scholarly journals Structured illumination microscopy artifacts caused by illumination scattering

2021 ◽  
Author(s):  
Yanquan Mo ◽  
Fan Feng ◽  
Heng Mao ◽  
Junchao Fan ◽  
Liangyi Chen
Keyword(s):  
Refractive Index ◽  
Incident Light ◽  
Super Resolution ◽  
Optical Path ◽  
Sample Thickness ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Subcellular Structure ◽  
Excitation Light ◽  
Noise Amplification

AbstractDespite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artifacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index (RI) from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artifacts caused by scattering in thick samples.

scholarly journals Structured illumination microscopy artefacts caused by illumination scattering

2021 ◽  
Vol 379 (2199) ◽  
Author(s):  
Yanquan Mo ◽  
Fan Feng ◽  
Heng Mao ◽  
Junchao Fan ◽  
Liangyi Chen
Keyword(s):  
Refractive Index ◽  
Incident Light ◽  
Super Resolution ◽  
Optical Path ◽  
Sample Thickness ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Subcellular Structure ◽  
Excitation Light ◽  
Noise Amplification

Despite its wide application in live-cell super-resolution (SR) imaging, structured illumination microscopy (SIM) suffers from aberrations caused by various sources. Although artefacts generated from inaccurate reconstruction parameter estimation and noise amplification can be minimized, aberrations due to the scattering of excitation light on samples have rarely been investigated. In this paper, by simulating multiple subcellular structure with the distinct refractive index from water, we study how different thicknesses of this subcellular structure scatter incident light on its optical path of SIM excitation. Because aberrant interference light aggravates with the increase in sample thickness, the reconstruction of the 2D-SIM SR image degraded with the change of focus along the axial axis. Therefore, this work may guide the future development of algorithms to suppress SIM artefacts caused by scattering in thick samples. This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 1)'.

scholarly journals Effect of light polariztion on pattern illumination super-resolution imaging

2016 ◽  
Vol 09 (03) ◽  
pp. 1641001 ◽  
Author(s):  
Caimin Qiu ◽  
Jianling Chen ◽  
Zexian Hou ◽  
Chaoxian Xu ◽  
Shusen Xie ◽  
...  
Keyword(s):  
Polarized Light ◽  
Super Resolution ◽  
Stimulated Emission ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Excitation Light ◽  
Imaging Technology ◽  
Circularly Polarized Light ◽  
Resolution Imaging ◽  
The Right

Far-field fluorescence microscopy has made great progress in the spatial resolution, limited by light diffraction, since the super-resolution imaging technology appeared. And stimulated emission depletion (STED) microscopy and structured illumination microscopy (SIM) can be grouped into one class of the super-resolution imaging technology, which use pattern illumination strategy to circumvent the diffraction limit. We simulated the images of the beads of SIM imaging, the intensity distribution of STED excitation light and depletion light in order to observe effects of the polarized light on imaging quality. Compared to fixed linear polarization, circularly polarized light is more suitable for SIM on reconstructed image. And right-handed circular polarization (CP) light is more appropriate for both the excitation and depletion light in STED system. Therefore the right-handed CP light would be the best candidate when the SIM and STED are combined into one microscope. Good understanding of the polarization will provide a reference for the patterned illumination experiment to achieve better resolution and better image quality.

scholarly journals Simulating digital micromirror devices for patterning coherent excitation light in structured illumination microscopy

2021 ◽  
Vol 379 (2199) ◽  
Author(s):  
Mario Lachetta ◽  
Hauke Sandmeyer ◽  
Alice Sandmeyer ◽  
Jan Schulte am Esch ◽  
Thomas Huser ◽  
...  
Keyword(s):  
High Speed ◽  
Super Resolution ◽  
Consumer Electronics ◽  
Light Sources ◽  
Structured Illumination ◽  
Coherent Light ◽  
Structured Illumination Microscopy ◽  
Excitation Light ◽  
Coherent Excitation ◽  
Digital Micromirror Devices

Digital micromirror devices (DMDs) are spatial light modulators that employ the electro-mechanical movement of miniaturized mirrors to steer and thus modulate the light reflected off a mirror array. Their wide availability, low cost and high speed make them a popular choice both in consumer electronics such as video projectors, and scientific applications such as microscopy. High-end fluorescence microscopy systems typically employ laser light sources, which by their nature provide coherent excitation light. In super-resolution microscopy applications that use light modulation, most notably structured illumination microscopy (SIM), the coherent nature of the excitation light becomes a requirement to achieve optimal interference pattern contrast. The universal combination of DMDs and coherent light sources, especially when working with multiple different wavelengths, is unfortunately not straight forward. The substructure of the tilted micromirror array gives rise to a blazed grating, which has to be understood and which must be taken into account when designing a DMD-based illumination system. Here, we present a set of simulation frameworks that explore the use of DMDs in conjunction with coherent light sources, motivated by their application in SIM, but which are generalizable to other light patterning applications. This framework provides all the tools to explore and compute DMD-based diffraction effects and to simulate possible system alignment configurations computationally, which simplifies the system design process and provides guidance for setting up DMD-based microscopes. This article is part of the Theo Murphy meeting ‘Super-resolution structured illumination microscopy (part 1)’.

scholarly journals Two-dimensional TIRF-SIM–traction force microscopy (2D TIRF-SIM-TFM)

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Liliana Barbieri ◽  
Huw Colin-York ◽  
Kseniya Korobchevskaya ◽  
Di Li ◽  
Deanna L. Wolfson ◽  
...  
Keyword(s):  
Resolution Enhancement ◽  
Traction Force ◽  
Super Resolution ◽  
Traction Force Microscopy ◽  
Two Dimensional ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Force Microscopy ◽  
Health And Disease ◽  
Spatio Temporal

AbstractQuantifying small, rapidly evolving forces generated by cells is a major challenge for the understanding of biomechanics and mechanobiology in health and disease. Traction force microscopy remains one of the most broadly applied force probing technologies but typically restricts itself to slow events over seconds and micron-scale displacements. Here, we improve >2-fold spatially and >10-fold temporally the resolution of planar cellular force probing compared to its related conventional modalities by combining fast two-dimensional total internal reflection fluorescence super-resolution structured illumination microscopy and traction force microscopy. This live-cell 2D TIRF-SIM-TFM methodology offers a combination of spatio-temporal resolution enhancement relevant to forces on the nano- and sub-second scales, opening up new aspects of mechanobiology to analysis.

scholarly journals Double moiré localized plasmon structured illumination microscopy

Nanophotonics ◽  
2020 ◽  
Vol 0 (0) ◽  
Author(s):  
Ruslan Röhrich ◽  
A. Femius Koenderink
Keyword(s):  
Near Field ◽  
Super Resolution ◽  
Reconstruction Algorithm ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Experimental Realization ◽  
Spatial Frequencies ◽  
Wide Range ◽  
Localized Plasmon ◽  
Plasmonic Grating

AbstractStructured illumination microscopy (SIM) is a well-established fluorescence imaging technique, which can increase spatial resolution by up to a factor of two. This article reports on a new way to extend the capabilities of structured illumination microscopy, by combining ideas from the fields of illumination engineering and nanophotonics. In this technique, plasmonic arrays of hexagonal symmetry are illuminated by two obliquely incident beams originating from a single laser. The resulting interference between the light grating and plasmonic grating creates a wide range of spatial frequencies above the microscope passband, while still preserving the spatial frequencies of regular SIM. To systematically investigate this technique and to contrast it with regular SIM and localized plasmon SIM, we implement a rigorous simulation procedure, which simulates the near-field illumination of the plasmonic grating and uses it in the subsequent forward imaging model. The inverse problem, of obtaining a super-resolution (SR) image from multiple low-resolution images, is solved using a numerical reconstruction algorithm while the obtained resolution is quantitatively assessed. The results point at the possibility of resolution enhancements beyond regular SIM, which rapidly vanishes with the height above the grating. In an initial experimental realization, the existence of the expected spatial frequencies is shown and the performance of compatible reconstruction approaches is compared. Finally, we discuss the obstacles of experimental implementations that would need to be overcome for artifact-free SR imaging.

scholarly journals High-fidelity structured illumination microscopy by point-spread-function engineering

2021 ◽  
Vol 10 (1) ◽  
Author(s):  
Gang Wen ◽  
Simin Li ◽  
Linbo Wang ◽  
Xiaohu Chen ◽  
Zhenglong Sun ◽  
...  
Keyword(s):  
Point Spread Function ◽  
Super Resolution ◽  
Reconstruction Algorithm ◽  
High Fidelity ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Imaging Tool ◽  
Point Spread ◽  
Spread Function ◽  
Point Spread Function Engineering

AbstractStructured illumination microscopy (SIM) has become a widely used tool for insight into biomedical challenges due to its rapid, long-term, and super-resolution (SR) imaging. However, artifacts that often appear in SIM images have long brought into question its fidelity, and might cause misinterpretation of biological structures. We present HiFi-SIM, a high-fidelity SIM reconstruction algorithm, by engineering the effective point spread function (PSF) into an ideal form. HiFi-SIM can effectively reduce commonly seen artifacts without loss of fine structures and improve the axial sectioning for samples with strong background. In particular, HiFi-SIM is not sensitive to the commonly used PSF and reconstruction parameters; hence, it lowers the requirements for dedicated PSF calibration and complicated parameter adjustment, thus promoting SIM as a daily imaging tool.

The FDTD Analysis of Near-Field Response for Microgroove Structure With Standing Wave Illumination for the Realization of Coherent Structured Illumination Microscopy

2021 ◽  
Author(s):  
Yizhao Guan ◽  
Hiromasa Kume ◽  
Shotaro Kadoya ◽  
Masaki Michihata ◽  
Satoru Takahashi
Keyword(s):  
Standing Wave ◽  
Incident Angle ◽  
Near Field ◽  
Super Resolution ◽  
Structured Illumination ◽  
Field Phase ◽  
Structured Illumination Microscopy ◽  
Depth Measurement ◽  
Field Response ◽  
Depth Dependency

Abstract Microstructures are widely used in the manufacture of functional surfaces. An optical-based super-resolution, non-invasive method is preferred for the inspection of surfaces with massive microstructures. The Structured Illumination Microscopy (SIM) uses standing-wave illumination to reach optical super-resolution. Recently, coherent SIM is being studied. It can obtain not only the super-resolved intensity distribution but also the phase and amplitude distribution of the sample surface beyond the diffraction limit. By analysis of the phase-depth dependency, the depth measurement for microgroove structures with coherent SIM is expected. FDTD analysis is applied for observing the near-field response of microgroove under the standing-wave illumination. The near-field phase shows depth dependency in this analysis. Moreover, the effects from microgroove width, the incident angle, and the relative position between the standing-wave peak and center of the microgroove are investigated. It is found the near-field phase change can measure depth until 200 nm (aspect ratio 1) with an error of up to 20.4 nm in the case that the microgroove width is smaller than half of the wavelength.

Super-Resolution Imaging in Fluid Mechanics Using New Illumination Approaches

2020 ◽  
Vol 52 (1) ◽  
pp. 369-393
Author(s):  
Minami Yoda
Keyword(s):  
Fluid Mechanics ◽  
Total Internal Reflection ◽  
Imaging Techniques ◽  
Super Resolution ◽  
Internal Reflection ◽  
Interfacial Flows ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Entire Volume ◽  
Resolution Imaging

Quantifying submillimeter flows using optical diagnostic techniques is often limited by a lack of spatial resolution and optical access. This review discusses two super-resolution imaging techniques, structured illumination microscopy and total internal reflection fluorescence or microscopy, which can visualize bulk and interfacial flows, respectively, at spatial resolutions below the classic diffraction limits. First, we discuss the theory and applications of structured illumination for optical sectioning, i.e., imaging a thin slice of a flow illuminated over its entire volume. Structured illumination can be used to visualize the interior of multiphase flows such as sprays by greatly reducing secondary scattering. Second, the theory underlying evanescent waves is introduced, followed by a review of how total internal reflection microscopy has been used to visualize interfacial flows over the last 15 years. Both techniques, which are starting to be used in fluid mechanics, could significantly improve quantitative imaging of microscale and macroscale flows.

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