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.

Základní údaje

Originální název

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

Autoři

MAŠKA, Martin (203 Česká republika, garant, domácí), Cristina EDERRA (724 Španělsko), Javier FERNÁNDEZ-MARQUÉS (724 Španělsko), Arrate MUÑOZ-BARRUTIA (724 Španělsko), Michal KOZUBEK (203 Česká republika, domácí) a Carlos ORTIZ-DE-SOLÓRZANO (724 Španělsko)

Vydání

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

Nakladatel

IEEE

Další údaje

Jazyk

angličtina

Typ výsledku

Stať ve sborníku

Obor

10201 Computer sciences, information science, bioinformatics

Stát vydavatele

Spojené státy

Utajení

není předmětem státního či obchodního tajemství

Forma vydání

elektronická verze "online"

Odkazy

URL

Kód RIV

RIV/00216224:14330/15:00080822

Organizační jednotka

Fakulta informatiky

ISBN

978-1-4799-8339-1

ISSN

DOI

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

UT WoS

000371977801182

Klíčová slova anglicky

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

Štítky

cbia-web, core_B, firank_A

Příznaky

Mezinárodní význam, Recenzováno

Změněno: 26. 5. 2016 00:26, doc. RNDr. Martin Maška, Ph.D.

Anotace

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.

Návaznosti

EE2.3.30.0009, projekt VaV

Název: Zaměstnáním čerstvých absolventů doktorského studia k vědecké excelenci

GBP302/12/G157, projekt VaV

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

Investor: Grantová agentura ČR, Dynamika a organizace chromosomů během buněčného cyklu a při diferenciaci v normě a patologii

Citovat

MAŠKA, Martin, Cristina EDERRA, Javier FERNÁNDEZ-MARQUÉS, Arrate MUÑOZ-BARRUTIA, Michal KOZUBEK a 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, s. 1791-1794. ISBN 978-1-4799-8339-1. Dostupné z: 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 a 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, s.~1791-1794. ISBN~978-1-4799-8339-1. Dostupné z: https://dx.doi.org/10.1109/ICIP.2015.7351109.

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