Artificial intelligence for microscopy: what you should know

被引:69
作者
von Chamier, Lucas [1 ]
Laine, Romain F. [1 ,2 ,3 ]
Henriques, Ricardo [1 ,2 ,3 ,4 ]
机构
[1] UCL, MRC, Lab Mol Cell Biol, London, England
[2] UCL, Dept Cell & Dev Biol, London, England
[3] Francis Crick Inst, London, England
[4] UCL, Inst Phys Living Syst, London, England
基金
英国生物技术与生命科学研究理事会; 英国惠康基金; 英国医学研究理事会;
关键词
DEEP; CLASSIFICATION; LOCALIZATION; INFORMATION; IMAGES;
D O I
10.1042/BST20180391
中图分类号
Q5 [生物化学]; Q7 [分子生物学];
学科分类号
071010 ; 081704 ;
摘要
Artificial Intelligence based on Deep Learning (DL) is opening new horizons in biomedical research and promises to revolutionize the microscopy field. It is now transitioning from the hands of experts in computer sciences to biomedical researchers. Here, we introduce recent developments in DL applied to microscopy, in a manner accessible to non-experts. We give an overview of its concepts, capabilities and limitations, presenting applications in image segmentation, classification and restoration. We discuss how DL shows an outstanding potential to push the limits of microscopy, enhancing resolution, signal and information content in acquired data. Its pitfalls are discussed, along with the future directions expected in this field.
引用
收藏
页码:1029 / 1040
页数:12
相关论文
共 92 条
[21]   Large-Scale Machine Learning with Stochastic Gradient Descent [J].
Bottou, Leon .
COMPSTAT'2010: 19TH INTERNATIONAL CONFERENCE ON COMPUTATIONAL STATISTICS, 2010, :177-186
[22]  
Boyd N., 2018, BioRxiv, DOI [DOI 10.1101/267096, 10.1101/ 267096, 10.1101/267096]
[23]   CellProfiler: image analysis software for identifying and quantifying cell phenotypes [J].
Carpenter, Anne E. ;
Jones, Thouis Ray ;
Lamprecht, Michael R. ;
Clarke, Colin ;
Kang, In Han ;
Friman, Ola ;
Guertin, David A. ;
Chang, Joo Han ;
Lindquist, Robert A. ;
Moffat, Jason ;
Golland, Polina ;
Sabatini, David M. .
GENOME BIOLOGY, 2006, 7 (10)
[24]   Deep Learning: A Primer for Radiologists [J].
Chartrand, Gabriel ;
Cheng, Phillip M. ;
Vorontsov, Eugene ;
Drozdzal, Michal ;
Turcotte, Simon ;
Pal, Christopher J. ;
Kadoury, Samuel ;
Tang, An .
RADIOGRAPHICS, 2017, 37 (07) :2113-2131
[25]   Deep Learning in Label-free Cell Classification [J].
Chen, Claire Lifan ;
Mahjoubfar, Ata ;
Tai, Li-Chia ;
Blaby, Ian K. ;
Huang, Allen ;
Niazi, Kayvan Reza ;
Jalali, Bahram .
SCIENTIFIC REPORTS, 2016, 6
[26]   DCAN: Deep Contour-Aware Networks for Accurate Gland Segmentation [J].
Chen, Hao ;
Qi, Xiaojuan ;
Yu, Lequan ;
Heng, Pheng-Ann .
2016 IEEE CONFERENCE ON COMPUTER VISION AND PATTERN RECOGNITION (CVPR), 2016, :2487-2496
[27]  
Chen Jiecao, 2016, Advances in Neural Information Processing Systems, V29
[28]   Not-so-supervised: A survey of semi-supervised, multi-instance, and transfer learning in medical image analysis [J].
Cheplygina, Veronika ;
de Bruijne, Marleen ;
Pluim, Josien P. W. .
MEDICAL IMAGE ANALYSIS, 2019, 54 :280-296
[29]   In Silico Labeling: Predicting Fluorescent Labels in Unlabeled Images [J].
Christiansen, Eric M. ;
Yang, Samuel J. ;
Ando, D. Michael ;
Javaherian, Ashkan ;
Skibinski, Gaia ;
Lipnick, Scott ;
Mount, Elliot ;
O'Neil, Alison ;
Shah, Kevan ;
Lee, Alicia K. ;
Goyal, Piyush ;
Fedus, William ;
Poplin, Ryan ;
Esteva, Andre ;
Berndl, Marc ;
Rubin, Lee L. ;
Nelson, Philip ;
Finkbeiner, Steven .
CELL, 2018, 173 (03) :792-+
[30]   SRRF: Universal live-cell super-resolution microscopy [J].
Culley, Sian ;
Tosheva, Kalina L. ;
Pereira, Pedro Matos ;
Henriques, Ricardo .
INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY, 2018, 101 :74-79