北京大学学报(医学版) ›› 2021, Vol. 53 ›› Issue (2): 425-433. doi: 10.19723/j.issn.1671-167X.2021.02.033
HUANG Xin-rui1,LI Sha2,GAO Song2,Δ()
中图分类号:
[1] |
Bajaj C, Goswami S, Zhang Q. Detection of secondary and supersecondary structures of proteins from cryo-electron microscopy[J]. J Struct Biol, 2012,177(2):367-381.
pmid: 22186625 |
[2] | Merino F, Raunser S. Electron cryo-microscopy as a tool for structure-based drug development[J]. Angew Chem Int Edit, 2017,56(11):2846-2860. |
[3] | Armbruster BL, Kawasaki M, Kersker M, et al. Advanced instrumentation for high resolution transmission cryo-electron microscopy[J]. Biophys J, 2002,82(1):489a. |
[4] |
Zhang X, Zhou ZH. Limiting factors in atomic resolution cryo electron microscopy: No simple tricks[J]. J Struct Biol, 2011,175(3):253-263.
doi: 10.1016/j.jsb.2011.05.004 pmid: 21627992 |
[5] | Frank J. Single-particle cryo-electron microscopy: the path toward atomic resolution[M]. New Jersey: World Scientific, 2018. |
[6] |
Wagner J, Schaffer M, Fernandez-Busnadiego R. Cryo-electron tomography: the cell biology that came in from the cold[J]. Febs Lett, 2017,591(17):2520-2533.
doi: 10.1002/1873-3468.12757 pmid: 28726246 |
[7] |
Al-Amoudi A, Chang JJ, Leforestier A, et al. Cryo-electron microscopy of vitreous sections[J]. Embo J, 2014,23(18):3583-3588.
pmid: 15318169 |
[8] |
Cabra V, Samso M. Do’s and don’ts of cryo-electron microscopy: A primer on sample preparation and high quality data collection for macromolecular 3D reconstruction[J]. J Vis Exp, 2015(95):52311.
pmid: 25651412 |
[9] | Bert W, Slos D, Leroux O, et al. Cryo-fixation and associated developments in transmission electron microscopy: a cool future for nematology[J]. Nematology, 2016,18(1):1-14. |
[10] | Mielanczyk L, Matysiak N, Michalski M, et al. Closer to the native state. Critical evaluation of cryo-techniques for transmission electron microscopy: preparation of biological samples[J]. Folia Histochem Cyto, 2014,52(1):1-17. |
[11] |
Beck M, Baumeister W. Cryo-electron tomography: Can it reveal the molecular sociology of cells in atomic detail?[J]. Trends Cell Biol, 2016,26(11):825-837.
pmid: 27671779 |
[12] | Schmidt-Krey I, Cheng Y. Electron crystallography of soluble and membrane proteins: methods and protocols[M]. New York: Humana Press, Springer, 2013. |
[13] |
Cheng Y, Grigorieff N, Penczek PA, et al. A primer to single-particle cryo-electron microscopy[J]. Cell, 2015,161(3):438-449.
pmid: 25910204 |
[14] |
Dubochet J, Knapek E. Ups and downs in early electron cryo-microscopy[J]. PLoS Biol, 2018,16(4):e2005550.
pmid: 29672565 |
[15] | Welter K. Nobel Price for Chemistry cryo-electron microscopy: Cool images in 3D[J]. Chem Unserer Zeit, 2017,51(6):366-368. |
[16] | Mocibob M. Nobel Prize for Chemistry for 2017: cryo-electron microscopy[J]. Kem Ind, 2017,66(10):703-705. |
[17] | Neumann E, Estrozi LF, Effantin G, et al. The resolution revolution in cryo-electron microscopy[J]. Med Sci (Paris), 2017,33(12):1111-1117. |
[18] | Chiu W, Downing KH. Editorial overview: Cryo electron microscopy: Exciting advances in CryoEM herald a new era in structural biology[J]. Curr Opin Struc Biol, 2017, 46(8): iv-viii. |
[19] | Karuppasamy M, Nejadasl FK, Vulovic M, et al. Radiation damage in single-particle cryo-electron microscopy: effects of dose and dose rate[J]. J Synchrotron Radiat, 2011,18(3):398-412. |
[20] |
Marchin S, Putaux JL, Pignon F, et al. Effects of the environmental factors on the casein micelle structure studied by cryo transmission electron microscopy and small-angle X-ray scattering/ultrasmall-angle X-ray scattering[J]. J Chem Phys, 2007,126(4):045101.
pmid: 17286511 |
[21] | Wang K, Doerschuk PC. Understanding dynamics of biological macromolecular complexes by estimating a mechanical model via statistical mechanics from cryo electron microscopy images: proceedings of the 2011 IEEE International Symposium on Biomedical Imaging: From Nano to Macro[C]. San Diego, CA: Biomedical Engineering, Cornell University, 2011: 1935-1938. |
[22] |
Vulovic M, Ravelli RBG, van Vliet LJ, et al. Image formation modeling in cryo-electron microscopy[J]. J Struct Biol, 2013,183(1):19-32.
pmid: 23711417 |
[23] | Doerschuk PC. Inverse problems for cryo electron microscopy of viruses: Randomly oriented projection images of random 3-D structures in noise[J]. Proc Spie, 2011,7873(4):565-568. |
[24] |
Penczek PA. Image restoration in cryo-electron microscopy[J]. Methods Enzymol, 2010,482:35-72.
pmid: 20888957 |
[25] | Lindert S, Stewart PL, Meiler J. Hybrid approaches: applying computational methods in cryo-electron microscopy[J]. Curr Opin Struc Biol, 2009,19(2):218-225. |
[26] | Hoffmann A, Perrier V, Grudinin S. A novel fast Fourier transform accelerated off-grid exhaustive search method for cryo-electron microscopy fitting[J]. J Appl Crystallogr, 2017,50(4):1036-1047. |
[27] |
McMullan G, Vinothkumar KR, Henderson R. Thon rings from amorphous ice and implications of beam-induced Brownian motion in single particle electron cryo-microscopy[J]. Ultramicroscopy, 2015,158:26-32.
doi: 10.1016/j.ultramic.2015.05.017 pmid: 26103047 |
[28] | Jing ZC, Li M. A wavelet based alternative iteration method for the orientation refinement of cryo-electron microscopy 3D reconstruction[J]. Math Model Anal, 2015,20(3):396-408. |
[29] | Lee J, Zheng YL, Yin Z, et al. Classification of cryo electron microscopy images, noisy tomographic images recorded with unknown projection directions, by simultaneously estimating reconstructions and application to an assembly mutant of cowpea chlorotic mottle virus and portals of the bacteriophage P22[C]// San Diego, CA: Conference on Image Reconstruction from Incomplete Data VI, 2010: 78000R. 1-10. |
[30] | Zheng YL, Doerschuk PC. Algorithms for sorting and reconstructing heterogeneous nanoscale biological objects from cryo electron microscopy images[C]. 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro, 2009: 169-172. |
[31] | Mielikainen T, Ravantti J. Sinogram denoising of cryo-electron microscopy images[J]. Lect Notes Comput Sc, 2005,3483:1251-1261. |
[32] |
Maiorca M, Hanssen E, Kazmierczak E, et al. Improving the quality of electron tomography image volumes using pre-reconstruction filtering[J]. J Struct Biol, 2012,180(1):132-142.
pmid: 22683346 |
[33] |
Starosolski Z, Szczepanski M, Wahle M, et al. Developing a denoising filter for electron microscopy and tomography data in the cloud[J]. Biophys Rev, 2012,4(3):223-229.
pmid: 23066432 |
[34] |
Henderson R. Avoiding the pitfalls of single particle cryo-electron microscopy: Einstein from noise[J]. Proc Natl Acad Sci USA, 2013,110(45):18037-18041.
pmid: 24106306 |
[35] | Prust CJ, Wang Q, Doerschuk PC, et al. Highly scalable methods for exploiting a label with unknown location in order to orient a set of single-particle cryo electron microscopy images[J]. Proc Spie, 2012,8296(3):4. |
[36] |
Bhamre T, Zhang T, Singer A. Denoising and covariance estimation of single particle cryo-EM images[J]. J Struct Biol, 2016,195(1):72-81.
pmid: 27129418 |
[37] |
Sindelar CV, Grigorieff N. Optimal noise reduction in 3D reconstructions of single particles using a volume-normalized filter[J]. J Struct Biol, 2012,180(1):26-38.
pmid: 22613568 |
[38] | Fernandez-Leiro R, Scheres SHW. A pipeline approach to single-particle processing in RELION[J]. Acta Crystallogr D, 2017,73(Pt6):496-502. |
[39] |
Campbell MG, Cheng AC, Brilot AF, et al. Movies of ice-embedded particles enhance resolution in electron cryo-microscopy[J]. Structure, 2012,20(11):1823-1828.
pmid: 23022349 |
[40] | Shigematsu H, Sigworth FJ. Noise models and cryo-EM drift correction with a direct-electron camera[J]. Ultramicroscopy, 2013,131(8):61-69. |
[41] | Nejadasl FK, Karuppasamy M, Newman ER, et al. Non-rigid image registration to reduce beam-induced blurring of cryo-electron microscopy images[J]. J Synchrotron Radiat, 2013,20(1):58-66. |
[42] | Brown A, Long F, Nicholls RA, et al. Tools for macromolecular model building and refinement into electron cryo-microscopy reconstructions[J]. Acta Crystallogr D, 2015,71(1):136-153. |
[43] | Jiang W, Baker ML, Wu Q, et al. Applications of a bilateral denoising filter in biological electron microscopy[J]. J Struct Biol, 2003,144(1):114-122. |
[44] | Asano S, Engel BD, Baumeister W. In situ cryo-electron tomography: A post-reductionist approach to structural biology[J]. J Mol Biol, 2016,428(2):332-343. |
[45] |
Evans JE, Hetherington C, Kirkland A, et al. Low-dose aberration corrected cryo-electron microscopy of organic specimens[J]. Ultramicroscopy, 2008,108(12):1636-1644.
doi: 10.1016/j.ultramic.2008.06.004 pmid: 18703285 |
[46] |
Burger V, Chennubhotla C. Nhs: Network-based hierarchical segmentation for cryo-electron microscopy density maps[J]. Biopolymers, 2012,97(9):732-741.
pmid: 22696408 |
[47] |
Anderson KL, Page C, Swift MF, et al. Marker-free method for accurate alignment between correlated light, cryo-light, and electron cryo-microscopy data using sample support features[J]. J Struct Biol, 2018,201(1):46-51.
doi: 10.1016/j.jsb.2017.11.001 pmid: 29113849 |
[48] |
Ali RA, Landsberg MJ, Knauth E, et al. A 3D image filter for parameter-free segmentation of macromolecular structures from electron tomograms[J]. PLoS One, 2012,7(3):e33697.
pmid: 22479430 |
[49] |
Grange M, Vasishtan D, Grunewald K. Cellular electron cryo tomography and in situ sub-volume averaging reveal the context of microtubule-based processes[J]. J Struct Biol, 2017,197(2):181-190.
pmid: 27374320 |
[50] |
Wan W, Briggs JAG. Cryo-electron tomography and subtomogram averaging[J]. Methods Enzymol, 2016,579:329-367.
pmid: 27572733 |
[51] |
Langlois R, Pallesen J, Ash JT, et al. Automated particle picking for low-contrast macromolecules in cryo-electron microscopy[J]. J Struct Biol, 2014,186(1):1-7.
doi: 10.1016/j.jsb.2014.03.001 pmid: 24607413 |
[52] | Kumar V, Heikkonen J, Engelhardt P, et al. Robust filtering and particle picking in micrograph images towards 3D reconstruction of purified proteins with cryo-electron microscopy[J]. J Struct Biol, 2004,145(1):41-51. |
[53] |
van der Heide P, Xu XP, Marsh BJ, et al. Efficient automatic noise reduction of electron tomographic reconstructions based on iterative median filtering[J]. J Struct Biol, 2007,158(2):196-204.
doi: 10.1016/j.jsb.2006.10.030 pmid: 17224280 |
[54] |
Baxter WT, Grassucci RA, Gao HX, et al. Determination of signal-to-noise ratios and spectral SNRs in cryo-EM low-dose imaging of molecules[J]. J Struct Biol, 2009,166(2):126-132.
doi: 10.1016/j.jsb.2009.02.012 pmid: 19269332 |
[55] |
Sindelar CV, Grigorieff N. An adaptation of the Wiener filter suitable for analyzing images of isolated single particles[J]. J Struct Biol, 2011,176(1):60-74.
pmid: 21757012 |
[56] |
Pantelic RS, Rothnagel R, Huang CY, et al. The discriminative bilateral filter: An enhanced denoising filter for electron microscopy data[J]. J Struct Biol, 2006,155(3):395-408.
doi: 10.1016/j.jsb.2006.03.030 pmid: 16774838 |
[57] |
Pantelic RS, Ericksson G, Hamilton N, et al. Bilateral edge filter: Photometrically weighted, discontinuity based edge detection[J]. J Struct Biol, 2007,160(1):93-102.
doi: 10.1016/j.jsb.2007.07.005 pmid: 17822922 |
[58] |
Wei DY, Yin CC. An optimized locally adaptive non-local means denoising filter for cryo-electron microscopy data[J]. J Struct Biol, 2010,172(3):211-218.
doi: 10.1016/j.jsb.2010.06.021 pmid: 20599508 |
[59] |
Wang J, Yin CC. A Zernike-moment-based non-local denoising filter for cryo-EM images[J]. Sci China Life Sci, 2013,56(4):384-390.
pmid: 23564187 |
[60] | Fernandez JJ, Li S. An improved algorithm for anisotropic nonli-near diffusion for denoising cryo-tomograms[J]. J Struct Biol, 2003,144(1):152-161. |
[61] |
Frangakis AS, Hegerl R. Noise reduction in electron tomographic reconstructions using nonlinear anisotropic diffusion[J]. J Struct Biol, 2001,135(3):239-250.
doi: 10.1006/jsbi.2001.4406 pmid: 11722164 |
[62] |
Zhong JM, Ning RL. Image denoising based on wavelets and multifractals for singularity detection[J]. IEEE Trans Image Process, 2005,14(10):1435-1447.
doi: 10.1109/tip.2005.849313 pmid: 16238050 |
[63] | Tian DZ, Ha MH. Applications of wavelet transform in medical image processing[C]// Machine Learning and Cybernetics, 2004. Proceedings of 2004 International Conference on. IEEE, 2004. |
[64] | Xie GH, Wang YL, Ming L. The application research of wavelet analysis in medical image processing[J]. Wavelet Analysis & Its Applications, 2003(1/2):751-756. |
[65] | Soumia SA, Messai Z, Ouahabi A, et al. Non parametric denoi-sing methods based on wavelets: Application to electron microscopy images in low exposure time[J]. AIP Conference Proceedings, 2015,1641(1):403-413. |
[66] | Moss WC, Haase S, Lyle JM, et al. A novel 3D wavelet-based filter for visualizing features in noisy biological data[J]. J Microsc-Oxford, 2005,219(2):43-49. |
[67] | Huang XR, Li S, Gao S. Applying a modified wavelet shrinkage filter to improve cryo-electron microscopy imaging[J]. J Comput Biol, 2018,25(9):1-9. |
[68] |
Huang X, Li S, Gao S. Exploring an optimal wavelet-based filter for cryo-ET imaging[J]. Sci Rep, 2018,8(1):2582.
pmid: 29416100 |
[1] | 刘思民,赵一姣,王晓燕,王祖华. 动态导航下不同深度环钻定位精确度的体外评价[J]. 北京大学学报(医学版), 2022, 54(1): 146-152. |
[2] | 李怡,王丽瑜,刘晓强,周倜,吕季喆,谭建国. 不同材料及厚度椅旁CAD/CAM瓷贴面的边缘特征[J]. 北京大学学报(医学版), 2022, 54(1): 140-145. |
[3] | 邱淑婷,朱玉佳,王时敏,王飞龙,叶红强,赵一姣,刘云松,王勇,周永胜. 姿势微笑位口唇对称参考平面的数字化构建及初步应用验证[J]. 北京大学学报(医学版), 2022, 54(1): 193-199. |
[4] | 任国勇,吴雪梅,李颖,李婕妤,孙伟平,黄一宁. 大血管闭塞性脑卒中亚急性期磁敏感血管征的表现[J]. 北京大学学报(医学版), 2021, 53(6): 1133-1138. |
[5] | 李媛,林红,张铁军. 对比传统成像与数字成像对牙科复合树脂X射线阻射性的影响[J]. 北京大学学报(医学版), 2021, 53(5): 995-1001. |
[6] | 杨刚,胡文杰,曹洁,柳登高. 牙周健康的上颌前牙唇侧嵴顶上牙龈的三维形态分析[J]. 北京大学学报(医学版), 2021, 53(5): 990-994. |
[7] | 邵振兴,宋庆法,赵宇晴,崔国庆. 一种结合线袢固定的关节镜下“嵌入式”喙突移位术:手术技术及术后影像学分析[J]. 北京大学学报(医学版), 2021, 53(5): 896-901. |
[8] | 吴一凡,张晓圆,任爽,玉应香,常翠青. 基于磁共振的青年男性股四头肌的测量和评估[J]. 北京大学学报(医学版), 2021, 53(5): 843-849. |
[9] | 李新飞, 彭意吉, 余霄腾, 熊盛炜, 程嗣达, 丁光璞, 杨昆霖, 唐琦, 米悦, 吴静云, 张鹏, 谢家馨, 郝瀚, 王鹤, 邱建星, 杨建, 李学松, 周利群. 肾部分切除术前CT三维可视化评估标准的初步探究[J]. 北京大学学报(医学版), 2021, 53(3): 613-622. |
[10] | 胡迪,张苗,康惠颖,彭芸. 0~2岁婴幼儿磁共振脑白质模板的建立及验证[J]. 北京大学学报(医学版), 2021, 53(2): 341-347. |
[11] | 陈迪,徐翔宇,汪明睿,李芮,臧根奥,张悦,钱浩楠,闫光荣,范田园. 熔融沉积成型3D打印盐酸维拉帕米胃漂浮制剂的制备与体外评价[J]. 北京大学学报(医学版), 2021, 53(2): 348-354. |
[12] | 穆海丽,田福聪,王晓燕,高学军. 玻璃体和通用型复合树脂耐磨性的临床对照研究[J]. 北京大学学报(医学版), 2021, 53(1): 120-125. |
[13] | 岳兆国,张海东,杨静文,侯建霞. 数字化评估CAD/CAM个性化基台与成品基台影响粘接剂残留的体外研究[J]. 北京大学学报(医学版), 2021, 53(1): 69-75. |
[14] | 徐啸翔,曹烨,赵一姣,贾璐,谢秋菲. 数字化个齿托盘制取下颌全牙列全冠预备体印模的体外评价[J]. 北京大学学报(医学版), 2021, 53(1): 54-61. |
[15] | 国丹妮,潘韶霞,衡墨笛,屈健,魏秀霞,周永胜. 应用于无牙颌种植修复设计的三维面部扫描配准方法的对比[J]. 北京大学学报(医学版), 2021, 53(1): 83-87. |
|