基本信息
陈曦  男  硕导  中国科学院自动化研究所
电子邮件: xi.chen@ia.ac.cn
通信地址: 北京市海淀区中关村东路95号
邮政编码: 100190

研究领域

生物组织高通量序列图像实时配准技术

招生信息

   
招生专业
081104-模式识别与智能系统

教育背景

2004-09--2009-07   中国科学院自动化研究所   博士
2000-09--2004-07   西安交通大学   学士

工作经历

   
工作简历
2021-04~现在, 中国科学院自动化研究所, 研究员
2012-10~2021-04,中国科学院自动化研究所, 高级工程师
2009-07~2012-10,中国科学院自动化研究所, 助理研究员

专利与奖励

   
专利成果
[1] 陈曦, 吕亚楠, 韩华, 沈丽君. 基于仿射变换的显微序列图像自动拼接方法、系统及装置. CN: CN112381718B, 2021-07-30.

[2] 沈丽君, 洪贝, 韩华, 陈曦. 基于电镜图像的集成电路金属圆孔自动识别方法及系统. CN: CN112200164B, 2021-02-23.

[3] 陈曦, 周芳旭, 韩华, 李琳琳, 马宏图. 基于X光图像的生物组织电镜图像校正方法、系统和装置. CN: CN112396608A, 2021-02-23.

[4] 沈丽君, 常胜, 韩华, 李琳琳, 陈曦. 扫描电镜透射模式与透射电镜联用的病毒快速检测系统. CN: CN112381817A, 2021-02-19.

[5] 马宏图, 李琳琳, 张丽娜, 陈曦, 韩华. 基于生物组织序列切片刻蚀减薄的三维图像库获取方法. CN: CN110533772B, 2021-02-02.

[6] 陈曦, 翟昊, 沈丽君, 谢启伟, 韩华. 基于孪生网络的笼养动物行为分析方法、系统、装置. CN: CN111582214A, 2020-08-25.

[7] 陈曦, 韩华, 李国庆, 谢启伟, 沈丽君. 面向序列切片的扫描电镜图像实时配准装置及方法. CN: CN108038874B, 2020-07-24.

[8] 陈曦, 韩华, 沈丽君, 马宏图. 大视场光学显微图像成像装置及方法. CN: CN109283679B, 2020-05-19.

[9] 陈曦, 韩华, 谢启伟, 沈丽君. 生物组织序列切片显微图像的配准方法及装置. CN: CN107545567B, 2020-05-19.

[10] 李国庆, 韩华, 陈曦, 孙国栋. 基于随机线段的图像特征分类方法及系统. CN: CN110991541A, 2020-04-10.

[11] 张丽娜, 马宏图, 李琳琳, 陈曦, 李国庆, 韩华. 超薄切片机及其刀台. CN: CN110887685A, 2020-03-17.

[12] 李国庆, 韩华, 马宏图, 陈曦. 低能量背散射电子探测器. CN: CN107917924B, 2020-01-10.

[13] 谢启伟, 韩华, 陈曦, 沈丽君, 李国庆. 基于电镜序列切片图像的突触检测方法. CN: CN106407988B, 2019-11-26.

[14] 张丽娜, 马宏图, 李琳琳, 陈曦, 韩华. 刀刃位置切换方法、装置及包括该装置的超薄切片机. CN: CN110328712A, 2019-10-15.

[15] 张丽娜, 马宏图, 李琳琳, 陈曦, 李国庆, 韩华. 超薄切片机及其刀台. CN: CN209132009U, 2019-07-19.

[16] 谢启伟, 韩华, 沈丽君, 陈曦, 李国庆. 基于双光子图像的突触检测方法. CN: CN106373116B, 2019-04-12.

[17] 陈曦, 舒畅, 韩华, 谢启伟. 生物样品三维结构的构建方法及装置. CN: CN109584368A, 2019-04-05.

[18] 陈曦, 韩华, 沈丽君, 谢启伟. 显微序列图像拼接方法及装置. CN: CN109584156A, 2019-04-05.

[19] 李国庆, 韩华, 马宏图, 陈曦. 低能量背散射电子探测器. 中国: CN107976458A, 2018-05-01.

[20] 陈曦, 周芳旭, 韩华, 沈丽君. 多幅显微图像拼接中的灰度校正方法及装置. 中国: CN107958442A, 2018-04-24.

[21] 曹会文, 韩华, 陈曦, 饶强, 肖驰. 基于线粒体结构的图像配准方法及装置、存储介质及设备. 中国: CN107481224A, 2017.12.15.

[22] 陈曦, 韩华, 谢启伟, 沈丽君. 小波邻域高斯模型图像复原方法. 中国: CN106508111B, 2014-10-22.

[23] 韩华, 胡敏, 陈涛, 陈曦, 谢启伟, 沈丽君. 一种基于多尺度基本形式的相似尺度图像融合方法. 中国: CN106508048B, 2014-08-27.

[24] 沈丽君, 陈涛, 韩华, 陈曦, 谢启伟. 利用自适应多尺度基本形式实现图像融合的方法. 中国: CN106508047B, 2014-08-27.

[25] 谢启伟, 韩华, 陈曦, 沈丽君. 一种基于图像边缘保持自适应分解的超分辨率重建方法. 中国: CN106508045B, 2014-08-27.

[26] 谢启伟, 韩华, 陈曦, 沈丽君. 基于带限二维EMD与Gabor自适应滤波的图像时频分析法. 中国: CN106508110B, 2014-07-23.

出版信息

   
发表论文
[1] Jiang, Yi, Li, Linlin, Chen, Xi, Liu, Jiazheng, Yuan, Jingbin, Xie, Qiwei, Han, Hua. Three-dimensional ATUM-SEM reconstruction and analysis of hepatic endoplasmic reticulum-organelle interactions. JOURNAL OF MOLECULAR CELL BIOLOGY(Cover)[J]. 2021, 13(9): 636-645, http://dx.doi.org/10.1093/jmcb/mjab032.
[2] Wang, Zejin, Liu, Jing, Chen, Xi, Li, Guoqing, Han, Hua. Sparse self-attention aggregation networks for neural sequence slice interpolation. BIODATA MINING[J]. 2021, 14(1): https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7852179/.
[3] Xiao, Chi, Chen, Xi, Xie, Qiwei, Li, Guoqing, Xiao, Hao, Song, Jingdong, Han, Hua. Virus identification in electron microscopy images by residual mixed attention network. COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE[J]. 2021, 198: http://dx.doi.org/10.1016/j.cmpb.2020.105766.
[4] Liu, Jing, Hong, Bei, Chen, Xi, Xie, Qiwei, Tang, Yuanyan, Han, Hua. An effective AI integrated system for neuron tracing on anisotropic electron microscopy volume. BIOMEDICAL SIGNAL PROCESSING AND CONTROL[J]. 2021, 69: http://dx.doi.org/10.1016/j.bspc.2021.102829.
[5] Zhou, Fangxu, Shen, Lijun, Chen, Bohao, Chen, Xi, Hua, Han. Human attention-inspired volume reconstruction method on serial section electron microscopy images. CYTOMETRY PART A[J]. 2021, 99(6): 575-585, http://dx.doi.org/10.1002/cyto.a.24332.
[6] Liu, Jing, Li, Linlin, Yang, Yang, Hong, Bei, Chen, Xi, Xie, Qiwei, Han, Hua. Automatic Reconstruction of Mitochondria and Endoplasmic Reticulum in Electron Microscopy Volumes by Deep Learning. FRONTIERS IN NEUROSCIENCE[J]. 2020, 14: https://doaj.org/article/15d204a109b54f9b9ae112dcf4e2ab6d.
[7] Shu, Chang, Xin, Tong, Zhou, Fangxu, Chen, Xi, Han, Hua. Dual Networks for High-Precision and High-Speed Registration of Brain Electron Microscopy Images. BRAIN SCIENCES[J]. 2020, 10(2): https://doaj.org/article/281eaee52c6c436fa179e9c36a6df4f3.
[8] Chang, Sheng, Zhou, Fangxu, Chen, Xi, Han, Hua, Pan, Z, Wang, X. Electron Microscopic Sequential Images Stitching Based on Belief Propagation. ELEVENTH INTERNATIONAL CONFERENCE ON GRAPHICS AND IMAGE PROCESSING (ICGIP 2019)null. 2020, 11373: [9] Liu, Danqian, Li, Weifu, Ma, Chenyan, Zheng, Weitong, Yao, Yuanyuan, Tso, Chak Foon, Zhong, Peng, Chen, Xi, Song, Jun Ho, Choi, Woochul, Paik, SeBum, Han, Hua, Dan, Yang. A common hub for sleep and motor control in the substantia nigra. SCIENCE[J]. 2020, 367(6476): 440-+, https://www.webofscience.com/wos/woscc/full-record/WOS:000509810200041.
[10] Xi Chen, Hao Zhai, Hua Han. SiamBOMB: A Real-time AI-based System for Home-cage Animal Tracking, Segmentation and Behavioral Analysis. International Conference on Artificial Intelligence(IJCAI)null. 2020, [11] Shu, Chang, Li, LinLin, Li, Guoqing, Chen, Xi, Han, Hua. A Noniterative Simultaneous Rigid Registration Method for Serial Sections of Biological Tissues. APPLIED SCIENCES-BASEL[J]. 2020, 10(3): http://dx.doi.org/10.3390/app10031156.
[12] Lv, Yanan, Chen, Xi, Shu, Chang, Han, Hua, IEEE. ROBUST GLOBAL OPTIMIZED AFFINE REGISTRATION METHOD FOR MICROSCOPIC IMAGES OF BIOLOGICAL TISSUE. 2020 IEEE INTERNATIONAL CONFERENCE ON ACOUSTICS, SPEECH, AND SIGNAL PROCESSINGnull. 2020, 1070-1074, [13] Chen, Bohao, Chang, Sheng, Chen, Xi, Han, Hua, Pan, Z, Wang, X. Using Scale Information to Improve SIFT-Based Electron Microscope Image Registration Method. ELEVENTH INTERNATIONAL CONFERENCE ON GRAPHICS AND IMAGE PROCESSING (ICGIP 2019)null. 2020, 11373: [14] Yu, Chong, Chen, Xi, Yin, Lei, Shu, Chang, Zhao, Li, Han, Hua. Image deformation based on contour using moving integral least squares. IET IMAGE PROCESSING[J]. 2019, 13(1): 152-160, http://ir.ia.ac.cn/handle/173211/25663.
[15] Xie, Qiwei, Chen, Xi, Zhang, Liming, Jiang, An, Cui, Feng. A Robust and Efficient Video Anti-Shaking Algorithm for Low-End Smartphone Platforms. IEEE TRANSACTIONS ON CONSUMER ELECTRONICS[J]. 2019, 65(1): 1-10, http://ir.ia.ac.cn/handle/173211/25277.
[16] Bourgoin, Thierry, Wang, RongRong, Szwedo, Jacek, Li, XinYu, Chen, Xi. A new early Miocene fossil genus from Dominican amber extends the Eastern Asia distribution of Paricanini (Hemiptera: Fulgoromorpha: Tropiduchidae) to the Neotropics. PALAEONTOLOGIA ELECTRONICA[J]. 2019, 22(3): http://dx.doi.org/10.26879/958.
[17] Chen, Xi, Shen, Lijun, Xie, Qiwei, Han, Hua, Tomaszewski, JE, Ward, AD. Skeleton-based Image Registration of Serial Electron Microscopy Sections. MEDICAL IMAGING 2019: DIGITAL PATHOLOGYnull. 2019, 10956: [18] Xiao, Chi, Chen, Xi, Li, Weifu, Li, Linlin, Wang, Lu, Xie, Qiwei, Han, Hua. Automatic Mitochondria Segmentation for EM Data Using a 3D Supervised Convolutional Network. FRONTIERS IN NEUROANATOMY[J]. 2018, 12: https://doaj.org/article/5586c0f8c96645d4bd4fe80280047c5a.
[19] Shu Chang, Chen Xi, Xie Qiwei, Xiao Chi, Han Hua, IEEE. NON-ITERATIVE SIMULTANEOUS RIGID REGISTRATION METHOD FOR SERIAL SECTIONS OF BIOLOGICAL TISSUE. 2018 IEEE 15TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI 2018)null. 2018, 436-440, [20] Sun, Rong, Chen, Xi, Yin, ChunYing, Qi, Lei, Lau, PakMing, Han, Hua, Bi, GuoQiang. Correlative light and electron microscopy for complex cellular structures on PDMS substrates with coded micro-patterns. LAB ON A CHIP[J]. 2018, 18(24): 3840-3848, http://ir.ia.ac.cn/handle/173211/25681.
[21] Xiao, Chi, Li, Weifu, Chen, Xi, Han, Hua, Xie, Qiwei. An Effective Fully Deep Convolutional Neural Networks for Mitochondria Segmentation Based on ATUM-SEM. MEDICAL IMAGING 2018: IMAGE PROCESSING[J]. 2018, 10574: [22] Chen Xi, Xie Qiwei, Shen Lijun, Han Hua, IEEE. MORPHOLOGY-RETAINED NON-LINEAR IMAGE REGISTRATION OF SERIAL ELECTRON MICROSCOPY SECTIONS. 2018 25TH IEEE INTERNATIONAL CONFERENCE ON IMAGE PROCESSING (ICIP)null. 2018, 3833-3837, [23] Shu Chang, Yu Chong, Chen Xi, Han Hua. A Refined Spatial Transformer Network. International Conference on Neural Information Processing (ICONIP 2018)null. 2018, http://ir.ia.ac.cn/handle/173211/21724.
[24] Zhou Fangxu, Chen Xi, Sun Rong, Han Hua, Yu H, Dong Y. Grayscale Inhomogeneity Correction Method for Multiple Mosaicked Electron Microscope Images. NINTH INTERNATIONAL CONFERENCE ON GRAPHIC AND IMAGE PROCESSING (ICGIP 2017)null. 2018, 10615: [25] Xiao Chi, Liu Jing, Chen Xi, Han Hua, Shu Chang, Xie Qiwei, IEEE. DEEP CONTEXTUAL RESIDUAL NETWORK FOR ELECTRON MICROSCOPY IMAGE SEGMENTATION IN CONNECTOMICS. 2018 IEEE 15TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI 2018)null. 2018, 378-381, [26] Xiao, Chi, Li, Weifu, Deng, Hao, Chen, Xi, Yang, Yang, Xie, Qiwei, Han, Hua. Effective automated pipeline for 3D reconstruction of synapses based on deep learning. BMC BIOINFORMATICS[J]. 2018, 19(1): http://ir.ia.ac.cn/handle/173211/23633.
[27] Shu, Chang, Chen, Xi, Xie, Qiwei, Han, Hua, Tomaszewski, JE, Gurcan, MN. An Unsupervised Network for Fast Microscopic Image Registration. MEDICAL IMAGING 2018: DIGITAL PATHOLOGYnull. 2018, 10581: [28] Li, Weifu, Zhang, Dandan, Xie, Qiwei, Chen, Xi, Han, Hua, Pham, TD, Vozenilek, V, Zeng, Z. An Automated Detection for Axonal Boutons in Vivo Two-photon Imaging of Mouse. EIGHTH INTERNATIONAL CONFERENCE ON GRAPHIC AND IMAGE PROCESSING (ICGIP 2016)null. 2017, 10225: [29] Hu, Jie, Xiao, Chi, Shen, Lijun, Xie, Qiwei, Chen, Xi, Han, Hua, IEEE. Automatical Detecting and Connecting the Mitochondria From the Serial EM Images. 2017 IEEE INTERNATIONAL CONFERENCE ON MECHATRONICS AND AUTOMATION (ICMA)null. 2017, 1632-1637, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000426271700284.
[30] Li, Weifu, Deng, Hao, Rao, Qiang, Xie, Qiwei, Chen, Xi, Han, Hua. An automated pipeline for mitochondrial segmentation on ATUM-SEM stacks. JOURNAL OF BIOINFORMATICS AND COMPUTATIONAL BIOLOGY[J]. 2017, 15(3): https://www.webofscience.com/wos/woscc/full-record/WOS:000404061500009.
[31] Li Xixia, Ji Gang, Chen Xi, Ding Wei, Sun Lei, Xu Wei, Han Hua, Sun Fei. Large scale three-dimensional reconstruction of an entire Caenorhabditis elegans larva using AutoCUTS-SEM. Journal of Structural Biology[J]. 2017, [32] Cao, Huiwen, Han, Hua, Rao, Qiang, Xiaol, Chi, Chen, Xi, Styner, MA, Angelini, ED. Microscopic neural image registration based on the structure of mitochondria. MEDICAL IMAGING 2017: IMAGE PROCESSINGnull. 2017, 10133: [33] Yin Lei, Xiao Chi, Xie Qiwei, Chen Xi, Shen Lijun, Han Hua, IEEE. An Efficient Method for Neuronal Tracking in Electron Microscopy Images. 2017 IEEE INTERNATIONAL CONFERENCE ON MECHATRONICS AND AUTOMATION (ICMA)null. 2017, 1865-1870, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000426271700325.
[34] Rao Qiang, Xiao Chi, Han Hua, Chen Xi, Shen Lijun, Xie Qiwei, Styner MA, Angelini ED. Deep Learning and Shapes Similarity for Joint Segmentation and Tracing single Neurons in SEM images. MEDICAL IMAGING 2017: IMAGE PROCESSINGnull. 2017, 10133: [35] 谢启伟, 陈曦, 沈丽君, 李国庆, 马宏图, 韩华. 脑微观重建系统研究. 系统工程理论与实践[J]. 2017, 37(11): 3006-3017, [36] Xiao Chi, Rao Qiang, Zhang Dandan, Chen Xi, Han Hua, Xie Qiwei. 3D-Reconstruction of Synapses with deep learning Based on EM. MEDICAL IMAGING 2017: PHYSICS OF MEDICAL IMAGING[J]. 2017, 10132: [37] Yu Chong, Chen Xi, Xie Qiwei, Li Guoqing, Yin Lei, Han Hua, IEEE. Image Deformation Using Modified Moving Least Squares with Outlines. 2017 IEEE INTERNATIONAL CONFERENCE ON MECHATRONICS AND AUTOMATION (ICMA)null. 2017, 1047-1051, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000426271700184.
[38] Xie, Qiwei, Chen, Xi, Deng, Hao, Liu, Danqian, Sun, Yingyu, Zhou, Xiaojuan, Yang, Yang, Han, Hua. An automated pipeline for bouton, spine, and synapse detection of in vivo two-photon images. BIODATA MINING[J]. 2017, 10(1): https://doaj.org/article/6f5ebf075a004776acc9f4996e5ed9c3.
[39] Li Weifu, Rao Qiang, Chen Xi, Li Guoqing, Zhang Dandan, IEEE. Segmentation of Mitochondria Based on SEM Images. 2016 IEEE INTERNATIONAL CONFERENCE ON MECHATRONICS AND AUTOMATIONnull. 2016, 1953-1958, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000387187800342.
[40] Rao Qiang, Han Hua, Li Weifu, Shen Lijun, Chen Xi, Xie Qiwei, IEEE. Automatically Segmenting and Reconstructing Neurons in SEM images. 2016 IEEE INTERNATIONAL CONFERENCE ON MECHATRONICS AND AUTOMATIONnull. 2016, 1908-1915, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000387187800334.
[41] Xie Q W, Chen X, Zhang L M, Jiang A, Cui F, IEEE. A Novel Rapid and Efficient Video Stabilization Algorithm for Mobile Platforms. 2016 30TH ANNIVERSARY OF VISUAL COMMUNICATION AND IMAGE PROCESSING (VCIP)null. 2016, http://apps.webofknowledge.com/CitedFullRecord.do?product=UA&colName=WOS&SID=5CCFccWmJJRAuMzNPjj&search_mode=CitedFullRecord&isickref=WOS:000392647500063.
[42] 谢启伟, 陈曦, 沈丽君, 李伟夫, 韩华, 饶强. Automatically Segmenting and Reconstructing Neurons in SEM images. ICMA2016 proceedingsnull. 2016, http://ir.ia.ac.cn/handle/173211/14642.
[43] Chen, Xi, Xie, Qiwei, Shen, Lijun, Han, Hua, Chbeir, R, Yetongnon, K, Dipanda, A. Wrinkle Image Registration for Serial Microscopy Sections. 2015 11TH INTERNATIONAL CONFERENCE ON SIGNAL-IMAGE TECHNOLOGY & INTERNET-BASED SYSTEMS (SITIS)null. 2015, 23-26, http://dx.doi.org/10.1109/SITIS.2015.14.
[44] Peng Silong, Chen Xi. Restoration of degraded image from partially-known mixed blur. Jisuanji Fuzhu Sheji Yu Tuxingxue Xuebao/Journal of Computer-Aided Design and Computer Graphics[J]. 2010, 22(2): 272-278, http://ir.ia.ac.cn/handle/173211/2892.
[45] WangYangang, 陈曦, PengSilong, 陈曦, 汪彦刚, 彭思龙, ChenXi. 部分模糊核已知的混合模糊图像复原算法. 计算机辅助设计与图形学学报. 2010, 272-278, http://lib.cqvip.com/Qikan/Article/Detail?id=32965481.
[46] Han Hua, Chen Xi, Peng Silong. An efficient algorithm and FPGA implementation of video luminance transient improvement. 高技术通讯:英文版[J]. 2010, 359-365, http://lib.cqvip.com/Qikan/Article/Detail?id=36296364.
[47] Chen Xi, Wang Yangang, Peng Silong, Han Hua, Yangang Wang. Video luminance transient improvement using difference-of-Gaussian. 2009, pp 249-253, http://ir.ia.ac.cn/handle/173211/12878.
[48] 陈曦. 图像复原算法的研究. 2009, http://www.irgrid.ac.cn/handle/1471x/976858.
[49] Xi Chen, Peng Silong, Chen Xi. A modified SLT denoising method. 2008, pp 430-434, http://ir.ia.ac.cn/handle/173211/12884.

科研活动

   
科研项目
( 1 ) 大目标场景下的电镜图像拼接方法研究, 主持, 国家级, 2013-01--2015-12
( 2 ) 智能汽车的视觉感知关键技术研究, 参与, 国家级, 2017-01--2020-12
( 3 ) 突触水平神经大数据重建与分析平台, 参与, 省级, 2016-05--2018-12
( 4 ) 生物切片序列高通量扫描电镜三维影像系统, 参与, 部委级, 2017-01--2018-12
( 5 ) 微观脑网络结构分析与重构, 参与, 部委级, 2015-07--2017-06
( 6 ) 果蝇脑超薄切片图像处理, 主持, 院级, 2014-10--2017-12
( 7 ) 大脑微观三维重建, 参与, 市地级, 2014-01--2015-06
( 8 ) 果蝇视觉系统的微观结构重建及网络分析, 参与, 国家级, 2017-07--2020-06
( 9 ) 面向超薄序列切片的三维电镜自动成像技术研究, 参与, 国家级, 2018-01--2020-12
( 10 ) 灵长类全脑神经联接图谱计划, 参与, 部委级, 2017-01--2021-12
( 11 ) 纳米级芯片智能分析系统研发及产业化, 主持, 省级, 2018-07--2020-06
( 12 ) 生物序列切片扫描电镜图像实时配准技术功能开发, 主持, 部委级, 2018-09--2020-08
( 13 ) 序列切片透射电镜电子断层成像数据配准系统研制, 主持, 部委级, 2020-09--2022-08
( 14 ) 笼养动物实时跟踪、分割和行为分析的智能化系统, 主持, 部委级, 2020-01--2024-12
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