Super-resolution microscopy and its applications in neuroscience

Optical microscopy promises researchers to soe most tiny substances directly.However,the resolution of conventional microscopy is resticted by the diffraction limit.This makes it a challenge to observe subcellular processes happened in nanoscale.The development of super-resolution microscopy provides a solution to this challenge.Here,we briefly review several commonly used super-resolution techniques,explicating their basic principles and applications in biological science,especially in neuroscience.In addition,characteristics and limitations of each techrique are compared to provide a guidance for biologists to choose the most suitable tool.

Super-resolution microscopy based on parallel detection

Image scanning microscopy based on pixel reassignment can improve the confocal resolution limit without losing the image signal-to-noise ratio(SNR)greatly[C.J.R.Sheppard,"Super resolution in confocal imaging,"Optik 80(2)53-54(1988).C.B.Miller,E.Jorg,"Image scanning microscopy,"Phys.Reu.Lett.104(19)198101(2010).C.J.R.Sheppard,s.B.Mehta,R Heintzmann,"Superresolution by image scanning microscopy using pixel reassignment,"Opt.Lett.38(15)28892892(2013)].Here,we use a tailor-made optical fiber and 19 avalanche pho-todiodes(APDs)as parallel detectors to upgrade our existing confocal microscopy,termed as parallel-detection super resolution(PDSR)microscopy.In order to obtain the correct shift value,we use the normalized 2D cross correlation to calculate the shifting value of each image.We characterized our system performance by imaging fuorescence beads and applied this system to observing the 3D structure of biological specimen.

Unleashing the potential:super-resolution microscopy as the key to advanced mitochondrial research

Investigating the fine structure of mitochondria and their dynamic interactions with other organelles is crucial for unraveling the mechanisms underlying mitochondrial-related diseases.The development of super-resolution techniques has provided powerful visualization tools for mitochondrial research,which is significant for investigating mitochondrial cristae structure,the localization of mitochondrial-related protein complex,and the interactions between mitochondria and other organelles.In this perspective,we introduce several advanced super-resolution techniques and their applications in mitochondrial research,and discuss the potential roles these techniques may play in future studies of mitochondria.

Numerical Simulation of Super-Resolution Structured Illumination Microscopy (SIM) Using Heintzmann-Cremer Algorithm with Non-Continuous Spatial Frequency Support

We report a comprehensive numerical study of super resolution (SR) structured illumination microscopy (SIM) utilizing the classic Heintzmann-Cremer SIM process and algorithm. In particular, we investigated the impact of the diffraction limit of the underlying imaging system on the optimal SIM grating frequency that can be used to obtain the highest SR enhancement with non-continuous spatial frequency support. Besides confirming the previous theoretical and experimental work that SR-SIM can achieve an enhancement close to 3 times the diffraction limit with grating pattern illuminations, we also observe and report a series of more subtle effects of SR-SIM with non-continuous spatial frequency support. Our simulations show that when the SIM grating frequency exceeds twice that of the diffraction limit, the higher SIM grating frequency can help achieve a higher SR enhancement for the underlying imaging systems whose diffraction limit is low, though this enhancement is obtained at the cost of losing resolution at some lower resolution targets. Our simulations also show that, for underlying imaging systems with high diffraction limits, however, SR-SIM grating frequencies above twice the diffraction limits tend to bring no significant extra enhancement. Furthermore, we observed that there exists a limit grating frequency above which the SR enhancement effect is lost, and the reconstructed images essentially have the same resolution as the one obtained directly from the underlying imaging system without using the SIM process.

Temporal compressive super-resolution microscopy at frame rate of 1200 frames per second and spatial resolution of 100 nm

Various super-resolution microscopy techniques have been presented to explore fine structures of biological specimens.However,the super-resolution capability is often achieved at the expense of reducing imaging speed by either point scanning or multiframe computation.The contradiction between spatial resolution and imaging speed seriously hampers the observation of high-speed dynamics of fine structures.To overcome this contradiction,here we propose and demonstrate a temporal compressive super-resolution microscopy(TCSRM)technique.This technique is to merge an enhanced temporal compressive microscopy and a deep-learning-based super-resolution image reconstruction,where the enhanced temporal compressive microscopy is utilized to improve the imaging speed,and the deep-learning-based super-resolution image reconstruction is used to realize the resolution enhancement.The high-speed super-resolution imaging ability of TCSRM with a frame rate of 1200 frames per second(fps)and spatial resolution of 100 nm is experimentally demonstrated by capturing the flowing fluorescent beads in microfluidic chip.Given the outstanding imaging performance with high-speed super-resolution,TCSRM provides a desired tool for the studies of high-speed dynamical behaviors in fine structures,especially in the biomedical field.

Multi-prior physics-enhanced neural network enables pixel super-resolution and twin-imagefree phase retrieval from single-shot hologram

Digital in-line holographic microscopy(DIHM)is a widely used interference technique for real-time reconstruction of living cells’morphological information with large space-bandwidth product and compact setup.However,the need for a larger pixel size of detector to improve imaging photosensitivity,field-of-view,and signal-to-noise ratio often leads to the loss of sub-pixel information and limited pixel resolution.Additionally,the twin-image appearing in the reconstruction severely degrades the quality of the reconstructed image.The deep learning(DL)approach has emerged as a powerful tool for phase retrieval in DIHM,effectively addressing these challenges.However,most DL-based strategies are datadriven or end-to-end net approaches,suffering from excessive data dependency and limited generalization ability.Herein,a novel multi-prior physics-enhanced neural network with pixel super-resolution(MPPN-PSR)for phase retrieval of DIHM is proposed.It encapsulates the physical model prior,sparsity prior and deep image prior in an untrained deep neural network.The effectiveness and feasibility of MPPN-PSR are demonstrated by comparing it with other traditional and learning-based phase retrieval methods.With the capabilities of pixel super-resolution,twin-image elimination and high-throughput jointly from a single-shot intensity measurement,the proposed DIHM approach is expected to be widely adopted in biomedical workflow and industrial measurement.

Shear Let Transform Residual Learning Approach for Single-Image Super-Resolution

Super-resolution techniques are employed to enhance image resolution by reconstructing high-resolution images from one or more low-resolution inputs.Super-resolution is of paramount importance in the context of remote sensing,satellite,aerial,security and surveillance imaging.Super-resolution remote sensing imagery is essential for surveillance and security purposes,enabling authorities to monitor remote or sensitive areas with greater clarity.This study introduces a single-image super-resolution approach for remote sensing images,utilizing deep shearlet residual learning in the shearlet transform domain,and incorporating the Enhanced Deep Super-Resolution network(EDSR).Unlike conventional approaches that estimate residuals between high and low-resolution images,the proposed approach calculates the shearlet coefficients for the desired high-resolution image using the provided low-resolution image instead of estimating a residual image between the high-and low-resolution image.The shearlet transform is chosen for its excellent sparse approximation capabilities.Initially,remote sensing images are transformed into the shearlet domain,which divides the input image into low and high frequencies.The shearlet coefficients are fed into the EDSR network.The high-resolution image is subsequently reconstructed using the inverse shearlet transform.The incorporation of the EDSR network enhances training stability,leading to improved generated images.The experimental results from the Deep Shearlet Residual Learning approach demonstrate its superior performance in remote sensing image recovery,effectively restoring both global topology and local edge detail information,thereby enhancing image quality.Compared to other networks,our proposed approach outperforms the state-of-the-art in terms of image quality,achieving an average peak signal-to-noise ratio of 35 and a structural similarity index measure of approximately 0.9.

AFBNet: A Lightweight Adaptive Feature Fusion Module for Super-Resolution Algorithms

At present,super-resolution algorithms are employed to tackle the challenge of low image resolution,but it is difficult to extract differentiated feature details based on various inputs,resulting in poor generalization ability.Given this situation,this study first analyzes the features of some feature extraction modules of the current super-resolution algorithm and then proposes an adaptive feature fusion block(AFB)for feature extraction.This module mainly comprises dynamic convolution,attention mechanism,and pixel-based gating mechanism.Combined with dynamic convolution with scale information,the network can extract more differentiated feature information.The introduction of a channel spatial attention mechanism combined with multi-feature fusion further enables the network to retain more important feature information.Dynamic convolution and pixel-based gating mechanisms enhance the module’s adaptability.Finally,a comparative experiment of a super-resolution algorithm based on the AFB module is designed to substantiate the efficiency of the AFB module.The results revealed that the network combined with the AFB module has stronger generalization ability and expression ability.

PSMFNet:Lightweight Partial Separation and Multiscale Fusion Network for Image Super-Resolution

The employment of deep convolutional neural networks has recently contributed to significant progress in single image super-resolution(SISR)research.However,the high computational demands of most SR techniques hinder their applicability to edge devices,despite their satisfactory reconstruction performance.These methods commonly use standard convolutions,which increase the convolutional operation cost of the model.In this paper,a lightweight Partial Separation and Multiscale Fusion Network(PSMFNet)is proposed to alleviate this problem.Specifically,this paper introduces partial convolution(PConv),which reduces the redundant convolution operations throughout the model by separating some of the features of an image while retaining features useful for image reconstruction.Additionally,it is worth noting that the existing methods have not fully utilized the rich feature information,leading to information loss,which reduces the ability to learn feature representations.Inspired by self-attention,this paper develops a multiscale feature fusion block(MFFB),which can better utilize the non-local features of an image.MFFB can learn long-range dependencies from the spatial dimension and extract features from the channel dimension,thereby obtaining more comprehensive and rich feature information.As the role of the MFFB is to capture rich global features,this paper further introduces an efficient inverted residual block(EIRB)to supplement the local feature extraction ability of PSMFNet.A comprehensive analysis of the experimental results shows that PSMFNet maintains a better performance with fewer parameters than the state-of-the-art models.

Efficient 2-D MUSIC algorithm for super-resolution moving target tracking based on an FMCW radar

Frequency modulated continuous wave(FMCW)radar is an advantageous sensor scheme for target estimation and environmental perception.However,existing algorithms based on discrete Fourier transform(DFT),multiple signal classification(MUSIC)and compressed sensing,etc.,cannot achieve both low complexity and high resolution simultaneously.This paper proposes an efficient 2-D MUSIC algorithm for super-resolution target estimation/tracking based on FMCW radar.Firstly,we enhance the efficiency of 2-D MUSIC azimuth-range spectrum estimation by incorporating 2-D DFT and multi-level resolution searching strategy.Secondly,we apply the gradient descent method to tightly integrate the spatial continuity of object motion into spectrum estimation when processing multi-epoch radar data,which improves the efficiency of continuous target tracking.These two approaches have improved the algorithm efficiency by nearly 2-4 orders of magnitude without losing accuracy and resolution.Simulation experiments are conducted to validate the effectiveness of the algorithm in both single-epoch estimation and multi-epoch tracking scenarios.

Improved spatiotemporal resolution of anti-scattering super-resolution label-free microscopy via synthetic wave 3D metalens imaging

Super-resolution(SR)microscopy has dramatically enhanced our understanding of biological processes.However,scattering media in thick specimens severely limits the spatial resolution,often rendering the images unclear or indistinguishable.Additionally,live-cell imaging faces challenges in achieving high temporal resolution for fast-moving subcellular structures.Here,we present the principles of a synthetic wave microscopy(SWM)to extract three-dimensional information from thick unlabeled specimens,where photobleaching and phototoxicity are avoided.SWM exploits multiple-wave interferometry to reveal the specimen’s phase information in the area of interest,which is not affected by the scattering media in the optical path.SWM achieves~0.42λ/NA resolution at an imaging speed of up to 106 pixels/s.SWM proves better temporal resolution and sensitivity than the most conventional microscopes currently available while maintaining exceptional SR and anti-scattering capabilities.Penetrating through the scattering media is challenging for conventional imaging techniques.Remarkably,SWM retains its efficacy even in conditions of low signal-to-noise ratios.It facilitates the visualization of dynamic subcellular structures in live cells,encompassing tubular endoplasmic reticulum(ER),lipid droplets,mitochondria,and lysosomes.

Faster split-based feedback network for image super-resolution

Although most of the existing image super-resolution(SR)methods have achieved superior performance,contrastive learning for high-level tasks has not been fully utilized in the existing image SR methods based on deep learning.This work focuses on two well-known strategies developed for lightweight and robust SR,i.e.,contrastive learning and feedback mechanism,and proposes an integrated solution called a split-based feedback network(SPFBN).The proposed SPFBN is based on a feedback mechanism to learn abstract representations and uses contrastive learning to explore high information in the representation space.Specifically,this work first uses hidden states and constraints in recurrent neural network(RNN)to implement a feedback mechanism.Then,use contrastive learning to perform representation learning to obtain high-level information by pushing the final image to the intermediate images and pulling the final SR image to the high-resolution image.Besides,a split-based feedback block(SPFB)is proposed to reduce model redundancy,which tolerates features with similar patterns but requires fewer parameters.Extensive experimental results demonstrate the superiority of the proposed method in comparison with the state-of-the-art methods.Moreover,this work extends the experiment to prove the effectiveness of this method and shows better overall reconstruction quality.

Deep-learning-based methods for super-resolution fluorescence microscopy

The algorithm used for reconstruction or resolution enhancement is one of the factors affectingthe quality of super-resolution images obtained by fluorescence microscopy.Deep-learning-basedalgorithms have achieved stateof-the-art performance in super-resolution fluorescence micros-copy and are becoming increasingly attractive.We firstly introduce commonly-used deep learningmodels,and then review the latest applications in terms of the net work architectures,the trainingdata and the loss functions.Additionally,we discuss the challenges and limits when using deeplearning to analyze the fluorescence microscopic data,and suggest ways to improve the reliability and robustness of deep learning applications.

SOFFLFM:Super-resolution optical fluctuation Fourierlight-field microscopy

Fourier light-field microscopy(FLFM)uses a microlens aray(MLA)to segment the Fourierplane of the microscopic objective lens to generate multiple two-dimensional perspective views,thereby reconstructing the threedimensional(3D)structure of the sample using 3D deconvo-lution calculation without scanning.However,the resolution of FLFM is stil limited by dif-fraction,and furthermore,it is dependent on the aperture division.In order to improve itsresolution,a super-resolution opticai fuctuation Fourier light-field microscopy(SOFFLFM)wasproposed here,in which the super-resolution optical fluctuation imaging(SOFI)with the abilityof super-resolution was introduced into FLFM.SOFFLFM uses higher-order cumulants statis-tical analysis on an image sequence collected by FLFM,and then carries out 3D deconvolutioncalculation to reconstruct the 3D structure of the sample.The theoretical basis of SOFFLFM onimproving resolution was explained and then verified with the simulations.Simulation resultsdemonstrated that SOFFLFM improved the lateral and axial resolution by more than V2 and 2times in the second-and fourth-order accumulations,compared with that of FLFM.

Spatiotemporal Isolation Based Super-Resolution Microscopy

Super-resolution microscopy(SRM)is a powerful imaging technique that overcomes the diffraction limit and allows imaging of the object structure in the nanoscale.However,SRM suffers from a tradeoff between spatial and temporal resolution,which prevents further exploration in scientific discoveries.In this review,we mainly focus on the development of improving spatiotemporal resolution of SRM,including 1)SRM based on physical and computational principles,2)physical and computational factors affecting SRM,from which we conclude some strategies for developing new types of SRM,3)the summary of the various types of SRM based on physical and computational principles,as well as,the analysis of the ordinary and developing SRM.Both SRMs based on physical principles and computational principles can be realized with spatial isolation and temporal isolation methods.We expect this review will offer some new ideas to improve the spatial and temporal resolution simultaneously,which may lead to more new discoveries in biology,chemistry,and materials science.

Computational methods in super-resolution microscopy

The broad applicability of super-resolution microscopy has been widely demonstrated in various areas and disciplines. The optimization and improvement of algorithms used in super-resolution microscopy are of great importance for achieving optimal quality of super-resolution imaging. In this review, we comprehensively discuss the computational methods in different types of super-resolution microscopy, including deconvolution microscopy, polarization-based super-resolution microscopy, structured illumination microscopy, image scanning microscopy, super-resolution optical fluctuation imaging microscopy, single-molecule localization microscopy, Bayesian super-resolution microscopy, stimulated emission depletion microscopy, and translation microscopy. The development of novel computational methods would greatly benefit super-resolution microscopy and lead to better resolution, improved accuracy, and faster image processing.

Rethinking resolution estimation in fluorescence microscopy: from theoretical resolution criteria to super-resolution microscopy

Resolution is undoubtedly the most important parameter in optical microscopy by providing an estimation on the maximum resolving power of a certain optical microscope. For centuries, the resolution of an optical microscope is generally considered to be limited only by the numerical aperture of the optical system and the wavelength of light. However, since the invention and popularity of various advanced fluorescence microscopy techniques, especially super-resolution fluorescence microscopy, many new methods have been proposed for estimating the resolution, leading to confusions for researchers who need to quantify the resolution of their fluorescence microscopes. In this paper, we firstly summarize the early concepts and criteria for predicting the resolution limit of an ideal optical system. Then, we discuss some important influence factors that deteriorate the resolution of a certain fluorescence microscope. Finally, we provide methods and examples on how to measure the resolution of a fluorescence microscope from captured fluorescence images. This paper aims to answer as best as possible the theoretical and practical issues regarding the resolution estimation in fluorescence microscopy.

Super-resolution microscopy reveals the distribution of targeted molecules in the complex matrix

With the support by the National Natural Science Foundation of China and the Chinese Academy of Sciences,the research team led by Prof.Li Junbai(李峻柏)at the CAS Key Lab of Colloid,Interface and Thermodynamics,Institute of Chemistry,Chinese Academy of Sciences,revealed the distribution of proteins in the transformation of inorganic/protein hybrid crystals by super-resolution microscopy,which

Hyperspectral Image Super-Resolution Meets Deep Learning:A Survey and Perspective

Hyperspectral image super-resolution,which refers to reconstructing the high-resolution hyperspectral image from the input low-resolution observation,aims to improve the spatial resolution of the hyperspectral image,which is beneficial for subsequent applications.The development of deep learning has promoted significant progress in hyperspectral image super-resolution,and the powerful expression capabilities of deep neural networks make the predicted results more reliable.Recently,several latest deep learning technologies have made the hyperspectral image super-resolution method explode.However,a comprehensive review and analysis of the latest deep learning methods from the hyperspectral image super-resolution perspective is absent.To this end,in this survey,we first introduce the concept of hyperspectral image super-resolution and classify the methods from the perspectives with or without auxiliary information.Then,we review the learning-based methods in three categories,including single hyperspectral image super-resolution,panchromatic-based hyperspectral image super-resolution,and multispectral-based hyperspectral image super-resolution.Subsequently,we summarize the commonly used hyperspectral dataset,and the evaluations for some representative methods in three categories are performed qualitatively and quantitatively.Moreover,we briefly introduce several typical applications of hyperspectral image super-resolution,including ground object classification,urban change detection,and ecosystem monitoring.Finally,we provide the conclusion and challenges in existing learning-based methods,looking forward to potential future research directions.

Contrastive Learning for Blind Super-Resolution via A Distortion-Specific Network

Previous deep learning-based super-resolution(SR)methods rely on the assumption that the degradation process is predefined(e.g.,bicubic downsampling).Thus,their performance would suffer from deterioration if the real degradation is not consistent with the assumption.To deal with real-world scenarios,existing blind SR methods are committed to estimating both the degradation and the super-resolved image with an extra loss or iterative scheme.However,degradation estimation that requires more computation would result in limited SR performance due to the accumulated estimation errors.In this paper,we propose a contrastive regularization built upon contrastive learning to exploit both the information of blurry images and clear images as negative and positive samples,respectively.Contrastive regularization ensures that the restored image is pulled closer to the clear image and pushed far away from the blurry image in the representation space.Furthermore,instead of estimating the degradation,we extract global statistical prior information to capture the character of the distortion.Considering the coupling between the degradation and the low-resolution image,we embed the global prior into the distortion-specific SR network to make our method adaptive to the changes of distortions.We term our distortion-specific network with contrastive regularization as CRDNet.The extensive experiments on synthetic and realworld scenes demonstrate that our lightweight CRDNet surpasses state-of-the-art blind super-resolution approaches.