TY - JOUR
T1 - Automated segmentation of electron tomograms for a quantitative description of actin filament networks
AU - Rigort, Alexander
AU - Günther, David
AU - Hegerl, Reiner
AU - Baum, Daniel
AU - Weber, Britta
AU - Prohaska, Steffen
AU - Medalia, Ohad
AU - Baumeister, Wolfgang
AU - Hege, Hans Christian
N1 - Funding Information:
The research leading to these results has received funding from an inter-institutional research initiative of the Max Planck Society . We thank Dr. Günther Gerisch and Mary Ecke for providing AX2 cells and we gratefully acknowledge Israel Patla for providing data on the stress fiber.
PY - 2012/1/1
Y1 - 2012/1/1
N2 - 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.
AB - 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.
KW - Actin branching
KW - Cryo-electron tomography
KW - Feature extraction
KW - Image processing
KW - Local shape analysis
UR - http://www.scopus.com/inward/record.url?scp=84855838451&partnerID=8YFLogxK
U2 - 10.1016/j.jsb.2011.08.012
DO - 10.1016/j.jsb.2011.08.012
M3 - Article
AN - SCOPUS:84855838451
SN - 1047-8477
VL - 177
SP - 135
EP - 144
JO - Journal of Structural Biology
JF - Journal of Structural Biology
IS - 1
ER -