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

被引：142

作者：

Rigort, Alexander ^{[1
]}

Guenther, David ^{[1
,2
]}

Hegerl, Reiner ^{[1
]}

Baum, Daniel ^{[2
]}

Weber, Britta ^{[2
]}

Prohaska, Steffen ^{[2
]}

Medalia, Ohad ^{[3
,4
,5
]}

Baumeister, Wolfgang ^{[1
]}

Hege, Hans-Christian ^{[2
]}

机构：

[1] Max Planck Inst Biochem, Dept Biol Struct, D-82152 Martinsried, Germany

[2] ZIB, Dept Visualizat & Data Anal, D-14195 Berlin, Germany

[3] Univ Zurich, Dept Biochem, CH-8057 Zurich, Switzerland

[4] Ben Gurion Univ Negev, Dept Life Sci, IL-82405 Beer Sheva, Israel

[5] Natl Inst Biotechnol, IL-82405 Beer Sheva, Israel

来源：

JOURNAL OF STRUCTURAL BIOLOGY | 2012年 / 177卷 / 01期

关键词：

Local shape analysis; Feature extraction; Cryo-electron tomography; Image processing; Actin branching; CRYOELECTRON TOMOGRAPHY; THERMAL FLUCTUATIONS; ARP2/3; COMPLEX; MICROSCOPY; IDENTIFICATION; LAMELLIPODIA; ALGORITHMS; CELLS; BACK;

D O I：

10.1016/j.jsb.2011.08.012

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

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. (C) 2011 Elsevier Inc. All rights reserved.

引用

页码：135 / 144

页数：10

共 37 条

[1] Rapid automated three-dimensional tracing of neurons from confocal image stacks [J].

Al-Kofahi, KA ;

Lasek, S ;

Szarowski, DH ;

Pace, CJ ;

Nagy, G ;

Turner, JN ;

Roysam, B .

IEEE TRANSACTIONS ON INFORMATION TECHNOLOGY IN BIOMEDICINE, 2002, 6 (02) :171-187

[2]

[Anonymous], THESIS U ILLES BALEA

[3]

[Anonymous], 1990, Introduction to Algorithms

[4] Toward detecting and identifying macromolecules in a cellular context:: Template matching applied to electron tomograms [J].

Böhm, J ;

Frangakis, AS ;

Hegerl, R ;

Nickell, S ;

Typke, D ;

Baumeister, W .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2000, 97 (26) :14245-14250

[5] A review of image denoising algorithms, with a new one [J].

Buades, A ;

Coll, B ;

Morel, JM .

MULTISCALE MODELING & SIMULATION, 2005, 4 (02) :490-530

[6] Identification of novel graded polarity actin filament bundles in locomoting heart fibroblasts: Implications for the generation of motile force [J].

Cramer, LP ;

Siebert, M ;

Mitchison, TJ .

JOURNAL OF CELL BIOLOGY, 1997, 136 (06) :1287-1305

[7] TOWARDS AUTOMATIC ELECTRON TOMOGRAPHY [J].

DIERKSEN, K ;

TYPKE, D ;

HEGERL, R ;

KOSTER, AJ ;

BAUMEISTER, W .

ULTRAMICROSCOPY, 1992, 40 (01) :71-87

[8]

DUBOCHET J, 1981, J MICROSC-OXFORD, V124, pRP3

[9] Macromolecular crowding: an important but neglected aspect of the intracellular environment [J].

Ellis, RJ .

CURRENT OPINION IN STRUCTURAL BIOLOGY, 2001, 11 (01) :114-119

[10] Path-based clustering for grouping of smooth curves and texture segmentation [J].

Fischer, B ;

Buhmann, JM .

IEEE TRANSACTIONS ON PATTERN ANALYSIS AND MACHINE INTELLIGENCE, 2003, 25 (04) :513-518

← 1 2 3 4 →