Segmentation and tracking of cytoskeletal filaments using open active contours

Matthew B. Smith, Hongsheng Li, Tian Shen, Xiaolei Huang, Eddy Yusuf, Dimitrios Vavylonis

Research output: Contribution to journalArticlepeer-review

137 Scopus citations


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.

Original languageEnglish (US)
Pages (from-to)693-705
Number of pages13
Issue number11
StatePublished - Nov 2010

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Cell Biology


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