arXiv subjects

Peng Xi

Publications and source records attributed to Peng Xi.

13 recordsLinked to original sources

arXiv2025

High Spatiotemporal Resolution Structured Illumination Microscopy: Principle, Instrumentation, and Applications

Among super-resolution microscopy techniques, structured illumination microscopy (SIM) shows great advances of low phototoxicity, high speed, and excellent performance in long-term dynamic observation, making it especially suitable for live cell imaging. This review delves into the principles, instrumentation, and applications of SIM, highlighting its capabilities in achieving high spatiotemporal resolution. Two types of structured illumination mechanics are employed: (1) stripe-based SIM, where the illumination stripes are formed through interference or projection, with extended resolution achieved through Fourier-domain extension; (2) point-scanning based SIM, where illumination pattern are generated through projection of the focal point or focal array, with extended resolution achieved through photon reassignment. We discuss the evolution of SIM from mechanical to high-speed photoelectric devices, such as spatial light modulators, digital micromirror devices, galvanometers, etc., which significantly enhance imaging speed, resolution, and modulation flexibility. The review also explores SIM's applications in biological research, particularly in live-cell imaging and cellular interaction studies, providing insights into disease mechanisms and cellular functions. We conclude by outlining the future directions of SIM in life sciences. With the advancement of imaging techniques and reconstruction algorithms, SIM is poised to bring revolutionary impacts to frontier research fields, offering new avenues for exploring the intricacies of cellular biology.

physics.optics↗

arXiv2021

FEDI: Few-shot learning based on Earth Mover's Distance algorithm combined with deep residual network to identify diabetic retinopathy

Diabetic retinopathy(DR) is the main cause of blindness in diabetic patients. However, DR can easily delay the occurrence of blindness through the diagnosis of the fundus. In view of the reality, it is difficult to collect a large amount of diabetic retina data in clinical practice. This paper proposes a few-shot learning model of a deep residual network based on Earth Mover's Distance algorithm to assist in diagnosing DR. We build training and validation classification tasks for few-shot learning based on 39 categories of 1000 sample data, train deep residual networks, and obtain experience maximization pre-training models. Based on the weights of the pre-trained model, the Earth Mover's Distance algorithm calculates the distance between the images, obtains the similarity between the images, and changes the model's parameters to improve the accuracy of the training model. Finally, the experimental construction of the small sample classification task of the test set to optimize the model further, and finally, an accuracy of 93.5667% on the 3way10shot task of the diabetic retina test set. For the experimental code and results, please refer to: https://github.com/panliangrui/few-shot-learning-funds.

eess.IV↗

arXiv2021

Axially Overlapped Multi-Focus Light Sheet with Enlarged Field of View

Light sheet fluorescence microscopy provides optical sectioning and is widely used in volumetric imaging of large specimens. However, the axial resolution and the lateral Field of View (FoV) of the system, defined by the light sheet, typically limit each other due to the spatial band product of the excitation objective. Here, we develop a simple multi-focus scheme to extend the FoV, where a Gaussian light sheet can be focused at three or more consecutive positions. Axially overlapped multiple light sheets significantly enlarge the FoV with improved uniformity and negligible loss in axial resolution. By measuring the point spread function of fluorescent beads, we demonstrated that the obtained light sheet has a FoV of 450 um and a maximum axial FWHM of 7.5 um. Compared with the conventional single-focus one, the multi-focus Gaussian light sheet displays a significantly improved optical sectioning ability over the full FoV when imaging cells and zebrafish.

physics.optics↗

arXiv2021

Full Poincar\'e polarimetry enabled through physical inference

While polarisation sensing is vital in many areas of research, with applications spanning from microscopy to aerospace, traditional approaches are limited by method-related error amplification or accumulation, placing fundamental limitations on precision and accuracy in single-shot polarimetry. Here, we put forward a new measurement paradigm to circumvent this, introducing the notion of a universal full Poincar\'e generator to map all polarisation analyser states into a single vectorially structured light field, allowing all vector components to be analysed in a single-shot with theoretically user-defined precision. To demonstrate the advantage of our approach, we use a common GRIN optic as our mapping device and show mean errors of <1% for each vector component, enhancing the sensitivity by around three times, allowing us to sense weak polarisation aberrations not measurable by traditional single-shot techniques. Our work paves the way for next-generation polarimetry, impacting a wide variety of applications relying on weak vector measurement.

physics.optics↗

arXiv2020

Two-photon MINFLUX with doubled localization precision

Achieving localization with molecular precision has been of great interest for extending fluorescence microscopy to nanoscopy. MINFLUX pioneers this transition through point spread function (PSF) engineering, yet its performance is primarily limited by the signal-to-background ratio. Here we demonstrate that applying two-photon excitation to MINFLUX would double its localization precision through PSF engineering by nonlinear effect. Cram\'er-Rao Bound (CRB) is studied as the maximum localization precision, and CRB of two-photon MINFLUX is halved compared to single-photon MINFLUX in all three dimensions. Meanwhile, in order to achieve same localization precision with single-photon MINFLUX, two-photon MINFLUX requires only 1/4 of fluorescence photons, contributing to a possible 4-fold temporal resolution. Benefitted from two-photon excitation, registration-free multicolor nanoscopy and ultrafast color tracking can be achieved. Localization precision of MINFLUX can also be doubled using excitation with second-order Laguerre-Gaussian beams but would suffer from high fluorescence background compared to single-photon and two-photon first-order MINFLUX.

physics.optics↗

arXiv2019

Structured Illumination Microscopy using Digital Micro-mirror Device and Coherent Light Source

Structured illumination microscopy (SIM) achieves doubled spatial resolution by exciting the specimen with a high-contrast, high-frequency sinusoidal pattern. Such an excitation pattern can be generated by interference between multiple laser beams, which are diffracted from a grating. In SIM, 2D imaging requires 9 patterns and 3D imaging requires 15 patterns. Compared to mechanical movement of gratings, opti-electro devices provide rapid switch of the excitation patterns, in which Digital Micro-mirror Device (DMD) is most common in industry. Here we model DMD as the blazed grating and report a fast and cost-efficient SIM. Our home-built DMD-based laser interference structured illumination microscopy (DMD-ISIM) system reveals the nuclear pore complex and microtubule in mammalian cells with doubled spatial resolution. We further proposed multi-color DMD-ISIM system with simulation, which could potentially exploit the full power of DMD-ISIM.

physics.optics↗

arXiv2019

Complex vectorial optics through gradient index lens cascades

Graded index (GRIN) lenses are commonly used for compact imaging systems. It is not widely appreciated that the ion-exchange process that creates the rotationally symmetric GRIN lens index profile also causes a symmetric birefringence variation. This property is usually considered a nuisance, such that manufacturing processes are optimized to keep it to a minimum. Here, rather than avoiding this birefringence, we understand and harness it by using GRIN lenses in cascade with other optical components to enable extra functionality in commonplace GRIN lens systems. We show how birefringence in the GRIN cascades can generate vector vortex beams and foci, and how it can be used advantageously to improve axial resolution. Through using the birefringence for analysis, we show that the GRIN cascades form the basis of a new single-shot Mueller matrix polarimeter with potential for endoscopic label-free cancer diagnostics. The versatility of these cascades opens up new technological directions.

physics.optics↗

arXiv2017

Super-resolution Imaging of the Fluorescent Dipole Assembly with Polarized Structured Illumination Microscopy

Fluorescence polarization microscopy images both the intensity and orientation of fluorescent dipoles, which plays a vital role in studying the molecular structure and dynamics of bio-complex. However, it is difficult to resolve the dipole assemblies on the subcellular structure and their dynamics in living cells with super-resolution. Here we report polarized structured illumination microscopy (pSIM), which decouples the entangled spatial and angular structured illumination through interpreting the dipoles in spatio-angular hyperspace. We demonstrate its application on a series of biological filamentous systems such as cytoskeleton networks and lambda-DNA, and report the dynamics of short actin sliding through myosin-coated surface. Further, pSIM reveals "side-by-side" organization of the actin ring structure in the membrane-associated periodic skeleton in hippocampal neurons. It also images the dipole dynamics of green fluorescent proteins labeled to the microtubules in live U2OS cells. pSIM can be applied directly to a large variety of commercial or home-built SIM systems.

physics.optics↗

arXiv2016

Structured illumination microscopy image reconstruction algorithm

Structured illumination microscopy (SIM) is a very important super-resolution microscopy technique, which provides high speed super-resolution with about two-fold spatial resolution enhancement. Several attempts aimed at improving the performance of SIM reconstruction algorithm have been reported. However, most of these highlight only one specific aspect of the SIM reconstruction -- such as the determination of the illumination pattern phase shift accurately -- whereas other key elements -- such as determination of modulation factor, estimation of object power spectrum, Wiener filtering frequency components with inclusion of object power spectrum information, translocating and the merging of the overlapping frequency components -- are usually glossed over superficially. In addition, most of the work reported lie scattered throughout the literature and a comprehensive review of the theoretical background is found lacking. The purpose of the present work is two-fold: 1) to collect the essential theoretical details of SIM algorithm at one place, thereby making them readily accessible to readers for the first time; and 2) to provide an open source SIM reconstruction code (named OpenSIM), which enables users to interactively vary the code parameters and study it's effect on reconstructed SIM image.

cs.CV↗

arXiv2015

Super-resolution deep imaging with hollow Bessel beam STED microscopy

Stimulated emission depletion (STED) microscopy has become a powerful imaging and localized excitation method beating the diffraction barrier for improved lateral spatial resolution in cellular imaging, lithography, etc. Due to specimen-induced aberrations and scattering distortion, it has been a great challenge for STED to maintain consistent lateral resolution deeply inside the specimens. Here we report on a deep imaging STED microscopy by using Gaussian beam for excitation and hollow Bessel beam for depletion (GB-STED). The proposed scheme shows the improved imaging depth up to ~155{\mu}m in solid agarose sample, ~115{\mu}m in PDMS and ~100{\mu}m in phantom of gray matter in brain tissue with consistent super resolution, while the standard STED microscopy shown a significantly reduced lateral resolution at the same imaging depth. The results indicate the excellent imaging penetration capability of GB-STED, making it a promising tool for deep 3D imaging optical nanoscopy and laser fabrication.

physics.optics↗

arXiv2015

Fast Super-Resolution Imaging with Ultra-High Labeling Density Achieved by Joint Tagging Super-Resolution Optical Fluctuation Imaging (JT-SOFI)

Previous stochastic localization-based super-resolution techniques are largely limited by the labeling density and the fidelity to the morphology of specimen. We report on an optical super-resolution imaging scheme implementing joint tagging using multiple fluorescent blinking dyes associated with super-resolution optical fluctuation imaging (JT-SOFI), achieving ultra-high labeling density super-resolution imaging. To demonstrate the feasibility of JT-SOFI, quantum dots with different emission spectra were jointly labeled to the tubulin in COS7 cells, creating ultra-high density labeling. After analyzing and combining the fluorescence intermittency images emanating from spectrally resolved quantum dots, the microtubule networks are capable of being investigated with high fidelity and remarkably enhanced contrast at sub-diffraction resolution. The spectral separation also significantly decreased the frame number required for SOFI, enabling fast super-resolution microscopy through simultaneous data acquisition. As the joint-tagging scheme can decrease the labeling density in each spectral channel, we can faithfully reflect the continuous microtubule structure with high resolution through collection of only 100 frames per channel. The improved continuity of the microtubule structure is quantitatively validated with image skeletonization, thus demonstrating the advantage of JT-SOFI over other localization-based super-resolution methods.

physics.optics↗

arXiv2014

Hundred-thousand light holes push nanoscopy to go parallel

The recent work by Chmyrov et al. (Nature Methods 2013) presents a capstone for the current major super-resolution microscopy techniques. In optical super-resolution microscopy, two pathways are commonly taken: targeted illumination modulation, or stochastic single-molecule localization. Incoherent cross-standing microscopy has utilized the concept of structured illumination in generating patterns, to generate effective 100,000 "doughnuts" as with STED; and used the photo-switchable dye to decrease the requirement of modulation intensity. It has combined the key elements of all these major super-resolution techniques.

physics.optics↗

arXiv2013

Analytical description of high-aperture STED resolution with 0-2$\pi$ vortex phase modulation

Stimulated emission depletion (STED) can achieve optical super-resolution, with the optical diffraction limit broken by the suppression on the periphery of the fluorescent focal spot. Previously, it is generally experimentally accepted that there exists an inverse square root relationship with the STED power and the resolution, yet without strict analytical description. In this paper, we have analytically verified the relationship between the STED power and the achievable resolution from vector optical theory for the widely used 0-2$\pi$ vortex phase modulation. Electromagnetic fields of the focal region of a high numerical aperture objective are calculated and approximated into polynomials, and analytical expression of resolution as a function of the STED intensity has been derived. As a result, the resolution can be estimated directly from the measurement of the saturation power of the dye and the STED power applied.

physics.optics↗