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MACS-W:A modified optical clearing agent for imaging 3D cell cultures

Journal of Innovative Optical Health Sciences 2024年第2期17卷 24-34页

作者： Xiang Zhong Chao Gao Hui Li Yuening He Peng Fei zaozao chen Zhongze Gu Dan Zhu Tingting Yu Britton Chance Center for Biomedical Photonics-MoE Key Laboratory for Biomedical Photonics Huazhong University of Science and Technology Wuhan Hubei 430074P.R.China Wuhan National Laboratory for Optoelectronics-Advanced Biomedical Imaging Facility Huazhong University of Science and Technology Wuhan Hubei 430074P.R.China School of Optical and Electronic Infrmation Huazhong University of Science and Technology Wuhan Hubei 430074P.R.China State Key Laboratory of Bioelectronics School of Biological Science and Medical Engineering Southeast University NanjingJiangsu 210096P.R.China Institute of Biomaterials and Medical Devices Southeast University Suzhou Jiangsu 215163P.R.China

Three-dimensional(3D)cell cultures have contributed to a variety of biological research fields by filling the gap between monolayers and animal models.The modern optical sectioning microscopic methods make it possible to probe the complexity of 3D cell cultures but are limited by the inherent opaqueness.While tissue optical clearing methods have emerged as powerful tools for investigating whole-mount tissues in 3D,they often have limitations,such as being too harsh for fragile 3D cell cultures,requiring complex handling protocols,or inducing tissue deformation with shrinkage or expansion.To address this issue,we proposed a modified optical clearing method for 3D cell cultures,called MACS-W,which is simple,highly efficient,and morphology-preserving.In our evaluation of MACS-W,we found that it exhibits excellent clearing capability in just 10 min,with minimal deformation,and helps drug evaluation on tumor spheroids.In summary,MACS-W is a fast,minimally-deformative and fluorescence compatible clearing method that has the potential to be widely used in the studies of 3D cell cultures.

关键词： Tissue optical clearing 3D cell cultures imaging

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Profile Compensation for Single-Point Diamond Turning of Microlens Array

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Nanomanufacturing and Metrology 2022年第4期5卷 403-411页

作者： Zhiyue Wang zaozao chen Xinquan Zhang National Key Laboratory of Science and Technology on Micro/Nano Fabrication Shanghai Jiao Tong UniversityShanghai200240China School of Mechanical Engineering Shanghai Jiao Tong UniversityShanghai200240China

To improve the efficiency and consistency of machined microlens array using single-point diamond turning technology,a theoretical model of surface form error is proposed in this paper.Then,a compensation method for this model is studied.In the proposed tool equivalent tilt angle model,the microlens array is regarded as a freeform surface.The corresponding curvature radius of the surface at each cutting point along the cutting direction is calculated by establishing a slow slide servo cutting model.In the spatial form error model,the assumption is that surface form error has a linear relationship with z-axis maximum speed vz.An empirical linear equation is obtained and verified,with a maximum deviation of 0.4μm.Then,after machining,the surface form error is measured and processed using on-machine measurement.The theoretical and measured surface form errors are consistent.The surface form error is compensated in the machining program.The peak-to-valley value is reduced from 5.4 to 0.6μm after compensation.Findings show that the single-point diamond turning and compensation method for the microlens array presented in this paper can predict the surface form error and significantly improve machining accuracy and consistency.

关键词： Microlens array Single-point diamond turning Slow slide servo On-machine measurement Compensation

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Organoids revealed:morphological analysis of the profound next generation in-vitro model with artificial intelligence

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Bio-Design and Manufacturing 2023年第3期6卷 319-339页

作者： Xuan Du zaozao chen Qiwei Li Sheng Yang Lincao Jiang Yi Yang Yanhui Li Zhongze Gu State Key Laboratory of Bioelectronics School of Biological Science and Medical EngineeringSoutheast UniversityNanjing 210096China State Key Laboratory for Novel Software Technology Nanjing UniversityNanjing 210008China Key Laboratory of Environmental Medicine Engineering Ministry of EducationSchool of Public HealthSoutheast UniversityNanjing 210009China

In modern terminology,“organoids”refer to cells that grow in a specific three-dimensional(3D)environment in vitro,sharing similar structures with their source organs or tissues.Observing themorphology or growth characteristics of organoids through a microscope is a commonly used method of organoid analysis.However,it is difficult,time-consuming,and inaccurate to screen and analyze organoids only manually,a problem which cannot be easily solved with traditional technology.Artificial intelligence(AI)technology has proven to be effective in many biological and medical research fields,especially in the analysis of single-cell or hematoxylin/eosin stained tissue slices.When used to analyze organoids,AI should also provide more efficient,quantitative,accurate,and fast solutions.In this review,we will first briefly outline the application areas of organoids and then discuss the shortcomings of traditional organoid measurement and analysis methods.Secondly,we will summarize the development from machine learning to deep learning and the advantages of the latter,and then describe how to utilize a convolutional neural network to solve the challenges in organoid observation and analysis.Finally,we will discuss the limitations of current AI used in organoid research,as well as opportunities and future research directions.

关键词： Artificial intelligence Organoids Morphology Growth characteristics Deep learning Convolutional neural network

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OOCDB:A Comprehensive,Systematic,and Real-time Organs-on-a-chip Database

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Genomics, Proteomics & Bioinformatics 2023年第2期21卷 243-258页

作者： Jian Li Weicheng Liang zaozao chen Xingyu Li Pan Gu Anna Liu Pin chen Qiwei Li Xueyin Mei Jing Yang Jun Liu Lincao Jiang Zhongze Gu School of Life Science and Technology Southeast UniversityNanjing 210096China School of Biological Science&Medical Engineering Southeast UniversityNanjing 210096China School of Computer Data&Information SciencesUniversity of Wisconsin-MadisonMadisonWI 53706USA

Organs-on-a-chip is a microfluidic microphysiological system that uses microfluidic technology to analyze the structure and function of living human cells at the tissue and organ levels in vitro.Organs-on-a-chip technology,as opposed to traditional two-dimensional cell culture and animal models,can more closely simulate pathologic and toxicologic interactions between different organs or tissues and reflect the collaborative response of multiple organs to drugs.Despite the fact that many organs-on-a-chip-related data have been published,none of the current databases have all of the following functions:searching,downloading,as well as analyzing data and results from the literature on organs-on-a-chip.Therefore,we created an organs-on-a-chip database(OOCDB)as a platform to integrate information about organs-on-a-chip from various sources,including literature,patents,raw data from microarray and transcriptome sequencing,several open-access datasets of organs-on-a-chip and organoids,and data generated in our laboratory.OOCDB contains dozens of sub-databases and analysis tools,and each sub-database contains various data associated with organs-on-a-chip,with the goal of providing researchers with a comprehensive,systematic,and convenient search engine.Furthermore,it offers a variety of other functions,such as mathematical modeling,three-dimensional modeling,and citation mapping,to meet the needs of organs-on-a-chip.

关键词： Organ Mathematical model Citation map Organs-on-a-chip

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microRNAs and ceRNAs: RNA networks in pathogenesis of cancer

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Chinese Journal of Cancer Research 2013年第2期25卷 235-239页

作者： Xiangqian Su Jiadi Xing zaozao Wang Lei chen Ming Cui Beihai Jiang Key Laboratory of Carcinogenesis and Translational Research (Ministry of Education) Department of Minimally Invasive Gastrointestinal Surgery Peking University Cancer Hospital & Institute

microRNAs （miRNAs） are a class of endogenous, single-stranded non-coding RNAs of 20- 23 nucleotides in length, functioning as negative regulators of gene expression at the post-transcriptional level. The dysregulation of miRNAs has been demonstrated to play critical roles in tumorigenesis, either through inhibiting tumor suppressor genes or activating oncogenes inappropriately. Besides their promising clinical applications in cancer diagnosis and treatment, recent studies have uncovered that miRNAs could act as a regulatory language, through which messenger RNAs, transcribed pseudogenes, and long noncoding RNAs crosstalk with each other and form a novel regulatory network. RNA transcripts involved in this network have been termed as competing endogenous RNAs （ceRNAs）, since they influence each other＇s level by competing for the same pool of miRNAs through miRNA response elements （MREs） on their target transcripts. The discovery of miRNA-ceRNA network not only provides the possibility of an additional level of post-transcriptional regulation, but also dictates a reassessment of the existing regulatory pathways involved in cancer initiation and progression.

关键词： miRNA ceRNA cancer

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微透镜阵列单点金刚石车削补偿技术

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光学精密工程 2022年第7期30卷 813-820页

作者：王之岳陈灶灶朱利民张鑫泉上海交通大学机械与动力工程学院上海200240

为了提高微透镜阵列单点金刚石车削的加工精度与一致性,提出了加工误差的理论模型,并针对其补偿方法进行了理论分析和实验研究。将微透镜阵列加工等效为自由曲面加工,通过建立单点金刚石慢刀伺服切削模型,计算了理论曲面在每一个切削点... 详细信息

为了提高微透镜阵列单点金刚石车削的加工精度与一致性,提出了加工误差的理论模型,并针对其补偿方法进行了理论分析和实验研究。将微透镜阵列加工等效为自由曲面加工,通过建立单点金刚石慢刀伺服切削模型,计算了理论曲面在每一个切削点处沿切削方向的曲率半径;结合刀具等效倾斜角模型和机床加工时延模型,进一步得到了慢刀伺服切削微透镜阵列误差面形的理论预测值。然后,使用原位测量设备测量处理得到实际加工误差,将面形误差理论值与实际加工误差测量值比较,并将面形误差理论值预补偿到加工程序中。实验结果表明,面形误差理论值与实际加工误差测量值具有一致性,两者偏差在[-0.7μm,0.3μm];补偿加工后微透镜阵列的PV值从5.4μm降低到0.6μm。所提出的微透镜阵列的单点金刚石车削加工与补偿方法能够预测误差面形,显著提升面形精度与一致性。

关键词：超精密加工微透镜阵列单点金刚石车削慢刀伺服原位测量加工补偿

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智能手机PCBA圆形焊点轮廓自适应提取

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计算机辅助设计与图形学学报 2023年第3期35卷 405-412页

作者：闫河刘伦宇陈早早莫佳迪刘继红重庆理工大学两江人工智能学院重庆401147

智能手机印刷电路板装配(printed circuit board assembly,PCBA)集成度高、焊点间隙小,小视场下成像易引入噪声,圆形焊点边缘粘合、断缺现象明显,导致圆形焊点轮廓提取准确性不高.为此,提出PCBA圆形焊点轮廓自适应提取算法.首先,采用引... 详细信息

智能手机印刷电路板装配(printed circuit board assembly,PCBA)集成度高、焊点间隙小,小视场下成像易引入噪声,圆形焊点边缘粘合、断缺现象明显,导致圆形焊点轮廓提取准确性不高.为此,提出PCBA圆形焊点轮廓自适应提取算法.首先,采用引导滤波算法,在有效地抑制噪声的同时捕捉圆形焊点边缘梯度信息;其次,依据自适应OTSU分割算法实现焊点区域分割,采用8邻域边界跟踪算法及Canny算子提取圆形焊点轮廓信息;最后,利用圆形焊点的轮廓几何特性和边缘滑动窗口机制对轮廓信息进行筛选,从而获得更精细的圆形焊点轮廓.在实验设备采集的90幅PCBA图像数据集上与3种典型方法进行实验的结果表明,所提算法的精确率、召回率、F值分别为96.96%,97.88%,97.42%,运行时间为310 ms,可快速、有效地提取出PCBA圆形焊点轮廓.

关键词： PCBA 自适应OTSU分割算法引导滤波边缘滑动窗口轮廓提取

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强噪声下自适应Canny算子边缘检测

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光学精密工程 2022年第3期30卷 350-362页

作者：刘宇涵闫河陈早早王潇棠黄骏滨重庆理工大学两江人工智能学院重庆401147

针对传统Canny算子不能有效滤除图像在解码处理和传输过程产生的椒盐噪声、无法保留边缘细节的问题,提出强噪声下Canny算子图像边缘检测算法。依据椒盐噪声的极值性、灰度差值性,将像元点划分为噪声点、疑似噪声点;根据分类之后的像元... 详细信息

针对传统Canny算子不能有效滤除图像在解码处理和传输过程产生的椒盐噪声、无法保留边缘细节的问题,提出强噪声下Canny算子图像边缘检测算法。依据椒盐噪声的极值性、灰度差值性,将像元点划分为噪声点、疑似噪声点;根据分类之后的像元点自适应地改变滤波器窗口的大小和权值,在降低噪声影响的同时能较好地保留图像细节。引入8个方向模板的Sobel算子计算梯度幅值以提高滤波后的边缘定位效果。使用迭代自适应阈值算法与Otsu算法选择最佳阈值,实现阈值自适应设定,提高边缘连接效果。实验结果表明:图像去噪后的结构相似度为0.949,峰值信噪比相较于传统算法提升了10.97 dB。边缘评价指标提高27.2%,F1值提高了34.6%。该算法能有效去除椒盐噪声,具有更好的边缘细节保护能力。

关键词：计算机视觉边缘检测图像去噪 Canny算法自适应滤波自适应阈值

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乌鲁木齐市采煤塌陷区地表沉降遥感监测

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全球定位系统 2023年第3期48卷 44-51页

作者：冯健杨早早徐莹陈灏新疆维吾尔自治区煤田地质局综合地质勘查队乌鲁木齐830091 山东科技大学测绘与空间信息学院山东青岛266590

乌鲁木齐市侏罗系含煤地层呈近东西向横穿城市主城区,具有含煤层数多、单层煤层巨厚且近乎直立的地质特点.数十年以来,煤炭资源的开采破坏了乌鲁木齐的城市环境,由此造成的塌陷区威胁着周边居民的生产生活,也严重制约着城市发展,限制了... 详细信息

乌鲁木齐市侏罗系含煤地层呈近东西向横穿城市主城区,具有含煤层数多、单层煤层巨厚且近乎直立的地质特点.数十年以来,煤炭资源的开采破坏了乌鲁木齐的城市环境,由此造成的塌陷区威胁着周边居民的生产生活,也严重制约着城市发展,限制了土地资源的开发利用.本文以乌鲁木齐市横跨水磨沟区和米东区的六道湾煤矿、苇湖梁煤矿等为研究区,以Sentinel-1A数据为主要数据源,采用短基线集合成孔径雷达干涉(SBAS-InSAR)技术监测研究区内2018-06-01-2022-06-30的历史废弃煤矿、现有开采煤矿和周边居民区的地表沉降现象.利用SBAS-InSAR技术处理SAR数据,获取研究区内地表时序形变结果,生成地理编码后的年均速率及累积形变量,发现多个矿区沉降漏斗范围扩大,且沉降漏斗中心的累积沉降量超过-150 mm.通过与全球卫星导航系统(GNSS)结果的对比分析发现,GNSS与SBAS结果整体沉降趋势一致,均方根误差(RMSE)为2~3 mm,因此SBAS-InSAR具有较高的可信度.

关键词：合成孔径雷达干涉(InSAR)测量短基线集InSAR(SBAS-InSAR) 全球卫星导航系统(GNSS) 矿区塌陷地乌鲁木齐市

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基于点自动对焦传感器的菲涅耳微结构超精密在位测量

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光学学报 2023年第13期43卷 140-151页

作者：杨知楷陈灶灶莫亮亮张鑫泉上海交通大学机械与动力工程学院上海200240

由于菲涅耳结构存在较大倾角且离线测量会引入原点误差,为实现菲涅耳微结构的超精密在位测量,构建了基于点自动对焦传感器的在位测量系统,并研究开发了配套的位置标定与温度补偿算法。首先,对于测量结果的核心影响因素——温度进行相关... 详细信息

由于菲涅耳结构存在较大倾角且离线测量会引入原点误差,为实现菲涅耳微结构的超精密在位测量,构建了基于点自动对焦传感器的在位测量系统,并研究开发了配套的位置标定与温度补偿算法。首先,对于测量结果的核心影响因素——温度进行相关性分析,并通过高斯过程对其进行补偿,使得测头测量误差下降至未补偿前的39%;其次,为保证测头扫描路径通过所测微结构中心,以避免曲面重构过程中引入对齐误差,在测量前利用标准球面对测头的位姿进行预标定;最后,利用该套设备对菲涅耳微结构进行测量并分析了测量结果。实验结果表明,所组建的系统相比基于光谱共聚焦的在位测量系统能够更有效地评估菲涅耳结构形貌,相比离线白光干涉测量系统可获得更精准的结果。

关键词：测量在位测量菲涅耳微结构高斯过程温度补偿

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