FM-Track: A fiducial marker tracking software for studying cell mechanics in a three-dimensional environment.
Cell mechanics
Fiducial markers
Open-source software
Particle tracking
Traction force microscopy
Journal
SoftwareX
ISSN: 2352-7110
Titre abrégé: SoftwareX
Pays: Netherlands
ID NLM: 101660267
Informations de publication
Date de publication:
Historique:
entrez:
22
7
2021
pubmed:
1
1
2020
medline:
1
1
2020
Statut:
ppublish
Résumé
Tracking the deformation of fiducial markers in the vicinity of living cells embedded in compliant synthetic or biological gels is a powerful means to study cell mechanics and mechanobiology in three-dimensional environments. However, current approaches to track and quantify three-dimensional (3D) fiducial marker displacements remain ad-hoc, can be difficult to implement, and may not produce reliable results. Herein, we present a compact software package entitled "FM-Track," written in the popular Python language, to facilitate feature-based particle tracking tailored for 3D cell micromechanical environment studies. FM-Track contains functions for pre-processing images, running fiducial marker tracking, and post-processing and visualization. FM-Track can thus aid the study of cellular mechanics and mechanobiology by providing an extensible software platform to more reliably extract complex local 3D cell contractile information in transparent compliant gel systems.
Identifiants
pubmed: 34291145
doi: 10.1016/j.softx.2020.100417
pmc: PMC8291167
mid: NIHMS1619196
pii:
doi:
Types de publication
Journal Article
Langues
eng
Subventions
Organisme : NHLBI NIH HHS
ID : R01 HL103723
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL119297
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL129077
Pays : United States
Organisme : NHLBI NIH HHS
ID : R01 HL142504
Pays : United States
Références
Methods. 2017 Feb 15;115:80-90
pubmed: 27713081
Exp Cell Res. 2013 Oct 1;319(16):2396-408
pubmed: 23806281
Nat Methods. 2016 Feb;13(2):171-6
pubmed: 26641311
J Cell Biol. 2014 Apr 14;205(1):83-96
pubmed: 24711500
PeerJ. 2014 Jun 19;2:e453
pubmed: 25024921
J Mol Cell Cardiol. 1987 Dec;19(12):1185-93
pubmed: 3327949
Nat Methods. 2010 Dec;7(12):969-71
pubmed: 21076420
Comput Methods Appl Mech Eng. 2019 Dec 1;357:
pubmed: 32831420
Nat Methods. 2008 Aug;5(8):695-702
pubmed: 18641657
PLoS One. 2012;7(3):e33476
pubmed: 22479403
Rev Sci Instrum. 2016 Feb;87(2):023905
pubmed: 26931864
J Theor Biol. 2017 Apr 7;418:1-7
pubmed: 28119022
Nat Methods. 2014 Mar;11(3):281-9
pubmed: 24441936
Biophys J. 2016 Apr 26;110(8):1845-1857
pubmed: 27119644
Methods Enzymol. 2012;504:183-200
pubmed: 22264535
Nat Cell Biol. 2017 Jul;19(7):742-751
pubmed: 28628082
Meas Sci Technol. 2014 May;25(5):
pubmed: 25530678
Soft Matter. 2017 Mar 15;13(11):2201-2206
pubmed: 28243646
Proc Natl Acad Sci U S A. 2016 Dec 6;113(49):14043-14048
pubmed: 27872289
Soft Matter. 2014 Jun 21;10(23):4047-55
pubmed: 24740485
Sci Rep. 2018 Apr 3;8(1):5581
pubmed: 29615650
Proc Natl Acad Sci U S A. 2003 Feb 18;100(4):1484-9
pubmed: 12552122
Acta Biomater. 2019 Sep 15;96:354-367
pubmed: 31323351
Biophys J. 2001 Oct;81(4):2378-88
pubmed: 11566807
Nat Methods. 2016 Apr 28;13(5):415-23
pubmed: 27123817
Nano Lett. 2019 Jul 10;19(7):4427-4434
pubmed: 31199151
Proc Natl Acad Sci U S A. 2013 Jan 15;110(3):881-6
pubmed: 23277584
Biophys J. 1999 Apr;76(4):2307-16
pubmed: 10096925
Am J Physiol Cell Physiol. 2002 Mar;282(3):C595-605
pubmed: 11832345
Biophys J. 2012 Jul 3;103(1):152-62
pubmed: 22828342
Sci Rep. 2013;3:2462
pubmed: 23955270
J Biomech. 2018 May 17;73:9-17
pubmed: 29622482