archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems

Benjamin Delory; Mao Li; Christopher Topp; Guillaume Lobet

doi:10.12688/f1000research.13541.1

archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems

Benjamin Delory
, Mao Li
, Christopher Topp
, Guillaume Lobet

Institute of Ecology

Research output: Journal contributions › Journal articles › Research › peer-review

22 Citations (Scopus)

Abstract

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.

Original language	English
Article number	22
Journal	Faculty of 1000 Research
Volume	7
Issue number	22
Number of pages	14
ISSN	2046-1402
DOIs	https://doi.org/10.12688/f1000research.13541.1
Publication status	Published - 08.01.2018

Bibliographical note

Publisher Copyright:
© 2018 Delory BM et al.

Research areas and keywords

Ecosystems Research
archiDart
plant root systems
topology
persistent homology
Fitter indices
Data Analysis of Root Tracings (DART)
Root System Markup Language (RSML)

ASJC Scopus Subject Areas

Medicine(all)
Immunology and Microbiology(all)
Pharmacology, Toxicology and Pharmaceutics(all)
Social Sciences (miscellaneous)
Library and Information Sciences
Biochemistry, Genetics and Molecular Biology(all)
Arts and Humanities (miscellaneous)

Access to Document

10.12688/f1000research.13541.1Licence: CC BY

VolltextFinal published version, 2.43 MBLicence: CC BY

archiDART 3.0
Delory, B. M. (Contributor), Li, M. (Contributor), Topp, C. N. (Contributor) & Lobet, G. (Contributor), ZENODO, 18.12.2017
DOI: 10.5281/zenodo.1117864, https://zenodo.org/record/1117864
Dataset
Data and R codes used in Delory et al (2017) F1000Research
Delory, B. M. (Contributor), Li, M. (Contributor), Topp, C. N. (Contributor) & Lobet, G. (Contributor), ZENODO, 18.12.2017
DOI: 10.5281/zenodo.1117824, https://zenodo.org/record/1117836
Dataset

Cite this

@article{5953ffa1a9104c7cbe9f9585b2327971,

title = "archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems",

abstract = "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. ",

keywords = "Ecosystems Research, archiDart, plant root systems, topology, persistent homology, Fitter indices, Data Analysis of Root Tracings (DART), Root System Markup Language (RSML)",

author = "Benjamin Delory and Mao Li and Christopher Topp and Guillaume Lobet",

note = "Publisher Copyright: {\textcopyright} 2018 Delory BM et al.",

year = "2018",

month = jan,

day = "8",

doi = "10.12688/f1000research.13541.1",

language = "English",

volume = "7",

journal = "Faculty of 1000 Research",

issn = "2046-1402",

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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

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 - https://www.scopus.com/pages/publications/85041458110

U2 - 10.12688/f1000research.13541.1

DO - 10.12688/f1000research.13541.1

M3 - Journal articles

C2 - 29636899

SN - 2046-1402

VL - 7

JO - Faculty of 1000 Research

JF - Faculty of 1000 Research

IS - 22

M1 - 22

ER -

archiDART v3.0: A new data analysis pipeline allowing the topological analysis of plant root systems

Abstract

Bibliographical note

Research areas and keywords

ASJC Scopus Subject Areas

Access to Document

Fingerprint

Datasets

archiDART 3.0

Data and R codes used in Delory et al (2017) F1000Research

Cite this