Quantification of the 3D Collagen Network Geometry in Confocal
Reflection Microscopy

D 2015

Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy

MAŠKA, Martin, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK et. al.

Basic information

Original name

Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy

Authors

MAŠKA, Martin (203 Czech Republic, guarantor, belonging to the institution), Cristina EDERRA (724 Spain), Javier FERNÁNDEZ-MARQUÉS (724 Spain), Arrate MUÑOZ-BARRUTIA (724 Spain), Michal KOZUBEK (203 Czech Republic, belonging to the institution) and Carlos ORTIZ-DE-SOLÓRZANO (724 Spain)

Edition

Québec City, 22nd IEEE International Conference on Image Processing, p. 1791-1794, 4 pp. 2015

Publisher

IEEE

Other information

Language

English

Type of outcome

Stať ve sborníku

Field of Study

10201 Computer sciences, information science, bioinformatics

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

Publication form

electronic version available online

References:

URL

RIV identification code

RIV/00216224:14330/15:00080822

Organization unit

Faculty of Informatics

ISBN

978-1-4799-8339-1

ISSN

DOI

http://dx.doi.org/10.1109/ICIP.2015.7351109

UT WoS

000371977801182

Keywords in English

collagen network geometry;confocal reflection microscopy;Matrigel;steerable filtering;pore size

Abstract

V originále

The geometry of 3D collagen networks is a key factor that influences the behavior of live cells within extracellular matrices. This paper presents a hybrid, two-step method for fully automatic quantification of the 3D collagen network geometry at fiber resolution in confocal reflection microscopy images. First, a coarse binary mask of the entire network is obtained using steerable filtering and local Otsu thresholding. Second, individual collagen fibers are reconstructed by~tracing maximum ridges in the Euclidean distance map of the binary mask. The proposed method, validated in a novel framework using 3D collagen gels with various collagen and Matrigel concentrations, reveal that Matrigel affects the collagen network geometry by decreasing the network pore size while preserving the fiber length and fiber persistence length.

Links

EE2.3.30.0009, research and development project

Name: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GBP302/12/G157, research and development project

Name: Dynamika a organizace chromosomů během buněčného cyklu a při diferenciaci v normě a patologii

Investor: Czech Science Foundation

Citovat

MAŠKA, Martin, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK and Carlos ORTIZ-DE-SOLÓRZANO. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. Online. In 22nd IEEE International Conference on Image Processing. Québec City: IEEE, 2015, p. 1791-1794. ISBN 978-1-4799-8339-1. Available from: https://dx.doi.org/10.1109/ICIP.2015.7351109.

@inproceedings{1300411,
   author = {Maška, Martin and Ederra, Cristina and FernándezandMarqués, Javier and MuñozandBarrutia, Arrate and Kozubek, Michal and OrtizanddeandSolórzano, Carlos},
   address = {Québec City},
   booktitle = {22nd IEEE International Conference on Image Processing},
   doi = {http://dx.doi.org/10.1109/ICIP.2015.7351109},
   keywords = {collagen network geometry;confocal reflection microscopy;Matrigel;steerable filtering;pore size},
   howpublished = {elektronická verze "online"},
   language = {eng},
   location = {Québec City},
   isbn = {978-1-4799-8339-1},
   pages = {1791-1794},
   publisher = {IEEE},
   title = {Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy},
   url = {http://dx.doi.org/10.1109/ICIP.2015.7351109},
   year = {2015}
}

TY  - JOUR
ID  - 1300411
AU  - Maška, Martin - Ederra, Cristina - Fernández-Marqués, Javier - Muñoz-Barrutia, Arrate - Kozubek, Michal - Ortiz-de-Solórzano, Carlos
PY  - 2015
TI  - Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy
PB  - IEEE
CY  - Québec City
SN  - 9781479983391
KW  - collagen network geometry;confocal reflection microscopy;Matrigel;steerable filtering;pore size
UR  - http://dx.doi.org/10.1109/ICIP.2015.7351109
N2  - The geometry of 3D collagen networks is a key factor that influences the behavior of live cells within extracellular matrices. This paper presents a hybrid, two-step method for fully automatic quantification of the 3D collagen network geometry at fiber resolution in confocal reflection microscopy images. First, a coarse binary mask of the entire network is obtained using steerable filtering and local Otsu thresholding. Second, individual collagen fibers are reconstructed by~tracing maximum ridges in the Euclidean distance map of the binary mask. The proposed method, validated in a novel framework using 3D collagen gels with various collagen and Matrigel concentrations, reveal that Matrigel affects the collagen network geometry by decreasing the network pore size while preserving the fiber length and fiber persistence length.
ER  -

MAŠKA, Martin, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK and Carlos ORTIZ-DE-SOLÓRZANO. Quantification of the 3D Collagen Network Geometry in Confocal Reflection Microscopy. Online. In \textit{22nd IEEE International Conference on Image Processing}. Québec City: IEEE, 2015, p.~1791-1794. ISBN~978-1-4799-8339-1. Available from: https://dx.doi.org/10.1109/ICIP.2015.7351109.

Detailed Information on Publication Record