anTraX, a software package for high-throughput video tracking of color-tagged insects.
ants
collective behavior
ethology
formicidae
machine learning
machine vision
neuroscience
social behavior
social insects
tracking
Journal
eLife
ISSN: 2050-084X
Titre abrégé: Elife
Pays: England
ID NLM: 101579614
Informations de publication
Date de publication:
19 11 2020
19 11 2020
Historique:
received:
22
04
2020
accepted:
29
10
2020
entrez:
19
11
2020
pubmed:
20
11
2020
medline:
19
3
2021
Statut:
epublish
Résumé
Recent years have seen a surge in methods to track and analyze animal behavior. Nevertheless, tracking individuals in closely interacting, group-living organisms remains a challenge. Here, we present anTraX, an algorithm and software package for high-throughput video tracking of color-tagged insects. anTraX combines neural network classification of animals with a novel approach for representing tracking data as a graph, enabling individual tracking even in cases where it is difficult to segment animals from one another, or where tags are obscured. The use of color tags, a well-established and robust method for marking individual insects in groups, relaxes requirements for image size and quality, and makes the software broadly applicable. anTraX is readily integrated into existing tools and methods for automated image analysis of behavior to further augment its output. anTraX can handle large-scale experiments with minimal human involvement, allowing researchers to simultaneously monitor many social groups over long time periods.
Identifiants
pubmed: 33211008
doi: 10.7554/eLife.58145
pii: 58145
pmc: PMC7676868
doi:
pii:
Types de publication
Evaluation Study
Journal Article
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't
Langues
eng
Sous-ensembles de citation
IM
Subventions
Organisme : NIGMS NIH HHS
ID : R35 GM127007
Pays : United States
Organisme : Howard Hughes Medical Institute
Pays : United States
Organisme : Human Frontier Science Program
ID : LT001049/2015
Pays : International
Informations de copyright
© 2020, Gal et al.
Déclaration de conflit d'intérêts
AG, JS, DK No competing interests declared
Références
Science. 2018 Nov 23;362(6417):941-945
pubmed: 30467168
J Exp Biol. 2019 Oct 8;222(Pt 19):
pubmed: 31413102
Phys Biol. 2017 Feb 16;14(1):015006
pubmed: 28140374
Science. 2018 Jul 27;361(6400):398-402
pubmed: 30049879
Cell. 2017 Aug 10;170(4):727-735.e10
pubmed: 28802042
Nat Neurosci. 2018 Sep;21(9):1281-1289
pubmed: 30127430
Proc Natl Acad Sci U S A. 2015 May 26;112(21):6706-11
pubmed: 25953335
Annu Rev Neurosci. 2016 Jul 8;39:217-36
pubmed: 27090952
Elife. 2019 Oct 01;8:
pubmed: 31570119
J Exp Biol. 2012 Aug 1;215(Pt 15):2653-9
pubmed: 22786642
Nat Methods. 2019 Dec;16(12):1233-1246
pubmed: 31133758
Curr Biol. 2018 Jan 8;28(1):R8-R12
pubmed: 29316423
Elife. 2018 Mar 06;7:
pubmed: 29506650
J Exp Biol. 2017 Jan 1;220(Pt 1):73-82
pubmed: 28057830
Nat Commun. 2017 Jun 01;8:15414
pubmed: 28569746
Neuron. 2017 Feb 8;93(3):480-490
pubmed: 28182904
J R Soc Interface. 2014 Oct 6;11(99):
pubmed: 25142523
PLoS Comput Biol. 2020 Oct 6;16(10):e1008230
pubmed: 33021989
Phys Biol. 2017 Feb 06;14(1):015002
pubmed: 28166059
IEEE Trans Pattern Anal Mach Intell. 2005 Nov;27(11):1805-19
pubmed: 16285378
Nat Methods. 2009 Jun;6(6):451-7
pubmed: 19412169
Nat Methods. 2019 Jan;16(1):117-125
pubmed: 30573820
Nat Commun. 2015 Jul 28;6:7729
pubmed: 26218613
Nat Methods. 2019 Feb;16(2):179-182
pubmed: 30643215
Nat Methods. 2014 Jul;11(7):743-8
pubmed: 24880877
Neuron. 2014 Oct 1;84(1):18-31
pubmed: 25277452
Nat Methods. 2009 Apr;6(4):297-303
pubmed: 19270697
Front Physiol. 2012 Nov 27;3:442
pubmed: 23205013
J Exp Biol. 2017 Jan 1;220(Pt 1):25-34
pubmed: 28057825
Trends Ecol Evol. 2014 Jul;29(7):417-28
pubmed: 24908439
Nat Commun. 2014;5:3363
pubmed: 24561920
Adv Genet. 2012;77:59-78
pubmed: 22902126
Nature. 2018 Aug;560(7720):635-638
pubmed: 30135576
Genome Res. 2018 Nov;28(11):1757-1765
pubmed: 30249741
PLoS Biol. 2014 Mar 11;12(3):e1001805
pubmed: 24618695
IEEE Trans Med Imaging. 2017 Feb;36(2):674-683
pubmed: 27845654
Annu Rev Entomol. 2001;46:511-43
pubmed: 11112178
Cold Spring Harb Protoc. 2009 Jul;2009(7):pdb.prot5240
pubmed: 20147205
Cell. 2017 Jul 13;170(2):393-406.e28
pubmed: 28709004
Nature. 2018 Jul;559(7715):564-569
pubmed: 29995860
BMC Biol. 2018 Feb 23;16(1):23
pubmed: 29475451
PLoS One. 2015 Sep 02;10(9):e0136487
pubmed: 26332211
Neuron. 2019 Oct 9;104(1):11-24
pubmed: 31600508
IEEE Trans Pattern Anal Mach Intell. 2017 Dec;39(12):2481-2495
pubmed: 28060704
Science. 2018 Aug 17;361(6403):672-677
pubmed: 30115804
J Exp Biol. 2018 Nov 19;221(Pt 22):
pubmed: 30266788
Biol Lett. 2014 Oct;10(10):20140749
pubmed: 25354920
Proc Biol Sci. 2020 Apr 8;287(1924):20192950
pubmed: 32228408
Nat Methods. 2013 Jan;10(1):64-7
pubmed: 23202433
Science. 2013 May 31;340(6136):1090-3
pubmed: 23599264
Curr Biol. 2014 Feb 17;24(4):451-8
pubmed: 24508170