Extraction and analysis of actin networks based on Open Active Contour models

Ting Xu, Hongsheng Li, Tian Shen, Nikola Ojkic, Dimitrios Vavylonis, Sharon Xiaolei Huang

Research output: Chapter in Book/Report/Conference proceedingConference contribution

16 Citations (Scopus)

Abstract

Network structures formed by actin filaments are present in many kinds of fluorescence microscopy images. In order to quantify the conformations and dynamics of such actin filaments, we propose a fully automated method to extract actin networks from images and analyze network topology. The method handles well intersecting filaments and, to some extent, overlapping filaments. First we automatically initialize a large number of Stretching Open Active Contours (SOACs) from ridge points detected by searching for plus-to-minus sign changes in the gradient map of the image. These initial SOACs then elongate simultaneously along the bright centerlines of filaments by minimizing an energy function. During their evolution, they may merge or stop growing, thus forming a network that represents the topology of the filament ensemble. We further detect junction points in the network and break the SOACs at junctions to obtain "SOAC segments". These segments are then re-grouped using a graph-cut spectral clustering method to represent the configuration of actin filaments. The proposed approach is generally applicable to extracting intersecting curvilinear structures in noisy images. We demonstrate its potential using two kinds of data: (1) actin filaments imaged by Total Internal Reflection Fluorescence Microscopy (TIRFM) in vitro; (2) actin cytoskeleton networks in fission yeast imaged by spinning disk confocal microscopy.

Original languageEnglish (US)
Title of host publication2011 8th IEEE International Symposium on Biomedical Imaging
Subtitle of host publicationFrom Nano to Macro, ISBI'11
Pages1334-1340
Number of pages7
DOIs
StatePublished - Nov 2 2011
Event2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11 - Chicago, IL, United States
Duration: Mar 30 2011Apr 2 2011

Publication series

NameProceedings - International Symposium on Biomedical Imaging
ISSN (Print)1945-7928
ISSN (Electronic)1945-8452

Other

Other2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11
CountryUnited States
CityChicago, IL
Period3/30/114/2/11

Fingerprint

Muscle Stretching Exercises
Actin Cytoskeleton
Stretching
Actins
Fluorescence microscopy
Fluorescence Microscopy
Topology
Confocal microscopy
Yeast
Schizosaccharomyces
Conformations
Confocal Microscopy
Cluster Analysis

All Science Journal Classification (ASJC) codes

  • Biomedical Engineering
  • Radiology Nuclear Medicine and imaging

Cite this

Xu, T., Li, H., Shen, T., Ojkic, N., Vavylonis, D., & Huang, S. X. (2011). Extraction and analysis of actin networks based on Open Active Contour models. In 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11 (pp. 1334-1340). [5872647] (Proceedings - International Symposium on Biomedical Imaging). https://doi.org/10.1109/ISBI.2011.5872647
Xu, Ting ; Li, Hongsheng ; Shen, Tian ; Ojkic, Nikola ; Vavylonis, Dimitrios ; Huang, Sharon Xiaolei. / Extraction and analysis of actin networks based on Open Active Contour models. 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11. 2011. pp. 1334-1340 (Proceedings - International Symposium on Biomedical Imaging).
@inproceedings{be890269c707480d896a262512bae6c0,
title = "Extraction and analysis of actin networks based on Open Active Contour models",
abstract = "Network structures formed by actin filaments are present in many kinds of fluorescence microscopy images. In order to quantify the conformations and dynamics of such actin filaments, we propose a fully automated method to extract actin networks from images and analyze network topology. The method handles well intersecting filaments and, to some extent, overlapping filaments. First we automatically initialize a large number of Stretching Open Active Contours (SOACs) from ridge points detected by searching for plus-to-minus sign changes in the gradient map of the image. These initial SOACs then elongate simultaneously along the bright centerlines of filaments by minimizing an energy function. During their evolution, they may merge or stop growing, thus forming a network that represents the topology of the filament ensemble. We further detect junction points in the network and break the SOACs at junctions to obtain {"}SOAC segments{"}. These segments are then re-grouped using a graph-cut spectral clustering method to represent the configuration of actin filaments. The proposed approach is generally applicable to extracting intersecting curvilinear structures in noisy images. We demonstrate its potential using two kinds of data: (1) actin filaments imaged by Total Internal Reflection Fluorescence Microscopy (TIRFM) in vitro; (2) actin cytoskeleton networks in fission yeast imaged by spinning disk confocal microscopy.",
author = "Ting Xu and Hongsheng Li and Tian Shen and Nikola Ojkic and Dimitrios Vavylonis and Huang, {Sharon Xiaolei}",
year = "2011",
month = "11",
day = "2",
doi = "10.1109/ISBI.2011.5872647",
language = "English (US)",
isbn = "9781424441280",
series = "Proceedings - International Symposium on Biomedical Imaging",
pages = "1334--1340",
booktitle = "2011 8th IEEE International Symposium on Biomedical Imaging",

}

Xu, T, Li, H, Shen, T, Ojkic, N, Vavylonis, D & Huang, SX 2011, Extraction and analysis of actin networks based on Open Active Contour models. in 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11., 5872647, Proceedings - International Symposium on Biomedical Imaging, pp. 1334-1340, 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11, Chicago, IL, United States, 3/30/11. https://doi.org/10.1109/ISBI.2011.5872647

Extraction and analysis of actin networks based on Open Active Contour models. / Xu, Ting; Li, Hongsheng; Shen, Tian; Ojkic, Nikola; Vavylonis, Dimitrios; Huang, Sharon Xiaolei.

2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11. 2011. p. 1334-1340 5872647 (Proceedings - International Symposium on Biomedical Imaging).

Research output: Chapter in Book/Report/Conference proceedingConference contribution

TY - GEN

T1 - Extraction and analysis of actin networks based on Open Active Contour models

AU - Xu, Ting

AU - Li, Hongsheng

AU - Shen, Tian

AU - Ojkic, Nikola

AU - Vavylonis, Dimitrios

AU - Huang, Sharon Xiaolei

PY - 2011/11/2

Y1 - 2011/11/2

N2 - Network structures formed by actin filaments are present in many kinds of fluorescence microscopy images. In order to quantify the conformations and dynamics of such actin filaments, we propose a fully automated method to extract actin networks from images and analyze network topology. The method handles well intersecting filaments and, to some extent, overlapping filaments. First we automatically initialize a large number of Stretching Open Active Contours (SOACs) from ridge points detected by searching for plus-to-minus sign changes in the gradient map of the image. These initial SOACs then elongate simultaneously along the bright centerlines of filaments by minimizing an energy function. During their evolution, they may merge or stop growing, thus forming a network that represents the topology of the filament ensemble. We further detect junction points in the network and break the SOACs at junctions to obtain "SOAC segments". These segments are then re-grouped using a graph-cut spectral clustering method to represent the configuration of actin filaments. The proposed approach is generally applicable to extracting intersecting curvilinear structures in noisy images. We demonstrate its potential using two kinds of data: (1) actin filaments imaged by Total Internal Reflection Fluorescence Microscopy (TIRFM) in vitro; (2) actin cytoskeleton networks in fission yeast imaged by spinning disk confocal microscopy.

AB - Network structures formed by actin filaments are present in many kinds of fluorescence microscopy images. In order to quantify the conformations and dynamics of such actin filaments, we propose a fully automated method to extract actin networks from images and analyze network topology. The method handles well intersecting filaments and, to some extent, overlapping filaments. First we automatically initialize a large number of Stretching Open Active Contours (SOACs) from ridge points detected by searching for plus-to-minus sign changes in the gradient map of the image. These initial SOACs then elongate simultaneously along the bright centerlines of filaments by minimizing an energy function. During their evolution, they may merge or stop growing, thus forming a network that represents the topology of the filament ensemble. We further detect junction points in the network and break the SOACs at junctions to obtain "SOAC segments". These segments are then re-grouped using a graph-cut spectral clustering method to represent the configuration of actin filaments. The proposed approach is generally applicable to extracting intersecting curvilinear structures in noisy images. We demonstrate its potential using two kinds of data: (1) actin filaments imaged by Total Internal Reflection Fluorescence Microscopy (TIRFM) in vitro; (2) actin cytoskeleton networks in fission yeast imaged by spinning disk confocal microscopy.

UR - http://www.scopus.com/inward/record.url?scp=80055038005&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=80055038005&partnerID=8YFLogxK

U2 - 10.1109/ISBI.2011.5872647

DO - 10.1109/ISBI.2011.5872647

M3 - Conference contribution

SN - 9781424441280

T3 - Proceedings - International Symposium on Biomedical Imaging

SP - 1334

EP - 1340

BT - 2011 8th IEEE International Symposium on Biomedical Imaging

ER -

Xu T, Li H, Shen T, Ojkic N, Vavylonis D, Huang SX. Extraction and analysis of actin networks based on Open Active Contour models. In 2011 8th IEEE International Symposium on Biomedical Imaging: From Nano to Macro, ISBI'11. 2011. p. 1334-1340. 5872647. (Proceedings - International Symposium on Biomedical Imaging). https://doi.org/10.1109/ISBI.2011.5872647