Segmentation and tracking of cytoskeletal filaments using open active contours.
We use open active contours to quantify cytoskeletal structures imaged by fluorescence microscopy in two and three dimensions. We developed an interactive software tool for segmentation, tracking, and visualization of individual fibers. Open active contours are parametric curves that deform to minimize the sum of an external energy derived from the image and an internal bending and stretching energy. The external energy generates (i) forces that attract the contour toward the central bright line of a filament in the image, and (ii) forces that stretch the active contour toward the ends of bright ridges. Images of simulated semiflexible polymers with known bending and torsional rigidity are analyzed to validate the method. We apply our methods to quantify the conformations and dynamics of actin in two examples: actin filaments imaged by TIRF microscopy in vitro, and actin cables in fission yeast imaged by spinning disk confocal microscopy.
Smith
Matthew B
MB
Department of Physics, Lehigh University, Bethlehem, Pennsylvania 18015, USA.
Li
Hongsheng
H
Shen
Tian
T
Huang
Xiaolei
X
Yusuf
Eddy
E
Vavylonis
Dimitrios
D
D003599:Cytoskeleton / Q000648:ultrastructure*; D007090:Image Interpretation, Computer-Assisted / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000379:methods*; D008962:Models, Theoretical; D010363:Pattern Recognition, Automated / Q000379:methods; D015203:Reproducibility of Results; D012984:Software
IEEE Trans Med Imaging. 2000 Mar;19(3):203-10
10875704
Proc IEEE Int Symp Biomed Imaging. 2009 Jun 28;2009:1302-1305
20072703
Biophys J. 2008 Dec 15;95(12):6072-80
18835899
Cell. 2003 Dec 12;115(6):705-13
14675535
IEEE Trans Inf Technol Biomed. 2006 Jul;10(3):608-17
16871731
J Cell Sci. 2008 Feb 15;121(Pt 4):496-503
18230647
Proc Natl Acad Sci U S A. 2007 Oct 9;104(41):16128-33
17911265
Biophys J. 2007 Jul 1;93(1):346-59
17416612
Biophys J. 1996 Feb;70(2):609-25
8789080
Med Image Comput Comput Assist Interv. 2009;12(Pt 2):673-81
20426170
J Mol Biol. 2008 Sep 5;381(3):550-8
18617188
Appl Environ Microbiol. 2008 Nov;74(21):6739-45
18791022
J Microsc. 2000 Apr;198(Pt 1):34-53
10781207
Mol Biol Cell. 2009 Jun;20(12):2943-53
19403700
Nat Biotechnol. 2010 Apr;28(4):348-53
20231818
Med Image Comput Comput Assist Interv. 2009;12(Pt 2):59-67
20426096
J Neurosci Methods. 2008 Feb 15;168(1):134-9
17936365
Biophys J. 2001 Jan;80(1):184-94
11159394
J Cell Biol. 2004 Nov 8;167(3):519-30
15534003
Biophys J. 2005 Feb;88(2):1387-402
15556992
J Cell Biol. 1993 Feb;120(4):923-34
8432732
Curr Biol. 2009 Sep 15;19(17):R749-61
19906577
J Microsc. 2008 Dec;232(3):463-75
19094023
J Microsc. 2010 Jul 1;239(1):1-16
20579265
Proc Natl Acad Sci U S A. 2007 May 22;104(21):8827-32
17517656
IEEE Trans Med Imaging. 2001 Dec;20(12):1411-21
11811840
IEEE Trans Image Process. 2001;10(7):1010-9
18249674
J Biol Chem. 1995 May 12;270(19):11437-44
7744781
Neuroinformatics. 2009 Dec;7(4):213-32
20012509
Phys Rev E Stat Nonlin Soft Matter Phys. 2007 May;75(5 Pt 1):050902
17677015
Med Image Comput Comput Assist Interv. 2005;8(Pt 1):246-53
16685852
Curr Biol. 2009 Sep 15;19(17):R812-22
19906583
Biophys J. 2006 May 15;90(10):3762-73
16500961
Methods Cell Biol. 2007;83:237-68
17613311
Science. 2009 Nov 27;326(5957):1208-12
19965462
Biophys J. 2004 Oct;87(4):2723-36
15454464
Phys Rev Lett. 2008 Mar 21;100(11):118104
18517833
Cytometry A. 2004 Apr;58(2):167-76
15057970
Phys Rev Lett. 2010 Jun 11;104(23):238104
20867276
Med Image Anal. 2008 Dec;12(6):689-702
18571462
IEEE Trans Image Process. 1998;7(3):359-69
18276256
J Cell Biol. 2006 May 8;173(3):383-94
16651381
Science. 2008 Jan 4;319(5859):97-100
18079366
PLoS One. 2008;3(12):e4078
19116660
IEEE Trans Med Imaging. 2001 Dec;20(12):1341-51
11811834