluorescent chemogenetic reporter with tunable optical and spectral properties. A collection of fluorogenic chromophores with various electronic properties enables to generate bimolecular fluorescent assemblies that cover the visible spectrum from blue to red using a single protein tag engineered and optimized by directed evolution and rational design. The ability to tune the fluorescence color and properties through simple molecular modulation provides a broad experimental versatility for imaging proteins in live cells, including neurons, and in multicellular organisms, and opens avenues for optimizing Förster resonance energy transfer (FRET) biosensors in live cells. The ability to tune the spectral properties and fluorescence performance enables furthermore to match the specifications and requirements of advanced super-resolution imaging techniques.

Imaging live cells at high spatiotemporal resolution for lab-on-a-chip applications

Lab on a Chip ◽  
2016 ◽  
Vol 16 (11) ◽  
pp. 2014-2024 ◽  
Author(s):  
Lip Ket Chin ◽  
Chau-Hwang Lee ◽  
Bi-Chang Chen
Keyword(s):  
Imaging Techniques ◽  
Super Resolution ◽  
Lab On A Chip ◽  
Live Cells ◽  
Spatiotemporal Resolution ◽  
Cellular Processes ◽  
High Spatiotemporal Resolution ◽  
Microfluidic Technology ◽  
Resolution Imaging

The synergy of novel super-resolution imaging techniques and microfluidic technology provides new biological and biomedical insights into sub-cellular processes.

Implantable hearing interfaces

2018 ◽  
Author(s):  
Torsten Lehmann ◽  
André van Schaik
Keyword(s):  
Cochlear Implants ◽  
Neural Activity ◽  
Dynamic Range ◽  
Systems Design ◽  
Fundamental Operation ◽  
Profound Hearing Loss ◽  
Biomedical Implant ◽  
Dynamic Range Compression ◽  
Hearing Function ◽  
Key Aspects

The chapter Implantable hearing interfaces describes the fundamental operation of a commonly available biohybrid system, the cochlear implant, or bionic ear. This neuro-stimulating biomedical implant is very successful in restoring hearing function to people with profound hearing loss. The fundamental operation of the biological cochlea is described and parallels are drawn between key aspects of the biological system and the biohybrid implementation: dynamic range compression, translation of sound to neural activity, and tonotopic mapping. Critical considerations are discussed for simultaneously meeting biological, surgical, and engineering restrictions in successful biohybrid systems design. Finally, challenges in present and future cochlear implants are outlined and directions of current research given.

scholarly journals Comparing Super-Resolution Microscopy Techniques to Analyze Chromosomes

2021 ◽  
Vol 22 (4) ◽  
pp. 1903
Author(s):  
Ivona Kubalová ◽  
Alžběta Němečková ◽  
Klaus Weisshart ◽  
Eva Hřibová ◽  
Veit Schubert
Keyword(s):  
Single Molecule ◽  
Imaging Techniques ◽  
Chromatin Condensation ◽  
Super Resolution ◽  
Stimulated Emission ◽  
Wide Field ◽  
Structured Illumination Microscopy ◽  
Metaphase Chromosomes ◽  
Localization Microscopy ◽  
Super Resolution Microscopy

The importance of fluorescence light microscopy for understanding cellular and sub-cellular structures and functions is undeniable. However, the resolution is limited by light diffraction (~200–250 nm laterally, ~500–700 nm axially). Meanwhile, super-resolution microscopy, such as structured illumination microscopy (SIM), is being applied more and more to overcome this restriction. Instead, super-resolution by stimulated emission depletion (STED) microscopy achieving a resolution of ~50 nm laterally and ~130 nm axially has not yet frequently been applied in plant cell research due to the required specific sample preparation and stable dye staining. Single-molecule localization microscopy (SMLM) including photoactivated localization microscopy (PALM) has not yet been widely used, although this nanoscopic technique allows even the detection of single molecules. In this study, we compared protein imaging within metaphase chromosomes of barley via conventional wide-field and confocal microscopy, and the sub-diffraction methods SIM, STED, and SMLM. The chromosomes were labeled by DAPI (4′,6-diamidino-2-phenylindol), a DNA-specific dye, and with antibodies against topoisomerase IIα (Topo II), a protein important for correct chromatin condensation. Compared to the diffraction-limited methods, the combination of the three different super-resolution imaging techniques delivered tremendous additional insights into the plant chromosome architecture through the achieved increased resolution.

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