Machine learning for cross-scale microscopy of viruses.
CP: Microbiology and CP: Imaging
SARS-CoV-2
adenovirus tracking and trafficking
artificial intelligence
deep learning
electron microscopy
fluorescence super-resolution microscopy
herpes simplex virus
human immunodeficiency virus
influenza virus
machine learning
nanoparticle
Journal
Cell reports methods
ISSN: 2667-2375
Titre abrégé: Cell Rep Methods
Pays: United States
ID NLM: 9918227360606676
Informations de publication
Date de publication:
25 09 2023
25 09 2023
Historique:
received:
06
02
2023
revised:
05
06
2023
accepted:
20
07
2023
medline:
28
9
2023
pubmed:
27
9
2023
entrez:
26
9
2023
Statut:
ppublish
Résumé
Despite advances in virological sciences and antiviral research, viruses continue to emerge, circulate, and threaten public health. We still lack a comprehensive understanding of how cells and individuals remain susceptible to infectious agents. This deficiency is in part due to the complexity of viruses, including the cell states controlling virus-host interactions. Microscopy samples distinct cellular infection stages in a multi-parametric, time-resolved manner at molecular resolution and is increasingly enhanced by machine learning and deep learning. Here we discuss how state-of-the-art artificial intelligence (AI) augments light and electron microscopy and advances virological research of cells. We describe current procedures for image denoising, object segmentation, tracking, classification, and super-resolution and showcase examples of how AI has improved the acquisition and analyses of microscopy data. The power of AI-enhanced microscopy will continue to help unravel virus infection mechanisms, develop antiviral agents, and improve viral vectors.
Identifiants
pubmed: 37751685
pii: S2667-2375(23)00201-1
doi: 10.1016/j.crmeth.2023.100557
pmc: PMC10545915
pii:
doi:
Substances chimiques
Antiviral Agents
0
Types de publication
Journal Article
Review
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Pagination
100557Informations de copyright
Copyright © 2023 The Author(s). Published by Elsevier Inc. All rights reserved.
Déclaration de conflit d'intérêts
Declaration of interests The authors declare no competing interests.
Références
Nat Commun. 2018 Dec 6;9(1):5217
pubmed: 30523263
Phys Rev E. 2021 Apr;103(4-1):042310
pubmed: 34005966
Life Sci Alliance. 2022 Jan 7;5(4):
pubmed: 34996842
Methods. 2017 Feb 15;115:80-90
pubmed: 27713081
Nat Commun. 2020 Oct 2;11(1):4938
pubmed: 33009401
Nat Protoc. 2016 Sep;11(9):1757-74
pubmed: 27560178
Sci Rep. 2020 Mar 19;10(1):5068
pubmed: 32193485
PLoS Biol. 2021 Dec 28;19(12):e3001490
pubmed: 34962926
Nature. 2020 Nov;587(7832):152-156
pubmed: 33087931
Elife. 2022 Jan 20;11:
pubmed: 35049501
Adv Virus Res. 1983;28:175-240
pubmed: 6362365
IEEE Trans Med Imaging. 2019 Feb;38(2):448-459
pubmed: 30716022
Science. 2019 Mar 29;363(6434):1463-1467
pubmed: 30923225
J Struct Biol. 2007 Jan;157(1):38-46
pubmed: 16859925
J Cell Biol. 1999 Feb 22;144(4):657-72
pubmed: 10037788
Cell Syst. 2020 May 20;10(5):453-458.e6
pubmed: 34222682
J Cell Sci. 2020 Nov 9;134(5):
pubmed: 32917739
Nature. 2013 Jun 20;498(7454):390-4
pubmed: 23783631
Cell Host Microbe. 2011 Aug 18;10(2):105-17
pubmed: 21843868
Nature. 1984 Mar 1-7;308(5954):32-6
pubmed: 6322001
Nat Rev Drug Discov. 2021 Feb;20(2):145-159
pubmed: 33353986
Nat Methods. 2019 Dec;16(12):1233-1246
pubmed: 31133758
Cell Rep. 2018 May 8;23(6):1779-1793
pubmed: 29742433
Comput Methods Programs Biomed. 2021 Jan;198:105766
pubmed: 33059061
STAR Protoc. 2021 Dec 11;2(4):101017
pubmed: 34950892
Nat Methods. 2018 Dec;15(12):1090-1097
pubmed: 30478326
Nat Rev Microbiol. 2020 Oct;18(10):559-570
pubmed: 32533130
Science. 2022 Jun 10;376(6598):eabm9506
pubmed: 35679397
Nature. 2015 May 28;521(7553):436-44
pubmed: 26017442
Proc IEEE Comput Soc Conf Comput Vis Pattern Recognit. 2018 Jun;2018:9309-9318
pubmed: 30918435
J Cell Biol. 2021 Feb 1;220(2):
pubmed: 33326005
Bioessays. 2021 Mar;43(3):e2000257
pubmed: 33377226
Science. 2020 Nov 13;370(6518):861-865
pubmed: 33082294
Nat Methods. 2010 Sep;7(9):747-54
pubmed: 20693996
iScience. 2021 May 15;24(6):102543
pubmed: 34151222
Nat Methods. 2014 Apr;11(4):417-22
pubmed: 24584193
Nat Rev Cancer. 2018 Aug;18(8):500-510
pubmed: 29777175
Q Rev Biophys. 1988 May;21(2):129-228
pubmed: 3043536
Nat Methods. 2019 Dec;16(12):1247-1253
pubmed: 31636459
PLoS One. 2013 Dec 02;8(12):e80999
pubmed: 24312513
Comput Struct Biotechnol J. 2021 Oct 05;19:5688-5700
pubmed: 34765089
Nat Biotechnol. 2022 Apr;40(4):606-617
pubmed: 34782739
Nat Methods. 2021 Jan;18(1):18-22
pubmed: 33408406
PLoS Pathog. 2022 May 23;18(5):e1010470
pubmed: 35605011
Mol Ther. 2011 Jul;19(7):1199-211
pubmed: 21654634
Nat Med. 2021 May;27(5):775-784
pubmed: 33990804
Microscopy (Oxf). 2023 Jun 8;72(3):204-212
pubmed: 37079744
Nat Methods. 2019 Dec;16(12):1226-1232
pubmed: 31570887
In Vitro Cell Dev Biol Anim. 2021 Feb;57(2):104-132
pubmed: 33175307
Nat Commun. 2021 Jul 30;12(1):4629
pubmed: 34330917
Nature. 2021 Nov;599(7883):141-146
pubmed: 34616042
Nat Methods. 2021 May;18(5):557-563
pubmed: 33963344
Nat Methods. 2021 May;18(5):551-556
pubmed: 33574612
Sci Rep. 2020 Dec 1;10(1):20937
pubmed: 33262363
Nat Microbiol. 2019 Feb;4(2):216-225
pubmed: 30420785
IEEE Trans Pattern Anal Mach Intell. 2017 Apr;39(4):640-651
pubmed: 27244717
Nat Commun. 2015 Jan 22;6:5980
pubmed: 25609143
Nature. 2020 Nov;587(7832):157-161
pubmed: 33087927
Nat Methods. 2020 Jul;17(7):734-740
pubmed: 32541853
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Cell. 2019 Jan 10;176(1-2):281-294.e19
pubmed: 30503209
BMC Biol. 2021 Aug 2;19(1):156
pubmed: 34334126
Nat Methods. 2021 Nov;18(11):1386-1394
pubmed: 34675434
BMC Bioinformatics. 2021 Sep 10;22(1):433
pubmed: 34507520
RSC Adv. 2021 Feb 18;11(14):7981-8002
pubmed: 35423337
J Virol. 2016 Mar 28;90(8):3802-3805
pubmed: 26842477
Bioinformatics. 2017 Jul 01;33(13):2010-2019
pubmed: 28203779
Bioinformatics. 2017 Aug 15;33(16):2555-2562
pubmed: 28379412
Nature. 2021 Aug;596(7873):583-589
pubmed: 34265844
Nature. 2010 Mar 11;464(7286):243-9
pubmed: 20190736
PLoS Comput Biol. 2022 Jan 18;18(1):e1009797
pubmed: 35041653
Cold Spring Harb Symp Quant Biol. 1962;27:1-24
pubmed: 14019094
IEEE Trans Pattern Anal Mach Intell. 2019 Sep;41(9):2251-2265
pubmed: 30028691
Sci Adv. 2021 Dec 17;7(51):eabl7150
pubmed: 34919430
Nat Biotechnol. 2018 Jun;36(5):460-468
pubmed: 29658943
Nat Methods. 2022 Dec;19(12):1634-1641
pubmed: 36344832
Nature. 2023 May;617(7962):711-716
pubmed: 37225882
Cell Host Microbe. 2023 Apr 12;31(4):616-633.e20
pubmed: 37003257
Viruses. 2018 Mar 31;10(4):
pubmed: 29614729
Nat Methods. 2022 Nov;19(11):1427-1437
pubmed: 36316563
J Biophys Biochem Cytol. 1955 Jan;1(1):1-12
pubmed: 14381423
Nat Methods. 2021 Feb;18(2):203-211
pubmed: 33288961
J Mol Biol. 1990 Jun 20;213(4):899-929
pubmed: 2359127
Nat Rev Mol Cell Biol. 2017 Nov;18(11):685-701
pubmed: 28875992
Nat Biotechnol. 2022 Apr;40(4):555-565
pubmed: 34795433
Nat Methods. 2023 Feb;20(2):284-294
pubmed: 36690741
PLoS Comput Biol. 2020 Apr 13;16(4):e1007673
pubmed: 32282792
Nat Methods. 2021 Oct;18(10):1192-1195
pubmed: 34594030
Science. 2012 Oct 26;338(6106):524-8
pubmed: 23112332
Sci Rep. 2019 May 22;9(1):7721
pubmed: 31118500
Histochem Cell Biol. 2019 Feb;151(2):101-114
pubmed: 30488339
Int J Biochem Cell Biol. 2018 Aug;101:74-79
pubmed: 29852248
Nat Biotechnol. 2021 Mar;39(3):313-319
pubmed: 33288904
Nat Methods. 2021 Jan;18(1):100-106
pubmed: 33318659
Nat Methods. 2017 Dec;14(12):1141-1152
pubmed: 29083403
Nat Commun. 2021 Apr 15;12(1):2276
pubmed: 33859193
Science. 2009 Nov 27;326(5957):1208-12
pubmed: 19965462
Viruses. 2021 Aug 09;13(8):
pubmed: 34452433
Science. 2018 Aug 3;361(6401):
pubmed: 30072512
Adv Virus Res. 1960;7:225-325
pubmed: 13756988
Nat Hum Behav. 2022 Sep;6(9):1257-1267
pubmed: 35817932
J Struct Biol. 2005 Aug;151(2):182-95
pubmed: 16043363
Elife. 2018 Dec 13;7:
pubmed: 30543181
Cell Host Microbe. 2013 Oct 16;14(4):468-80
pubmed: 24139403
Methods Mol Biol. 2018;1836:609-631
pubmed: 30151595
Nat Methods. 2022 Oct;19(10):1262-1267
pubmed: 36076039
J Struct Biol. 1996 Jan-Feb;116(1):190-9
pubmed: 8742743
Nat Methods. 2018 Apr;15(4):263-266
pubmed: 29457791
Nat Methods. 2021 Jan;18(1):43-45
pubmed: 33398191
Viruses. 2018 Apr 18;10(4):
pubmed: 29670029
J Med Virol. 2021 Feb;93(2):820-830
pubmed: 32691881
Nat Cell Biol. 2019 Jan;21(1):72-84
pubmed: 30602772
Cell. 1978 Jul;14(3):695-711
pubmed: 688389
Nat Methods. 2021 Sep;18(9):1082-1090
pubmed: 34480155
Curr Opin Virol. 2021 Jun;48:49-56
pubmed: 33892224
Science. 2006 Sep 15;313(5793):1642-5
pubmed: 16902090
Nat Commun. 2022 Dec 5;13(1):7492
pubmed: 36470883
Nature. 2019 Apr;568(7751):235-239
pubmed: 30911168
J Clin Immunol. 2022 Oct;42(7):1473-1507
pubmed: 35748970
Nat Methods. 2019 Jan;16(1):67-70
pubmed: 30559429
Cell Microbiol. 2021 Feb;23(2):e13280
pubmed: 33073426
Curr Opin Virol. 2011 Aug;1(2):118-24
pubmed: 22440622
Cell Host Microbe. 2018 Sep 12;24(3):417-428.e5
pubmed: 30146390
Immunity. 2022 Jun 14;55(6):1118-1134.e8
pubmed: 35447093
Molecules. 2019 Jan 29;24(3):
pubmed: 30700005
Chem Rev. 2020 Feb 12;120(3):1936-1979
pubmed: 31951121
Nat Methods. 2022 Jul;19(7):829-832
pubmed: 35654950
Bioinformatics. 2017 Aug 01;33(15):2424-2426
pubmed: 28369169
J Exp Med. 1960 Aug 1;112:373-82
pubmed: 13772565
Nat Commun. 2016 Aug 12;7:12471
pubmed: 27514992
Comput Methods Programs Biomed. 2019 Sep;178:31-39
pubmed: 31416558
J Virol. 2012 Sep;86(18):10123-37
pubmed: 22787215
Nat Methods. 2017 Oct;14(10):983-985
pubmed: 28846087
Nat Methods. 2008 Aug;5(8):695-702
pubmed: 18641657
Nature. 2020 Nov;587(7832):109-114
pubmed: 32908309
Genome Biol. 2006;7(10):R100
pubmed: 17076895