archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems
Publikation: Beiträge in Zeitschriften › Zeitschriftenaufsätze › Forschung › begutachtet
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archiDART v3.0 : A new data analysis pipeline allowing the topological analysis of plant root systems. / Delory, Benjamin; Li, Mao; Topp, Christopher et al.
in: Faculty of 1000 Research, Jahrgang 7, Nr. 22, 22, 08.01.2018.Publikation: Beiträge in Zeitschriften › Zeitschriftenaufsätze › Forschung › begutachtet
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TY - JOUR
T1 - archiDART v3.0
T2 - A new data analysis pipeline allowing the topological analysis of plant root systems
AU - Delory, Benjamin
AU - Li, Mao
AU - Topp, Christopher
AU - Lobet, Guillaume
N1 - Publisher Copyright: © 2018 Delory BM et al.
PY - 2018/1/8
Y1 - 2018/1/8
N2 - Quantifying plant morphology is a very challenging task that requires methods able to capture the geometry and topology of plant organs at various spatial scales. Recently, the use of persistent homology as a mathematical framework to quantify plant morphology has been successfully demonstrated for leaves, shoots, and root systems. In this paper, we present a new data analysis pipeline implemented in the R package archiDART to analyse root system architectures using persistent homology. In addition, we also show that both geometric and topological descriptors are necessary to accurately compare root systems and assess their natural complexity.
AB - Quantifying plant morphology is a very challenging task that requires methods able to capture the geometry and topology of plant organs at various spatial scales. Recently, the use of persistent homology as a mathematical framework to quantify plant morphology has been successfully demonstrated for leaves, shoots, and root systems. In this paper, we present a new data analysis pipeline implemented in the R package archiDART to analyse root system architectures using persistent homology. In addition, we also show that both geometric and topological descriptors are necessary to accurately compare root systems and assess their natural complexity.
KW - Ecosystems Research
KW - archiDart
KW - plant root systems
KW - topology
KW - persistent homology
KW - Fitter indices
KW - Data Analysis of Root Tracings (DART)
KW - Root System Markup Language (RSML)
UR - http://www.scopus.com/inward/record.url?scp=85041458110&partnerID=8YFLogxK
U2 - 10.12688/f1000research.13541.1
DO - 10.12688/f1000research.13541.1
M3 - Journal articles
C2 - 29636899
VL - 7
JO - F1000Research
JF - F1000Research
SN - 2046-1402
IS - 22
M1 - 22
ER -