U-Net-based deep learning for tracking and quantitative analysis of intracellular vesicles in time-lapse microscopy images

Fluorescence microscopy has become an essential tool for biologists,to visualize the dynamics of intracellular structures with specific labeling.Quantitatively measuring the dynamics of moving objects inside the cell is pivotal for understanding of the underlying regulatory mechanism.Protein-containing vesicles are involved in various biological processes such as material transportation,organelle interaction,and hormonal regulation,whose dynamic characteristics are signi¯cant to disease diagnosis and drug screening.Although some algorithms have been developed for vesicle tracking,most of them have limited performance when dealing with images with low resolution,poor signal-to-noise ratio(SNR)and complicated motion.Here,we proposed a novel deep learning-based method for intracellular vesicle tracking.We trained the U-Net for vesicle localization and motion classification,with demonstrates great performance in both simulated datasets and real biological samples.By combination with fan-shaped tracker(FsT)we have previously developed,this hybrid new algorithm significantly improved the performance of particle tracking with the function of subsequently automated vesicle motion classification.Furthermore,its performance was further demonstrated in analyzing with vesicle dynamics in different temperature,which achieved reasonable outcomes.Thus,we anticipate that this novel method would have vast applications in analyzing the vesicle dynamics in living cells.

Monitoring the change in horizontal stress with multi-wave time-lapse seismic response based on nonlinear elasticity theory

Monitoring the change in horizontal stress from the geophysical data is a tough challenge, and it has a crucial impact on broad practical scenarios which involve reservoir exploration and development, carbon dioxide (CO_(2)) injection and storage, shallow surface prospecting and deep-earth structure description. The change in in-situ stress induced by hydrocarbon production and localized tectonic movements causes the changes in rock mechanic properties (e.g. wave velocities, density and anisotropy) and further causes the changes in seismic amplitudes, phases and travel times. In this study, the nonlinear elasticity theory that regards the rock skeleton (solid phase) and pore fluid as an effective whole is used to characterize the effect of horizontal principal stress on rock overall elastic properties and the stress-dependent anisotropy parameters are therefore formulated. Then the approximate P-wave, SV-wave and SH-wave angle-dependent reflection coefficient equations for the horizontal-stress-induced anisotropic media are proposed. It is shown that, on the different reflectors, the stress-induced relative changes in reflectivities (i.e., relative difference) of elastic parameters (i.e., P- and S-wave velocities and density) are much less than the changes in contrasts of anisotropy parameters. Therefore, the effects of stress change on the reflectivities of three elastic parameters are reasonably neglected to further propose an AVO inversion approach incorporating P-, SH- and SV-wave information to estimate the change in horizontal principal stress from the corresponding time-lapse seismic data. Compared with the existing methods, our method eliminates the need for man-made rock-physical or fitting parameters, providing more stable predictive power. 1D test illustrates that the estimated result from time-lapse P-wave reflection data shows the most reasonable agreement with the real model, while the estimated result from SH-wave reflection data shows the largest bias. 2D test illustrates the feasibility of the proposed inversion method for estimating the change in horizontal stress from P-wave time-lapse seismic data.

Estimation-free spatial-domain image reconstruction of structured illumination microscopy

Structured illumination microscopy(SIM)achieves super-resolution(SR)by modulating the high-frequency information of the sample into the passband of the optical system and subsequent image reconstruction.The traditional Wiener-filtering-based reconstruction algorithm operates in the Fourier domain,it requires prior knowledge of the sinusoidal illumination patterns which makes the time-consuming procedure of parameter estimation to raw datasets necessary,besides,the parameter estimation is sensitive to noise or aberration-induced pattern distortion which leads to reconstruction artifacts.Here,we propose a spatial-domain image reconstruction method that does not require parameter estimation but calculates patterns from raw datasets,and a reconstructed image can be obtained just by calculating the spatial covariance of differential calculated patterns and differential filtered datasets(the notch filtering operation is performed to the raw datasets for attenuating and compensating the optical transfer function(OTF)).Experiments on reconstructing raw datasets including nonbiological,biological,and simulated samples demonstrate that our method has SR capability,high reconstruction speed,and high robustness to aberration and noise.

Probing the Nucleation and Growth Kinetics of Bismuth Nanoparticles via In-situ Transmission Electron Microscopy

The nucleation and growth mechanism of nanoparticles is an important theory,which can guide the preparation of nanomaterials.However,it is still lacking in direct observation on the details of the evolution of intermediate state structure during nucleation and growth.In this work,the evolution process of bismuth nanoparticles induced by electron beam was revealed by in-situ transmission electron microscopy(TEM)at atomic scale.The experimental results demonstrate that the size,stable surface and crystallographic defect have important influences on the growth of Bi nanoparticles.Two non-classical growth paths including single crystal growth and polycrystalline combined growth,as well as,corresponding layer-by-layer growth mechanism along{012}stable crystal plane of Bi nanoparticles with dodecahedron structure were revealed by in-situ TEM directly.These results provide important guidance and a new approach for in-depth understanding of the nucleation and growth kinetics of nanoparticles.

Ultrafast photoemission electron microscopy:A multidimensional probe of nonequilibrium physics

Exploring the realms of physics that extend beyond thermal equilibrium has emerged as a crucial branch of condensed matter physics research.It aims to unravel the intricate processes involving the excitations,interactions,and annihilations of quasi-and many-body particles,and ultimately to achieve the manipulation and engineering of exotic non-equilibrium quantum phases on the ultrasmall and ultrafast spatiotemporal scales.Given the inherent complexities arising from many-body dynamics,it therefore seeks a technique that has efficient and diverse detection degrees of freedom to study the underlying physics.By combining high-power femtosecond lasers with real-or momentum-space photoemission electron microscopy(PEEM),imaging excited state phenomena from multiple perspectives,including time,real space,energy,momentum,and spin,can be conveniently achieved,making it a unique technique in studying physics out of equilibrium.In this context,we overview the working principle and technical advances of the PEEM apparatus and the related laser systems,and survey key excited-state phenomena probed through this surface-sensitive methodology,including the ultrafast dynamics of electrons,excitons,plasmons,spins,etc.,in materials ranging from bulk and nano-structured metals and semiconductors to low-dimensional quantum materials.Through this review,one can further envision that time-resolved PEEM will open new avenues for investigating a variety of classical and quantum phenomena in a multidimensional parameter space,offering unprecedented and comprehensive insights into important questions in the field of condensed matter physics.

Recent progress about transmission electron microscopy characterizations on lithium-ion batteries

With the rapid development of portable electronics,new energy vehicles,and smart grids,ion batteries are becoming one of the most widely used energy storage devices,while the safety concern of ion batteries has always been an urgent problem to be solved.To develop a safety-guaranteed battery,the characterization of the internal structure is indispensable,where electron microscopy plays a crucial role.Based on this,this paper summarizes the application of transmission electron microscopy(TEM)in battery safety,further concludes and analyzes the aspects of dendrite growth and solid electrolyte interface(SEI)formation that affect the safety of ion batteries,and emphasizes the importance of electron microscopy in battery safety research and the potential of these techniques to promote the future development of this field.These advanced electron microscopy techniques and their prospects are also discussed.

Investigation of reflection anisotropy induced by micropipe defects on the surface of a 4H-SiC single crystal using scanning anisotropy microscopy

Optical reflection anisotropy microscopy mappings of micropipe defects on the surface of a 4H-SiC single crystal are studied by the scanning anisotropy microscopy(SAM)system.The reflection anisotropy(RA)image with a'butterfly pattern'is obtained around the micropipes by SAM.The RA image of the edge dislocations is theoretically simulated based on dislocation theory and the photoelastic principle.By comparing with the Raman spectrum,it is verified that the micropipes consist of edge dislocations.The different patterns of the RA images are due to the different orientations of the Burgers vectors.Besides,the strain distribution of the micropipes is also deduced.One can identify the dislocation type,the direction of the Burgers vector and the optical anisotropy from the RA image by using SAM.Therefore,SAM is an ideal tool to measure the optical anisotropy induced by the strain field around a defect.

A review of understanding electrocatalytic reactions in energy conversion and energy storage systems via scanning electrochemical microscopy

To address climate change and promote environmental sustainability,electrochemical energy conversion and storage systems emerge as promising alternative to fossil fuels,catering to the escalating demand for energy.Achieving optimal energy efficiency and cost competitiveness in these systems requires the strategic design of electrocatalysts,coupled with a thorough comprehension of the underlying mechanisms and degradation behavior occurring during the electrocatalysis processes.Scanning electrochemical microscopy(SECM),an analytical technique for studying surface electrochemically,stands out as a powerful tool offering electrochemical insights.It possesses remarkable spatiotemporal resolution,enabling the visualization of the localized electrochemical activity and surface topography.This review compiles crucial research findings and recent breakthroughs in electrocatalytic processes utilizing the SECM methodology,specifically focusing on applications in electrolysis,fuel cells,and metal–oxygen batteries within the realm of energy conversion and storage systems.Commencing with an overview of each energy system,the review introduces the fundamental principles of SECM,and aiming to provide new perspectives and broadening the scope of applied research by describing the major research categories within SECM.

Characterization of local chemical ordering and deformation behavior in high entropy alloys by transmission electron microscopy

Short-range ordering(SRO)is one of the most important structural features of high entropy alloys(HEAs).However,the chemical and structural analyses of SROs are very difficult due to their small size,complexed compositions,and varied locations.Transmission electron microscopy(TEM)as well as its aberration correction techniques are powerful for characterizing SROs in these compositionally complex alloys.In this short communication,we summarized recent progresses regarding characterization of SROs using TEM in the field of HEAs.By using advanced TEM techniques,not only the existence of SROs was confirmed,but also the effect of SROs on the deformation mechanism was clarified.Moreover,the perspective related to application of TEM techniques in HEAs are also discussed.

Microscopic Analysis of Cementitious Sand and Gravel Damming Materia

The mechanical properties of cementitious sand and gravel damming material have been experimentally determined by means of microscopic SEM(Scanning Electron Microscopy)image analysis.The results show that the combination of fly ash and water can fill the voids in cemented sand and gravel test blocks because of the presence of hydrated calcium silicate and other substances;thereby,the compactness and mechanical properties of these materials can be greatly improved.For every 10 kg/m^(3) increase in the amount of cementitious material,the density increases by about 2%,and the water content decreases by 0.2%.The amount of cementitious material used in the sand and gravel in these tests was 80-110 kg/m^(3),the water-binder ratio was 1-1.50.Moreover,the splitting tensile strength was 1/10 of the compressive strength,and the maximum strength was 7.42 MPa at 90 d.The optimal mix ratio has been found to be 50 kg of cement,60 kg of fly ash and 120 kg of water(C50F60W120).The related dry density was 2.6 g/cm^(3),the water content was 6%,and the water-binder ratio was 1.09.

Capturing the non-equilibrium state in light–matter–free-electron interactions through ultrafast transmission electron microscopy

Ultrafast transmission electron microscope(UTEM) with the multimodality of time-resolved diffraction, imaging,and spectroscopy provides a unique platform to reveal the fundamental features associated with the interaction between free electrons and matter. In this review, we summarize the principles, instrumentation, and recent developments of the UTEM and its applications in capturing dynamic processes and non-equilibrium transient states. The combination of the transmission electron microscope with a femtosecond laser via the pump–probe method guarantees the high spatiotemporal resolution, allowing the investigation of the transient process in real, reciprocal and energy spaces. Ultrafast structural dynamics can be studied by diffraction and imaging methods, revealing the coherent acoustic phonon generation and photoinduced phase transition process. In the energy dimension, time-resolved electron energy-loss spectroscopy enables the examination of the intrinsic electronic dynamics of materials, while the photon-induced near-field electron microscopy extends the application of the UTEM to the imaging of optical near fields with high real-space resolution. It is noted that light–free-electron interactions have the ability to shape electron wave packets in both longitudinal and transverse directions, showing the potential application in the generation of attosecond electron pulses and vortex electron beams.

Correlation of work function and stacking fault energy through Kelvin probe force microscopy and nanohardness in diluteα-magnesium

Electronic interactions of the Group 2A elements with magnesium have been studied through the dilute solid solutions in binary Mg-Ca,Mg-Sr and Mg-Ba systems.This investigation incorporated the difference in the‘Work Function'(ΔWF)measured via Kelvin Probe Force Microscopy(KPFM),as a property directly affected by interatomic bond types,i.e.the electronic structure,nanoindentation measurements,and Stacking Fault Energy values reported in the literature.It was shown that the nano-hardness of the solid-solutionα-Mg phase changed in the order of Mg-Ca>Mg-Sr>Mg-Ba.Thus,it was shown,by also considering the nano-hardness levels,that SFE of a solid-solution is closely correlated with its‘Work Function'level.Nano-hardness measurements on the eutectics andΔWF difference between eutectic phases enabled an assessment of the relative bond strength and the pertinent electronic structures of the eutectics in the three alloys.Correlation withΔWF and at least qualitative verification of those computed SFE values with some experimental measurement techniques were considered important as those computational methods are based on zero Kelvin degree,relatively simple atomic models and a number of assumptions.As asserted by this investigation,if the results of measurement techniques can be qualitatively correlated with those of the computational methods,it can be possible to evaluate the electronic structures in alloys,starting from binary systems,going to ternary and then multi-elemental systems.Our investigation has shown that such a qualitative correlation is possible.After all,the SFE values are not treated as absolute values but rather become essential in comparative investigations when assessing the influences of alloying elements at a fundamental level,that is,free electron density distributions.Our study indicated that the principles of‘electronic metallurgy'in developing multi-elemental alloy systems can be followed via practical experimental methods,i.e.ΔWF measurements using KPFM and nanoindentation.

Microscopic growth mechanism and edge states of monolayer 1T'-MoTe_(2)

Transition metal ditellurides(TMTDs)have versatile physical properties,including non-trivial topology,Weyl semimetal states and unique spin texture.Controlled growth of high-quality and large-scale monolayer TMTDs with preferred crystal phases is crucial for their applications.Here,we demonstrate the epitaxial growth of 1T'-MoTe_(2) on Au(111)and graphitized silicon carbide(Gr/SiC)by molecular beam epitaxy(MBE).We investigate the morphology of the grown1T'-MoTe_(2) at the atomic level by scanning tunnelling microscopy(STM)and reveal the corresponding microscopic growth mechanism.It is found that the unique ordered Te structures preferentially deposited on Au(111)regulate the growth of monolayer single crystal 1T'-MoTe_(2),while the Mo clusters were preferentially deposited on the Gr/SiC substrate,which impedes the ordered growth of monolayer MoTe_(2).We confirm that the size of single crystal 1T'-MoTe_(2) grown on Au(111)is nearly two orders of magnitude larger than that on Gr/SiC.By scanning tunnelling spectroscopy(STS),we observe that the STS spectrum of the monolayer 1T'-MoTe_(2) nano-island at the edge is different from that at the interior,which exhibits enhanced conductivity.

Confocal laser endomicroscopy as a new diagnostic tool for poorly differentiated gastric adenocarcinoma

Gastric cancer(GC)is a multifactorial disease,where both environmental and genetic features can have an impact on its occurrence and development.GC represents one of the leading causes of cancer-related deaths worldwide.GC is most frequent in males and is believed to arise from a series of premalignant lesions.The detection of GC at an early stage is crucial because early GC,which is an invasive stomach cancer confined to the mucosal or submucosal lining,may be curable with a reported 5-year survival rate of more than 90%.Advanced GC usually has a poor prognosis despite current treatment standards.The diagnostic efficacy of conventional endoscopy(with light endoscopy)is currently limited.Confocal laser endomicroscopy is a novel imaging technique that allows real-time in vivo histological examination of mucosal surfaces during endoscopy.Confocal laser endomicroscopy may be of great importance in the surveillance of precancerous gastric lesions and in the diagnosis of GC.In this editorial we commented on the article about this topic published by Lou et al in the recent issue of the World Journal of Clinical Cases.

使用time-lapse筛选早期IVF/ICSI胚胎及其临床结局

目的通过比较使用time-lapse（延迟摄像）和传统形态学方法筛选IVF/ICSI胚胎的临床结局,评价time-lapse用于早期胚胎观察和筛选的价值。方法回顾性分析139个IVF/ICSI周期的资料,根据胚胎的筛选方法,分为time-lapse monitoring组（TLM组）（n=68）和对照组（n=71）,比较两组间的βHCG阳性率、临床妊娠率和胚胎着床率,并根据女方年龄、受精方式进行亚组分析。结果 TLM组的βHCG阳性率、临床妊娠率、胚胎着床率分别为：66.2%、61.8%、47.1%;对照组的βHCG阳性率、临床妊娠率、胚胎着床率分别为：47.9%、43.7%、30.3%;TLM组的βHCG阳性率、临床妊娠率、胚胎着床率均高于对照组,且差异均有统计学意义（P〈0.05）。亚组分析显示：相较于年龄≤30岁的患者,年龄31~35岁的患者利用time-lapse更能明显改善临床结局;利用time-lapse能明显提高IVF周期的βHCG阳性率、临床妊娠率、胚胎着床率,但对于ICSI和TESA周期,效果则不理想。结论使用time-lapse动态监测胚胎并根据胚胎的形态动力学参数对胚胎进行评价和筛选,与传统方法相比,能获得更好的临床结局;年龄较大的（〉30岁）或者是进行IVF周期的患者更能从中获益。

利用Time-lapse技术筛选早期胚胎对IVF-ET妊娠结局的影响

目的探索利用Time-lapse系统筛选早期胚胎的临床应用价值。方法回顾性分析本中心2016年7月至2017年12月,第一次新鲜或复苏周期D3卵裂期胚胎移植的患者资料,根据胚胎评估方法分为Time-lapse系统组(TLM组,n=74)和传统形态学评分组(CMA组,n=951),比较这两种不同胚胎筛选方法对临床结局的影响。结果患者的不孕年限、体重指数、基础FSH、基础LH、E2、AMH、窦卵泡数、内膜厚度和周期类型等一般情况,在TLM组和CMA组均无显著差异(P均>0.05);TLM组年龄显著高于CMA组[(31.8±4.2)vs.(30.8±4.4),P<0.05],而平均移植胚胎数显著少于CMA组[(1.7±0.5)vs.(1.9±0.3),P<0.05];患者的临床结局,包括临床妊娠率、种植率、流产率、宫外孕率、双胎率和移植两个胚胎的双胎率等在两组间均无显著差异(P均>0.05)。进一步按照年龄分层分析,在<35岁患者,患者的一般情况在两组间均无显著差异(P均>0.05),TML组的平均移植胚胎数显著少于CMA组[(1.7±0.5)vs.(1.9±0.3),P<0.05],而患者临床结局在两组间亦无显著差异(P>0.05);在≥35岁患者,TML组的平均移植胚胎数显著少于CMA组[(1.7±0.5)vs.(1.9±0.4),P<0.05],而患者的一般情况和临床结局在两组间亦无显著差异(P>0.05)。结论利用Time-lapse技术选择早期胚胎,可以在显著减少移植胚胎数的基础上,维持稳定的临床妊娠结局。因此,认为Time-lapse技术可以在一定程度上优选出更具发育潜能的胚胎,为早期胚胎单胚胎移植提供新方法。

Time-lapse是否能预测胚胎染色体整倍性？

Time-lapse技术推进了胚胎评估的方法学,为胚胎评估带来了新的视角。Time-lapse系统理论上应具有预测胚胎染色体整倍性的潜力,但还需临床研究证实。

应用time-lapse技术探讨7～10细胞D3优质胚胎的发育潜能

目的：探讨人体外受精-胚胎移植（IVF-ET）中第3天细胞数目为7、8、9、10优质胚胎的发育潜能。方法：选取2014年11月至2015年10月于山东大学附属生殖医院行IVF-ET患者的D3（授精后第三天）胚胎,利用time-lapse（延时摄像）技术分析7~10细胞优质胚胎的早期分裂行为,进而探讨胚胎早期分裂行为对囊胚形成率和临床结局的影响。结果：（1）四种细胞数胚胎早期的分裂行为不同：大多数8细胞胚胎为发育正常（NB）的胚胎;9细胞和10细胞中发生直接分裂（DC,一种异常分裂）的胚胎比例高于发育正常胚胎;所有7细胞胚胎均存在异常分裂,其中主要为逆分裂（RC,一种异常分裂）和同步分裂延迟（t8-t5,S3,胚胎由5细胞分裂为8细胞的时间）。（2）与NB相比,每一种异常分裂（DC,RC,S3）的发生均不同程度降低了胚胎的发育潜能。（3）四种细胞数胚胎的发育结局显示,8细胞胚胎有最高的囊胚形成率和胚胎着床率,其次为9细胞和10细胞胚胎,7细胞胚胎的囊胚形成率和着床率最低。结论：7、8、9、10四种细胞数胚胎早期发育过程中异常分裂的类型和所占比重不同,最终导致其发育潜能的差异。8细胞胚胎的发育潜能最高,其次为9细胞和10细胞胚胎,7细胞胚胎发育潜能最低。

Purposeless repeated acquisition time-lapse seismic data processing

In China, most oil fields are continental sedimentation with strong heterogeneity, which on one side makes the reservoir prospecting and development more difficult, but on the other side provides more space for searching residual oil in matured fields. Time-lapse seismic reservoir monitoring technique is one of most important techniques to define residual oil distribution. According to the demand for and development of time-lapse seismic reservoir monitoring in China, purposeless repeated acquisition time-lapse seismic data processing was studied. The four key steps in purposeless repeated acquisition time-lapse seismic data processing, including amplitude-preserved processing with relative consistency, rebinning, match filtering and difference calculation, were analyzed by combining theory and real seismic data processing. Meanwhile, quality control during real time-lapse seismic processing was emphasized.

应用Time-lapse研究人3PN胚胎的卵裂模式

目的比较IVF3PN、IVF2PN、ICSI3PN和ICSI2PN胚胎的卵裂模式和胚胎动力学参数的差异。方法回顾性分析2017年7月至2018年6月在我院生殖中心就诊经时差胚胎监测(Time-lapse)培养箱培养的393个胚胎发育动力学参数,根据受精结局分为4组:IVF3PN组(n=132)、IVF2PN组(n=150)、ICSI3PN组(n=11)和ICSI2PN组(n=100),分析比较各组胚胎的卵裂模式和原核出现时间、原核消失时间、第一次卵裂时间、t4、t3-t5等胚胎动力学参数。结果IVF3PN组胚胎第一次卵裂模式异常率(100%)显著高于IVF2PN组胚胎(4.67%)、ICSI3PN组胚胎(18.18%)和ICSI2PN组胚胎(5.00%)(P<0.001),而ICSI3PN组、ICSI2PN组和IVF2PN组胚胎之间的第一次卵裂模式异常率无显著差异(P>0.05)。IVF3PN组胚胎原核消失时间[(25.76±1.33)h]显著长于IVF2PN组[(21.43±1.76)h]、ICSI3PN组[(21.86±1.63)h]和ICSI2PN组[(20.14±1.78)h](P<0.05),IVF3PN胚胎第一次卵裂时间亦显著长于其余3组[(27.06±1.59)hvs.(22.64±1.38)h、(22.32±1.56)h、(22.78±1.66)h](P<0.05);ICSI3PN组、ICSI2PN组和IVF2PN组胚胎之间的原核消失时间和第一次卵裂时间均无显著差异(P>0.05)。结论IVF3PN胚胎与IVF2PN、ICSI3PN和ICSI2PN胚胎的卵裂模式和原核消失时间、第一次卵裂时间等动力学参数不同。