title: Open source software for quantification of cell migration, protrusions, and fluorescence intensities.
abstract: Cell migration is frequently accompanied by changes in cell morphology (morphodynamics) on a range of spatial and temporal scales. Despite recent advances in imaging techniques, the application of unbiased computational image analysis methods for morphodynamic quantification is rare. For example, manual analysis using kymographs is still commonplace, often caused by lack of access to user-friendly, automated tools. We now describe software designed for the automated quantification of cell migration and morphodynamics. Implemented as a plug-in for the open-source platform, ImageJ, ADAPT is capable of rapid, automated analysis of migration and membrane protrusions, together with associated fluorescently labeled proteins, across multiple cells. We demonstrate the ability of the software by quantifying variations in cell population migration rates on different extracellular matrices. We also show that ADAPT can detect and morphologically profile filopodia. Finally, we have used ADAPT to compile an unbiased description of a "typical" bleb formed at the plasma membrane and quantify the effect of Arp2/3 complex inhibition on bleb retraction.
authors.affiliation: The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, England, UK.
authors.forename: David J
authors.initials: DJ
authors.lastname: Barry
authors.affiliation: The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, England, UK.
authors.forename: Charlotte H
authors.initials: CH
authors.lastname: Durkin
authors.affiliation: The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, England, UK.
authors.forename: Jasmine V
authors.initials: JV
authors.lastname: Abella
authors.affiliation: The Francis Crick Institute, Lincoln's Inn Fields Laboratories, London WC2A 3LY, England, UK michael.way@crick.ac.uk.
authors.forename: Michael
authors.initials: M
authors.lastname: Way
mesh_terms: D051376:Actin-Related Protein 2-3 Complex / Q000378:metabolism; D017209:Apoptosis; D002465:Cell Movement; D048430:Cell Shape; D058948:Cell Tracking; D006367:HeLa Cells; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008856:Microscopy, Fluorescence; D011554:Pseudopodia / Q000648:ultrastructure; D059010:Single-Cell Analysis; D012984:Software
chemical_list: D051376:Actin-Related Protein 2-3 Complex
references.citation: Cell Motil Cytoskeleton. 2002 Aug;52(4):221-30
references.pmid: 12112136
references.citation: Dev Cell. 2015 Jan 12;32(1):43-53
references.pmid: 25543282
references.citation: Science. 2003 Dec 5;302(5651):1704-9
references.pmid: 14657486
references.citation: Biophys J. 2005 Jul;89(1):724-33
references.pmid: 15879479
references.citation: J Cell Biol. 2006 May 8;173(3):383-94
references.pmid: 16651381
references.citation: Phys Rev Lett. 2006 Jul 21;97(3):038102
references.pmid: 16907546
references.citation: Traffic. 2006 Oct;7(10):1352-67
references.pmid: 16899087
references.citation: J Cell Biol. 2006 Nov 6;175(3):477-90
references.pmid: 17088428
references.citation: Nat Cell Biol. 2007 Oct;9(10):1110-21
references.pmid: 17909522
references.citation: Cell Host Microbe. 2007 May 17;1(3):213-26
references.pmid: 18005700
references.citation: PLoS Biol. 2007 Nov;5(11):e317
references.pmid: 18044991
references.citation: Biophys J. 2008 Mar 1;94(5):1836-53
references.pmid: 17921219
references.citation: Nat Rev Mol Cell Biol. 2008 Jun;9(6):446-54
references.pmid: 18464790
references.citation: J Cell Biol. 2008 Jun 16;181(6):879-84
references.pmid: 18541702
references.citation: Nat Rev Mol Cell Biol. 2008 Sep;9(9):730-6
references.pmid: 18628785
references.citation: Cell Motil Cytoskeleton. 2009 Mar;66(3):156-65
references.pmid: 19206151
references.citation: Nature. 2009 Aug 20;460(7258):1031-4
references.pmid: 19648907
references.citation: Nature. 2009 Sep 3;461(7260):99-103
references.pmid: 19693013
references.citation: Proc Natl Acad Sci U S A. 2009 Nov 3;106(44):18581-6
references.pmid: 19846787
references.citation: Chem Biol. 2009 Nov 25;16(11):1158-68
references.pmid: 19942139
references.citation: J Biol Chem. 2010 Apr 9;285(15):11607-16
references.pmid: 20139076
references.citation: Cell Adh Migr. 2010 Jan-Mar;4(1):46-55
references.pmid: 19949291
references.citation: Nat Methods. 2010 Sep;7(9):747-54
references.pmid: 20693996
references.citation: Dev Cell. 2012 Mar 13;22(3):530-43
references.pmid: 22421043
references.citation: Curr Biol. 2012 Apr 10;22(7):553-61
references.pmid: 22386315
references.citation: J Cell Biol. 2012 Apr 16;197(2):239-51
references.pmid: 22492726
references.citation: Nat Methods. 2012 Jul;9(7):659-60
references.pmid: 22743769
references.citation: Nat Methods. 2012 Jul;9(7):666-70
references.pmid: 22743771
references.citation: Nat Methods. 2012 Jul;9(7):671-5
references.pmid: 22930834
references.citation: Proc Natl Acad Sci U S A. 2012 Sep 4;109(36):14434-9
references.pmid: 22786929
references.citation: Cell Host Microbe. 2012 Sep 13;12(3):346-59
references.pmid: 22980331
references.citation: Mol Biol Cell. 2012 Dec;23(23):4601-10
references.pmid: 23051739
references.citation: Chem Biol. 2013 May 23;20(5):701-12
references.pmid: 23623350
references.citation: Nat Cell Biol. 2013 Jul;15(7):751-62
references.pmid: 23792690
references.citation: Curr Opin Cell Biol. 2013 Oct;25(5):582-90
references.pmid: 23786923
references.citation: Nature. 2013 Nov 14;503(7475):281-4
references.pmid: 24132237
references.citation: J Cell Biol. 2014 Feb 3;204(3):443-60
references.pmid: 24493591
references.citation: Cytoskeleton (Hoboken). 2013 Nov;70(11):741-54
references.pmid: 24136886
references.citation: Nat Methods. 2014 Mar;11(3):281-9
references.pmid: 24441936
references.citation: J Cell Biol. 2014 Mar 17;204(6):1027-44
references.pmid: 24616222
references.citation: Curr Biol. 2014 Jul 21;24(14):1628-35
references.pmid: 25017211
references.citation: Nat Rev Mol Cell Biol. 2014 Sep;15(9):577-90
references.pmid: 25145849
references.citation: Dev Cell. 2014 Sep 8;30(5):569-84
references.pmid: 25203209
references.citation: Biophys J. 2014 Dec 2;107(11):2652-61
references.pmid: 25468344
references.citation: Dev Cell. 2015 Jan 12;32(1):54-67
references.pmid: 25543281
references.citation: Nat Cell Biol. 2003 Aug;5(8):711-9
references.pmid: 12844144