Structured illumination microscopy for super-resolution and optical sectioning

Structured illumination microscopy with a phase-modulated spinning disk for optical sectioning

Among various super-resolution microscopic techniques, structured illumination microscopy (SIM) stands out for live-cell imaging because of its higher imaging speed. However, conventional SIM lacks optical sectioning capability. Here we demonstrate a new, to the best of our knowledge, approach using a phase-modulated spinning disk (PMSD) that enhances the optical sectioning capability of SIM. The PMSD consists of a pinhole array for confocal imaging and a transparent polymer layer for light phase modulation. The light phase modulation was designed to cancel the zeroth-order diffracted beam and create a sharp lattice illumination pattern using the interference of four first-order diffracted beams. In the detection optical path, the PMSD serves as a spatial filter to physically reject about 80% of the out-of-focus signals, an approach that allows for real-time optical reconstruction of super-resolved images with enhanced contrast. Furthermore, the simplicity of the design makes it easy to upgrade a conventional fluorescence microscope to a PMSD SIM system.

High-order spatial phase shift method realizes modulation analysis through a single-frame image

For the modulation-based structured illumination microscopy system, how to obtain modulation distribution with an image has been a research hotspot. However, the existing frequency-domain single-frame algorithms (mainly including the Fourier transform method, wavelet method, etc.) suffer from different degrees of analytical error due to the loss of high-frequency information. Recently, a modulation-based spatial area phase-shifting method was proposed; it can obtain higher precision by retaining high-frequency information effectively. But for discontinuous (such as step) topography, it would be somewhat smooth. To solve the problem, we propose a high-order spatial phase shift algorithm that realizes robust modulation analysis of a discontinuous surface with a single-frame image. At the same time, this technique proposes a residual optimization strategy, so that it can be applied to the measurement of complex topography, especially discontinuous topography. Simulation and experimental results demonstrate that the proposed method can provide higher-precision measurement.

An LED-Based structured illumination microscope using a digital micromirror device and GPU accelerated image reconstruction

When combined with computational approaches, fluorescence imaging becomes one of the most powerful tools in biomedical research. It is possible to achieve resolution figures beyond the diffraction limit, and improve the performance and flexibility of high-resolution imaging systems with techniques such as structured illumination microscopy (SIM) reconstruction. In this study, the hardware and software implementation of an LED-based super-resolution imaging system using SIM employing GPU accelerated parallel image reconstruction is presented. The sample is illuminated with two-dimensional sinusoidal patterns with various orientations and lateral phase shifts generated using a digital micromirror device (DMD). SIM reconstruction is carried out in frequency space using parallel CUDA kernel functions. Furthermore, a general purpose toolbox for the parallel image reconstruction algorithm and an infrastructure that allows all users to perform parallel operations on images without developing any CUDA kernel code is presented. The developed image reconstruction algorithm was run separately on a CPU and a GPU. Two different SIM reconstruction algorithms have been developed for the CPU as mono-thread CPU algorithm and multi-thread OpenMP CPU algorithm. SIM reconstruction of 1024 × 1024 px images was achieved in 1.49 s using GPU computation, indicating an enhancement by ∼28 and ∼20 in computation time when compared with mono-thread CPU computation and multi-thread OpenMP CPU computation, respectively.

Comparison of Two- and Three-Beam Interference Pattern Generation in Structured Illumination Microscopy

Structured illumination microscopy (SIM) provides wide-field optical sectioning in the focal plane by modulating the imaging information using fringe pattern illumination. For generating the fringe pattern illumination, a digital micro-mirror device (DMD) is commonly used due to its flexibility and fast refresh rate. However, the benefit of different pattern generation, for example, the two-beam interference mode and the three-beam interference mode, has not been clearly investigated. In this study, we systematically analyze the optical sectioning provided by the two-beam inference mode and the three-beam interference mode of DMD. The theoretical analysis and imaging results show that the two-beam interference mode is suitable for fast imaging of the superficial dynamic target due to reduced number of phase shifts needed to form the image, and the three-beam interference mode is ideal for imaging three-dimensional volume due to its superior optical sectioning by the improved modulation of the illumination patterns. These results, we believe, will provide better guidance for the use of DMD for SIM imaging and also for the choice of beam patterns in SIM application in the future.

Structured illumination microscopy with partially coherent illumination for phase and fluorescent imaging

This study presents a partially coherent illumination based (PCI-based) SIM apparatus for dual-modality (phase and fluorescent) microscopic imaging. The partially coherent illumination (PCI) is generated by placing a rotating diffuser on a monochromatic laser beam, which suppresses speckle noise in the dual-modality images and endows the apparatus with sound sectioning capability. With this system, label-free quantitative phase and super-resolved/sectioned fluorescent images can be obtained for the same sample. We have demonstrated the superiority of the system in phase imaging of transparent cells with high endogenous contrast and in a quantitative manner. In the meantime, we have also demonstrated fluorescent imaging of fluorescent beads, rat tail crosscut, wheat anther, and hibiscus pollen with super-resolution and optical sectioning. We envisage that the proposed method can be applied to many fields, including but not limited to biomedical, industrial, chemistry fields.

Super-Resolution Microscopy: Shedding New Light on In Vivo Imaging

Over the past two decades, super-resolution microscopy (SRM), which offered a significant improvement in resolution over conventional light microscopy, has become a powerful tool to visualize biological activities in both fixed and living cells. However, completely understanding biological processes requires studying cells in a physiological context at high spatiotemporal resolution. Recently, SRM has showcased its ability to observe the detailed structures and dynamics in living species. Here we summarized recent technical advancements in SRM that have been successfully applied to in vivo imaging. Then, improvements in the labeling strategies are discussed together with the spectroscopic and chemical demands of the fluorophores. Finally, we broadly reviewed the current applications for super-resolution techniques in living species and highlighted some inherent challenges faced in this emerging field. We hope that this review could serve as an ideal reference for researchers as well as beginners in the relevant field of in vivo super resolution imaging.

Fast structured illumination microscopy with a large dynamic measurement range

Fast structured illumination microscopy plays an important role in micro-nano detection due to the features of high accuracy, high efficiency, and excellent adaptability. The existing method utilizes the linear region of the axial modulation response curve (AMR), and by building the relationship between the modulation and the real height, achieves topography recovery. However, the traditional method is limited to narrow dynamic measurement range due to the linear region of the AMR being very short. In this paper, a double-differential fast structured illumination microscopy (DDFSIM) is proposed. By introducing two additional detectable branches for building the double-differential axial modulation response curve (DDAMR), the proposed method can obtain a large dynamic measurement range. In the measurement, three charge-coupled devices are respectively placed in and behind and before the focal plane to generate three axial modulation response curves. Three AMRs are used to set up the DDAMR, which has a large dynamic measurement range. Through simulation and experimental verification, the measurement range of DDFSIM is twice that of the conventional method under the same system parameters.

Full-color optically-sectioned imaging by wide-field microscopy via deep-learning

Wide-field microscopy (WFM) is broadly used in experimental studies of biological specimens. However, combining the out-of-focus signals with the in-focus plane reduces the signal-to-noise ratio (SNR) and axial resolution of the image. Therefore, structured illumination microscopy (SIM) with white light illumination has been used to obtain full-color 3D images, which can capture high SNR optically-sectioned images with improved axial resolution and natural specimen colors. Nevertheless, this full-color SIM (FC-SIM) has a data acquisition burden for 3D-image reconstruction with a shortened depth-of-field, especially for thick samples such as insects and large-scale 3D imaging using stitching techniques. In this paper, we propose a deep-learning-based method for full-color WFM, i.e., FC-WFM-Deep, which can reconstruct high-quality full-color 3D images with an extended optical sectioning capability directly from the FC-WFM z-stack data. Case studies of different specimens with a specific imaging system are used to illustrate this method. Consequently, the image quality achievable with this FC-WFM-Deep method is comparable to the FC-SIM method in terms of 3D information and spatial resolution, while the reconstruction data size is 21-fold smaller and the in-focus depth is doubled. This technique significantly reduces the 3D data acquisition requirements without losing detail and improves the 3D imaging speed by extracting the optical sectioning in the depth-of-field. This cost-effective and convenient method offers a promising tool to observe high-precision color 3D spatial distributions of biological samples.

Multi-plane, wide-field fluorescent microscopy for biodynamic imaging in vivo

Wide-field fluorescent microscopy (WFFM) is widely employed in biomedical studies, due to its inherent advantages in high-speed imaging of biological dynamics noninvasively and specifically. However, WFFM suffers from the loss of axial resolution and the poor resistance to light scattering in deep tissue imaging. Here we propose a novel WFFM which has the capability in optical sectioning and volumetric imaging. We perform speckle illumination with a digital-micromirror-device for optical sectioning and employ an electrically tunable lens for defocusing modulation so as to quickly switch the image planes. We demonstrate its applications in multi-plane, wide-field imaging of biological dynamics in both zebrafish brains and mouse brains in vivo.

Optical Imaging Approaches to Monitor Static and Dynamic Cell-on-Chip Platforms: A Tutorial Review

Miniaturized laboratories on chip platforms play an important role in handling life sciences studies. The platforms may contain static or dynamic biological cells. Examples are a fixed medium of an organ-on-a-chip and individual cells moving in a microfluidic channel, respectively. Due to feasibility of control or investigation and ethical implications of live targets, both static and dynamic cell-on-chip platforms promise various applications in biology. To extract necessary information from the experiments, the demand for direct monitoring is rapidly increasing. Among different microscopy methods, optical imaging is a straightforward choice. Considering light interaction with biological agents, imaging signals may be generated as a result of scattering or emission effects from a sample. Thus, optical imaging techniques could be categorized into scattering-based and emission-based techniques. In this review, various optical imaging approaches used in monitoring static and dynamic platforms are introduced along with their optical systems, advantages, challenges, and applications. This review may help biologists to find a suitable imaging technique for different cell-on-chip studies and might also be useful for the people who are going to develop optical imaging systems in life sciences studies.

Accurate surface profilometry using differential optical sectioning microscopy with structured illumination

A differential optical sectioning microscopy with structured-illumination (DOSM-SI) with enhanced axial precision is explored in this paper for three-dimensional (3D) measurement. As the segment of data on the linear region of the contrast depth response curve (CDR) is very sensitive to variation of the height information, the DOSM-SI introduces a new CDR2 with an axial shift to intersect the linear region of the CDR1, which is achieved by using two charge-coupled detectors (CCDs) in the optical path. The CCD1 is located on the imaging plane and the CCD2 is displaced from the imaging plane. The difference between the CDR1 and CDR2 for each pixel is defined as the differential depth response curve (DCDR). Further, the zero-crossing point of the DCDR for each pixel is accurately extracted using the line-fitting technique, and finally, the sample surface can be reconstructed with a high resolution and precision. Since the slope around the zero-crossing point of the DCDR is apparently larger than that of near the focal position, an enhanced resolution and precision can be realized in DOSM-SI. The experiments and theoretical analysis are elaborated to demonstrate the feasibility of DOSM-SI.

Structured illumination imaging without grating rotation based on mirror operation on 1D Fourier spectrum

Structured illumination microscopy (SIM) is a rapidly developing a super-resolution optical microscopy technique. With SIM, the grating is needed in order to rotate several angles for illuminating the sample in different directions. Multiple rotations reduce the imaging speed and grating rotation angle errors damage the image recovery quality. We introduce mirror transformation on one-dimension (1D) Fourier spectrum to SIM for resolving the problems of low imaging speed and severe impact on image reconstruction quality by grating rotation angle errors. When mirror operation and SIM are combined, the grating is placed at an orientation for obtaining three shadow images. The three shadow images are acquired by CCD at three different phase shift for a direction of grating. Thus, the SIM imaging speed is faster and the effect on image reconstruction quality by grating rotation angle errors is greatly reduced.

Improving resolution of second harmonic generation microscopy via scanning structured illumination

Second harmonic generation microscopy (SHGM) is a well-known technique for examining the noncentrosymmetric structures in biomedical research. However, without real-state transitions, fluorescence-based superresolution methods cannot be applied. To improve the resolution, fringe-scanning SHGM (FS-SHGM), which combines SHGM with structured illumination based on point-scanning, is introduced in this paper. The scanning path was modulated to generate illumination patterns. For the coherent parts of SHG signals, a mathematical model of image formation and reconstruction was established. Both simulations and experiments showed a resolution improvement factor of ~1.4 in the lateral and 1.56 in the axial directions for chicken tendons and mouse skin.

Parallel detection experiment of fluorescence confocal microscopy using DMD

Parallel detection of fluorescence confocal microscopy (PDFCM) system based on Digital Micromirror Device (DMD) is reported in this paper in order to realize simultaneous multi-channel imaging and improve detection speed. DMD is added into PDFCM system, working to take replace of the single traditional pinhole in the confocal system, which divides the laser source into multiple excitation beams. The PDFCM imaging system based on DMD is experimentally set up. The multi-channel image of fluorescence signal of potato cells sample is detected by parallel lateral scanning in order to verify the feasibility of introducing the DMD into fluorescence confocal microscope. In addition, for the purpose of characterizing the microscope, the depth response curve is also acquired. The experimental result shows that in contrast to conventional microscopy, the DMD-based PDFCM system has higher axial resolution and faster detection speed, which may bring some potential benefits in the biology and medicine analysis. SCANNING 38:234-239, 2016. © 2015 Wiley Periodicals, Inc.

Double-exposure optical sectioning structured illumination microscopy based on Hilbert transform reconstruction

Structured illumination microscopy (SIM) with axially optical sectioning capability has found widespread applications in three-dimensional live cell imaging in recent years, since it combines high sensitivity, short image acquisition time, and high spatial resolution. To obtain one sectioned slice, three raw images with a fixed phase-shift, normally 2π/3, are generally required. In this paper, we report a data processing algorithm based on the one-dimensional Hilbert transform, which needs only two raw images with arbitrary phase-shift for each single slice. The proposed algorithm is different from the previous two-dimensional Hilbert spiral transform algorithm in theory. The presented algorithm has the advantages of simpler data processing procedure, faster computation speed and better reconstructed image quality. The validity of the scheme is verified by imaging biological samples in our developed DMD-based LED-illumination SIM system.