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


Rigort, Alexander; Günther, David; Hegerl, Reiner; Baum, Daniel; Weber, Britta; Prohaska, Steffen; Medalia, Ohad; Baumeister, Wolfgang; Hege, Hans-Christian (2012). Automated segmentation of electron tomograms for a quantitative description of actin filament networks. Journal of Structural Biology, 177(1):135-144.

Abstract

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.

Abstract

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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Additional indexing

Item Type:Journal Article, refereed, original work
Communities & Collections:04 Faculty of Medicine > Department of Biochemistry
07 Faculty of Science > Department of Biochemistry
Dewey Decimal Classification:570 Life sciences; biology
Language:English
Date:2012
Deposited On:30 Oct 2012 16:03
Last Modified:05 Apr 2016 16:02
Publisher:Elsevier
ISSN:1047-8477
Publisher DOI:https://doi.org/10.1016/j.jsb.2011.08.012
PubMed ID:21907807

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