3D actin network centerline extraction with multiple active contours

Ting Xu, Dimitrios Vavylonis, Sharon Xiaolei Huang

Research output: Contribution to journalArticle

26 Citations (Scopus)

Abstract

Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and actin cables. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate quantitative, reproducible and objective analysis of the image data, we propose a semi-automated method to extract actin networks and retrieve their topology in 3D. Our method uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then evolve along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. The proposed approach is generally applicable to images of curvilinear networks with low SNR. We demonstrate its potential by extracting the centerlines of synthetic meshwork images, actin networks in 2D Total Internal Reflection Fluorescence Microscopy images, and 3D actin cable meshworks of live fission yeast cells imaged by spinning disk confocal microscopy. Quantitative evaluation of the method using synthetic images shows that for images with SNR above 5.0, the average vertex error measured by the distance between our result and ground truth is 1 voxel, and the average Hausdorff distance is below 10 voxels.

Original languageEnglish (US)
Pages (from-to)272-284
Number of pages13
JournalMedical Image Analysis
Volume18
Issue number2
DOIs
StatePublished - Feb 1 2014

Fingerprint

Fluorescence microscopy
Stretching
Actins
Cables
Muscle Stretching Exercises
Confocal microscopy
Fluorescence Microscopy
Yeast
Cells
Topology
Imaging techniques
Schizosaccharomyces
Fibers
Polymers
Chemical analysis
Actin Cytoskeleton
Confocal Microscopy

All Science Journal Classification (ASJC) codes

  • Radiological and Ultrasound Technology
  • Radiology Nuclear Medicine and imaging
  • Computer Vision and Pattern Recognition
  • Health Informatics
  • Computer Graphics and Computer-Aided Design

Cite this

Xu, Ting ; Vavylonis, Dimitrios ; Huang, Sharon Xiaolei. / 3D actin network centerline extraction with multiple active contours. In: Medical Image Analysis. 2014 ; Vol. 18, No. 2. pp. 272-284.
@article{4581c8245ca34f73a0294871a961e5ec,
title = "3D actin network centerline extraction with multiple active contours",
abstract = "Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and actin cables. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate quantitative, reproducible and objective analysis of the image data, we propose a semi-automated method to extract actin networks and retrieve their topology in 3D. Our method uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then evolve along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. The proposed approach is generally applicable to images of curvilinear networks with low SNR. We demonstrate its potential by extracting the centerlines of synthetic meshwork images, actin networks in 2D Total Internal Reflection Fluorescence Microscopy images, and 3D actin cable meshworks of live fission yeast cells imaged by spinning disk confocal microscopy. Quantitative evaluation of the method using synthetic images shows that for images with SNR above 5.0, the average vertex error measured by the distance between our result and ground truth is 1 voxel, and the average Hausdorff distance is below 10 voxels.",
author = "Ting Xu and Dimitrios Vavylonis and Huang, {Sharon Xiaolei}",
year = "2014",
month = "2",
day = "1",
doi = "10.1016/j.media.2013.10.015",
language = "English (US)",
volume = "18",
pages = "272--284",
journal = "Medical Image Analysis",
issn = "1361-8415",
publisher = "Elsevier",
number = "2",

}

3D actin network centerline extraction with multiple active contours. / Xu, Ting; Vavylonis, Dimitrios; Huang, Sharon Xiaolei.

In: Medical Image Analysis, Vol. 18, No. 2, 01.02.2014, p. 272-284.

Research output: Contribution to journalArticle

TY - JOUR

T1 - 3D actin network centerline extraction with multiple active contours

AU - Xu, Ting

AU - Vavylonis, Dimitrios

AU - Huang, Sharon Xiaolei

PY - 2014/2/1

Y1 - 2014/2/1

N2 - Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and actin cables. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate quantitative, reproducible and objective analysis of the image data, we propose a semi-automated method to extract actin networks and retrieve their topology in 3D. Our method uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then evolve along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. The proposed approach is generally applicable to images of curvilinear networks with low SNR. We demonstrate its potential by extracting the centerlines of synthetic meshwork images, actin networks in 2D Total Internal Reflection Fluorescence Microscopy images, and 3D actin cable meshworks of live fission yeast cells imaged by spinning disk confocal microscopy. Quantitative evaluation of the method using synthetic images shows that for images with SNR above 5.0, the average vertex error measured by the distance between our result and ground truth is 1 voxel, and the average Hausdorff distance is below 10 voxels.

AB - Fluorescence microscopy is frequently used to study two and three dimensional network structures formed by cytoskeletal polymer fibers such as actin filaments and actin cables. While these cytoskeletal structures are often dilute enough to allow imaging of individual filaments or bundles of them, quantitative analysis of these images is challenging. To facilitate quantitative, reproducible and objective analysis of the image data, we propose a semi-automated method to extract actin networks and retrieve their topology in 3D. Our method uses multiple Stretching Open Active Contours (SOACs) that are automatically initialized at image intensity ridges and then evolve along the centerlines of filaments in the network. SOACs can merge, stop at junctions, and reconfigure with others to allow smooth crossing at junctions of filaments. The proposed approach is generally applicable to images of curvilinear networks with low SNR. We demonstrate its potential by extracting the centerlines of synthetic meshwork images, actin networks in 2D Total Internal Reflection Fluorescence Microscopy images, and 3D actin cable meshworks of live fission yeast cells imaged by spinning disk confocal microscopy. Quantitative evaluation of the method using synthetic images shows that for images with SNR above 5.0, the average vertex error measured by the distance between our result and ground truth is 1 voxel, and the average Hausdorff distance is below 10 voxels.

UR - http://www.scopus.com/inward/record.url?scp=84889595686&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84889595686&partnerID=8YFLogxK

U2 - 10.1016/j.media.2013.10.015

DO - 10.1016/j.media.2013.10.015

M3 - Article

C2 - 24316442

AN - SCOPUS:84889595686

VL - 18

SP - 272

EP - 284

JO - Medical Image Analysis

JF - Medical Image Analysis

SN - 1361-8415

IS - 2

ER -