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J Struct Biol. 2012 Jan;177(1):135-44. doi: 10.1016/j.jsb.2011.08.012. Epub 2011 Sep 1.

Automated segmentation of electron tomograms for a quantitative description of actin filament networks.

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Max Planck Institute of Biochemistry, Department of Structural Biology, Am Klopferspitz 18, D-82152 Martinsried, Germany.


Cryo-electron tomography allows to visualize individual actin filaments and to describe the three-dimensional organization of actin networks in the context of unperturbed cellular environments. For a quantitative characterization of actin filament networks, the tomograms must be segmented in a reproducible manner. Here, we describe an automated procedure for the segmentation of actin filaments, which combines template matching with a new tracing algorithm. The result is a set of lines, each one representing the central line of a filament. As demonstrated with cryo-tomograms of cellular actin networks, these line sets can be used to characterize filament networks in terms of filament length, orientation, density, stiffness (persistence length), or the occurrence of branching points.

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