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Quanfima: An open source Python package for automated fiber analysis of biomaterials

Shkarin, Roman 1,2; Shkarin, Andrei 2; Shkarina, Svetlana 3; Cecilia, Angelica 3; Surmenev, Roman A.; Surmeneva, Maria A.; Weinhardt, Venera 2,3; Baumbach, Tilo 2,3; Mikut, Ralf ORCID iD icon 1
1 Fakultät für Maschinenbau – Institut für Angewandte Informatik/Automatisierungstechnik (AIA), Karlsruher Institut für Technologie (KIT)
2 Laboratorium für Applikationen der Synchrotronstrahlung (LAS), Karlsruher Institut für Technologie (KIT)
3 Institut für Photonenforschung und Synchrotronstrahlung (IPS), Karlsruher Institut für Technologie (KIT)

Abstract:

Hybrid 3D scaffolds composed of different biomaterials with fibrous structure or enriched with different inclusions (i.e., nano- and microparticles) have already demonstrated their positive effect on cell integration and regeneration. The analysis of fibers in hybrid biomaterials, especially in a 3D space is often difficult due to their various diameters (from micro to nanoscale) and compositions. Though biomaterials processing workflows are implemented, there are no software tools for fiber analysis that can be easily integrated into such workflows. Due to the demand for reproducible science with Jupyter notebooks and the broad use of the Python programming language, we have developed the new Python package quanfima offering a complete analysis of hybrid biomaterials, that include the determination of fiber orientation, fiber and/or particle diameter and porosity. Here, we evaluate the provided tensor-based approach on a range of generated datasets under various noise conditions. Also, we show its application to the X-ray tomography datasets of polycaprolactone fibrous scaffolds pure and containing silicate-substituted hydroxyapatite microparticles, hydrogels enriched with bioglass contained strontium and alpha-tricalcium phosphate microparticles for bone tissue engineering and porous cryogel 3D scaffold for pancreatic cell culturing. ... mehr


Verlagsausgabe §
DOI: 10.5445/IR/1000093999
Veröffentlicht am 26.04.2019
Originalveröffentlichung
DOI: 10.1371/journal.pone.0215137
Scopus
Zitationen: 14
Web of Science
Zitationen: 13
Dimensions
Zitationen: 15
Cover der Publikation
Zugehörige Institution(en) am KIT Institut für Automation und angewandte Informatik (IAI)
Institut für Photonenforschung und Synchrotronstrahlung (IPS)
Laboratorium für Applikationen der Synchrotronstrahlung (LAS)
Publikationstyp Zeitschriftenaufsatz
Publikationsjahr 2019
Sprache Englisch
Identifikator ISSN: 1932-6203
KITopen-ID: 1000093999
HGF-Programm 56.03.30 (POF III, LK 01) Soft Matter, Health and Life Sciences
Weitere HGF-Programme 47.01.02 (POF III, LK 01) Biol.Netzwerke u.Synth.Regulat. IAI
Erschienen in PLOS ONE
Verlag Public Library of Science (PLoS)
Band 14
Heft 4
Seiten e0215137
Bemerkung zur Veröffentlichung Gefördert durch den KIT-Publikationsfonds
Vorab online veröffentlicht am 11.04.2019
Nachgewiesen in Scopus
Dimensions
Web of Science
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