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

2020 ◽  
Author(s):  
Mario Lachetta ◽  
Hauke Sandmeyer ◽  
Alice Sandmeyer ◽  
Jan Schulte am Esch ◽  
Thomas Huser ◽  
...  
Keyword(s):  
High Speed ◽  
Consumer Electronics ◽  
Light Sources ◽  
Structured Illumination ◽  
Light Modulation ◽  
Coherent Light ◽  
Structured Illumination Microscopy ◽  
Excitation Light ◽  
Coherent Excitation ◽  
Digital Micromirror Devices

SummaryDigital micromirror devices (DMDs) are spatial light modulators that employ the electro-mechanical movement of miniaturized mirrors to steer and thus modulate the light reflected of 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.

scholarly journals DMD-based super-resolution structured illumination microscopy visualizes live cell dynamics at high speed and low cost

2019 ◽  
Author(s):  
Alice Sandmeyer ◽  
Mario Lachetta ◽  
Hauke Sandmeyer ◽  
Wolfgang Hübner ◽  
Thomas Huser ◽  
...  
Keyword(s):  
High Speed ◽  
Fluorescent Protein ◽  
Low Cost ◽  
Super Resolution ◽  
Live Cell ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Blazed Grating ◽  
High Modulation ◽  
Digital Micromirror Devices

Structured illumination microscopy (SIM) is among the most widely used super-resolution fluorescence microscopy techniques for visualizing the dynamics of cellular organelles, such as mitochondria, the endoplasmic reticulum, or the cytoskeleton. In its most wide-spread implementation, SIM relies on the creation of an interference pattern at the diffraction limit using the coherent addition of laser beams created by a diffraction pattern.Spatial light modulators based on liquid crystal displays allow SIM micro-scopes to run at image rates of up to hundreds of super-resolved images per second. Digital micromirror devices are another natural choice for creating interference-based SIM patterns, but are not used to their fullest potential because of the blazed grating effect. This effect arises due to the fixed angles between which the mirrors can be switched, creating a sawtooth arrangement of mirrors and thus leading to a change in the intensity distribution of the diffracted beams. This results in SIM patterns with varying modulation contrast which are prone to reconstruction artifacts.We have carefully studied the blazed grating effect of DMDs by simulations, varying a range of parameters and compared the simulation results with experiments. This allowed us to identify settings which result in very high modulation contrast across all angles and phases required to generate 2-beam SIM pattern. The use of inexpensive industry-grade CMOS cameras as well as low-cost lasers enabled us to construct a cost-effective, high-speed SIM system. Reconstruction of the super-resolved SIM images is achieved on a recently demonstrated parallel-computing platform, which allowed us to visualize living cells with super-resolution at multiple reconstructed frames per second in real time. We demonstrate the versatility of this new platform by imaging cellular organelle dynamics based on live-cell fluorescent stains as well as with fluorescent protein stained samples.

scholarly journals High-speed multiplane structured illumination microscopy of living cells using an image-splitting prism

Nanophotonics ◽  
2019 ◽  
Vol 9 (1) ◽  
pp. 143-148
Author(s):  
Adrien Descloux ◽  
Marcel Müller ◽  
Vytautas Navikas ◽  
Andreas Markwirth ◽  
Robin van den Eynde ◽  
...  
Keyword(s):  
High Speed ◽  
Three Dimensional ◽  
Super Resolution ◽  
Optical Element ◽  
Spatial Light Modulators ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Image Stack ◽  
Light Modulators ◽  
3D Information

AbstractSuper-resolution structured illumination microscopy (SR-SIM) can be conducted at video-rate acquisition speeds when combined with high-speed spatial light modulators and sCMOS cameras, rendering it particularly suitable for live-cell imaging. If, however, three-dimensional (3D) information is desired, the sequential acquisition of vertical image stacks employed by current setups significantly slows down the acquisition process. In this work, we present a multiplane approach to SR-SIM that overcomes this slowdown via the simultaneous acquisition of multiple object planes, employing a recently introduced multiplane image splitting prism combined with high-speed SIM illumination. This strategy requires only the introduction of a single optical element and the addition of a second camera to acquire a laterally highly resolved 3D image stack. We demonstrate the performance of multiplane SIM by applying this instrument to imaging the dynamics of mitochondria in living COS-7 cells.

scholarly journals Advances in High-Speed Structured Illumination Microscopy

2021 ◽  
Vol 9 ◽  
Author(s):  
Tianyu Zhao ◽  
Zhaojun Wang ◽  
Tongsheng Chen ◽  
Ming Lei ◽  
Baoli Yao ◽  
...  
Keyword(s):  
Live Cell Imaging ◽  
High Speed ◽  
Cell Imaging ◽  
Super Resolution ◽  
Live Cell ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Light Power ◽  
Recent Developments ◽  
Super Resolution Microscopy

Super-resolution microscopy surpasses the diffraction limit to enable the observation of the fine details in sub-cellular structures and their dynamics in diverse biological processes within living cells. Structured illumination microscopy (SIM) uses a relatively low illumination light power compared with other super-resolution microscopies and has great potential to meet the demands of live-cell imaging. However, the imaging acquisition and reconstruction speeds limit its further applications. In this article, recent developments all targeted at improving the overall speed of SIM are reviewed. These comprise both hardware and software improvements, which include a reduction in the number of raw images, GPU acceleration, deep learning and the spatial domain reconstruction. We also discuss the application of these developments in live-cell imaging.

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.

Localized plasmon assisted structured illumination microscopy for wide-field high-speed dispersion-independent super resolution imaging

Nanoscale ◽  
2014 ◽  
Vol 6 (11) ◽  
pp. 5807-5812 ◽  
Author(s):  
Joseph Louis Ponsetto ◽  
Feifei Wei ◽  
Zhaowei Liu
Keyword(s):  
Antenna Array ◽  
High Speed ◽  
Super Resolution ◽  
Fluorescent Imaging ◽  
Wide Field ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Resolution Imaging ◽  
Localized Plasmon ◽  
Imaging Resolution

Fluorescent imaging resolution down to 51 nm is shown by generating tunable localized plasmon excitations on a nano-antenna array.

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 Multicolor structured illumination microscopy and quantitative control of polychromatic coherent light with a digital micromirror device

2020 ◽  
Author(s):  
Peter T Brown ◽  
Rory Kruithoff ◽  
Gregory J Seedorf ◽  
Douglas P Shepherd
Keyword(s):  
Closed Form Solution ◽  
Forward Model ◽  
Live Cells ◽  
Optical Transfer Function ◽  
Structured Illumination ◽  
Coherent Light ◽  
Structured Illumination Microscopy ◽  
Excitation Light ◽  
Promising Alternative ◽  
Diffractive Optic

Structured illumination microscopy (SIM) is a broadly applicable super-resolution microscopy technique which does not impose photophysics requirements on fluorescent samples. Multicolor SIM implementations typically rely on liquid crystal on silicon (LCoS) spatial light modulators (SLM's) for precise patterning of the excitation light, but digital micromirror devices (DMD's) are a promising alternative, owing to their lower cost, increased imaging rate, and simplified experimental timings. Given these advantages, why do existing DMD SIM implementations either rely on incoherent projection, resulting in an order of magnitude lower signal-to-noise, or utilize coherent light at only a single wavelength? The primary obstacle to realizing a multicolor coherent DMD SIM microscope is the lack of an efficient approach for dealing with the blazed grating effect. To address this challenge, we developed quantitative tools applicable to a single DMD acting as a polychromatic diffractive optic. These include a closed form solution of the blaze and diffraction conditions, a forward model of DMD diffraction, and a forward model of coherent pattern projection. We applied these to identify experimentally feasible configurations using a single DMD as a polychromatic diffractive optic for combinations of three and four common fluorophore wavelengths. Based on these advances, we constructed a DMD SIM microscope for coherent light which we used to validate these models, develop a high-resolution optical transfer function measurement technique, and demonstrate SIM resolution enhancement for calibration samples, fixed cells, and live cells. This low-cost setup opens the door to applying DMD's in polychromatic applications which were previously restricted to LCoS SLM's.

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 mmSIM: an open toolbox for accessible structured illumination microscopy

2021 ◽  
Vol 379 (2199) ◽  
Author(s):  
Craig T. Russell ◽  
Michael Shaw
Keyword(s):  
Open Source ◽  
Open Source Software ◽  
High Speed ◽  
Super Resolution ◽  
Software Tools ◽  
Structured Illumination ◽  
Structured Illumination Microscopy ◽  
Light Modulator ◽  
Wide Range ◽  
Hardware Designs

Since the first practical super-resolution structured illumination fluorescence microscopes (SIM) were demonstrated more than two decades ago, the method has become increasingly popular for a wide range of bioimaging applications. The high cost and relative inflexibility of commercial systems, coupled with the conceptual simplicity of the approach and the desire to exploit and customize existing hardware, have led to the development of a large number of home-built systems. Several detailed hardware designs are available in the scientific literature, complemented by open-source software tools for SIM image validation and reconstruction. However, there remains a lack of simple open-source software to control these systems and manage the synchronization between hardware components, which is critical for effective SIM imaging. This article describes a new suite of software tools based on the popular Micro-Manager package, which enable the keen microscopist to develop and run a SIM system. We use the software to control two custom-built, high-speed, spatial light modulator-based SIM systems, evaluating their performance by imaging a range of fluorescent samples. By simplifying the process of SIM hardware development, we aim to support wider adoption of the technique. This article is part of the Theo Murphy meeting issue ‘Super-resolution structured illumination microscopy (part 1)’.

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