Using positional information to provide context for biological image analysis with MorphoGraphX 2.0.
A. thaliana
convolutional neural networks
developmental biology
morphogenesis
plant biology
positional information
quantification
segmentation
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
05 05 2022
05 05 2022
Historique:
received:
12
08
2021
accepted:
03
05
2022
pubmed:
6
5
2022
medline:
7
6
2022
entrez:
5
5
2022
Statut:
epublish
Résumé
Positional information is a central concept in developmental biology. In developing organs, positional information can be idealized as a local coordinate system that arises from morphogen gradients controlled by organizers at key locations. This offers a plausible mechanism for the integration of the molecular networks operating in individual cells into the spatially coordinated multicellular responses necessary for the organization of emergent forms. Understanding how positional cues guide morphogenesis requires the quantification of gene expression and growth dynamics in the context of their underlying coordinate systems. Here, we present recent advances in the MorphoGraphX software (Barbier de Reuille et al., 2015) that implement a generalized framework to annotate developing organs with local coordinate systems. These coordinate systems introduce an organ-centric spatial context to microscopy data, allowing gene expression and growth to be quantified and compared in the context of the positional information thought to control them.
Identifiants
pubmed: 35510843
doi: 10.7554/eLife.72601
pii: 72601
pmc: PMC9159754
doi:
pii:
Banques de données
Dryad
['10.5061/dryad.m905qfv1r']
Types de publication
Journal Article
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/S002804/1
Pays : United Kingdom
Organisme : Biotechnology and Biological Sciences Research Council
ID : BB/P013511/1
Pays : United Kingdom
Informations de copyright
© 2022, Strauss et al.
Déclaration de conflit d'intérêts
SS, AR, BL, DE, NB, NT, AR, SY, SR, AV, RT, MM, EE, CL, HB, MA, KS, GB, DK, JS, MT, RS No competing interests declared
Références
Plant Physiol. 2004 Dec;136(4):3905-19
pubmed: 15557102
Proc Natl Acad Sci U S A. 2006 Jan 31;103(5):1301-6
pubmed: 16432192
Elife. 2014 Feb 11;3:e01567
pubmed: 24520159
Nat Plants. 2020 Jun;6(6):686-698
pubmed: 32451448
Plant Cell. 2012 Aug;24(8):3186-92
pubmed: 22923673
Curr Biol. 2016 Apr 12;:
pubmed: 27151660
Nat Methods. 2015 Mar;12(3):207-10, 2 p following 210
pubmed: 25643149
Methods Mol Biol. 2017;1497:99-123
pubmed: 27864762
Cell. 2019 May 2;177(4):957-969.e13
pubmed: 31051107
Plant Cell. 2005 Feb;17(2):525-36
pubmed: 15659621
Plant Physiol. 2022 Feb 4;188(2):769-781
pubmed: 34618064
Plant Methods. 2019 Apr 4;15:33
pubmed: 30988692
Cold Spring Harb Perspect Biol. 2017 Jul 5;9(7):
pubmed: 28246181
Elife. 2020 Jul 29;9:
pubmed: 32723478
J Theor Biol. 1969 Oct;25(1):1-47
pubmed: 4390734
Plant Cell. 2015 Apr;27(4):1018-33
pubmed: 25901089
Nature. 1995 Nov 2;378(6552):62-5
pubmed: 7477287
Elife. 2018 Feb 27;7:
pubmed: 29482719
Proc Natl Acad Sci U S A. 2016 Jul 26;113(30):E4294-303
pubmed: 27436908
Plant J. 2014 Mar;77(5):806-14
pubmed: 24417645
Elife. 2017 Jul 06;6:
pubmed: 28682235
Curr Biol. 2021 Nov 22;31(22):4946-4955.e4
pubmed: 34610273
Proc Natl Acad Sci U S A. 2019 Dec 10;116(50):25333-25342
pubmed: 31757847
Plant Physiol. 2022 Jun 27;189(3):1278-1295
pubmed: 35348744
Elife. 2021 Jan 06;10:
pubmed: 33404501
Nat Protoc. 2014 Feb;9(2):457-63
pubmed: 24481272
Nature. 2003 Nov 20;426(6964):255-60
pubmed: 14628043
Nat Methods. 2019 Dec;16(12):1226-1232
pubmed: 31570887
Nat Genet. 2008 Sep;40(9):1136-41
pubmed: 19165928
Proc Natl Acad Sci U S A. 2011 Apr 12;108(15):6294-9
pubmed: 21383128
Cell Syst. 2019 Jan 23;8(1):53-65.e3
pubmed: 30660611
Nature. 2018 Mar 22;555(7697):529-533
pubmed: 29539635
PLoS One. 2014 Feb 27;9(2):e90036
pubmed: 24587204
Development. 2012 Sep;139(17):3221-31
pubmed: 22833127
Cell. 2019 May 30;177(6):1405-1418.e17
pubmed: 31130379
Nat Methods. 2012 Jun 28;9(7):676-82
pubmed: 22743772
Cell. 2003 Nov 26;115(5):591-602
pubmed: 14651850
PLoS Biol. 2010 Nov 09;8(11):e1000537
pubmed: 21085690
Curr Biol. 2018 Mar 5;28(5):666-675.e5
pubmed: 29456142
Dev Cell. 2016 Jan 25;36(2):225-40
pubmed: 26812020
Open Biol. 2019 May 31;9(5):190057
pubmed: 31138099
Curr Biol. 2020 Dec 21;30(24):4857-4868.e6
pubmed: 33035489
Curr Biol. 2016 Feb 22;26(4):439-49
pubmed: 26832441
Science. 2014 Feb 14;343(6172):780-3
pubmed: 24531971
Science. 2012 Mar 2;335(6072):1096-9
pubmed: 22383847
Methods Mol Biol. 2019;1992:269-290
pubmed: 31148045
Nat Plants. 2021 Nov;7(11):1475-1484
pubmed: 34782771
Bioinformatics. 2016 Jan 15;32(2):315-7
pubmed: 26415725
Dev Cell. 2016 Jul 11;38(1):15-32
pubmed: 27404356
Elife. 2015 May 06;4:05864
pubmed: 25946108
Dev Cell. 2014 Apr 14;29(1):75-87
pubmed: 24684831
J Cell Biol. 2010 May 31;189(5):777-82
pubmed: 20513764
Development. 2016 Sep 15;143(18):3394-406
pubmed: 27624834
Nat Methods. 2010 Jul;7(7):547-53
pubmed: 20543845
Proc Natl Acad Sci U S A. 2016 Dec 20;113(51):E8238-E8246
pubmed: 27930326
Science. 2020 Jan 3;367(6473):91-96
pubmed: 31753850
Plant Cell. 2015 Sep;27(9):2484-500
pubmed: 26296967
Arabidopsis Book. 2002;1:e0101
pubmed: 22303222
Science. 2012 Mar 2;335(6072):1092-6
pubmed: 22383846
Curr Biol. 2017 Mar 20;27(6):877-883
pubmed: 28285992
Am J Bot. 2018 Feb;105(2):257-265
pubmed: 29578288
Development. 2017 Dec 1;144(23):4398-4405
pubmed: 29183944
Proc Natl Acad Sci U S A. 2016 Jan 12;113(2):452-7
pubmed: 26715743
Methods Mol Biol. 2017;1544:103-125
pubmed: 28050833
Curr Biol. 2022 May 9;32(9):1974-1985.e3
pubmed: 35354067