title: phenoVein-A Tool for Leaf Vein Segmentation and Analysis.
abstract: Precise measurements of leaf vein traits are an important aspect of plant phenotyping for ecological and genetic research. Here, we present a powerful and user-friendly image analysis tool named phenoVein. It is dedicated to automated segmenting and analyzing of leaf veins in images acquired with different imaging modalities (microscope, macrophotography, etc.), including options for comfortable manual correction. Advanced image filtering emphasizes veins from the background and compensates for local brightness inhomogeneities. The most important traits being calculated are total vein length, vein density, piecewise vein lengths and widths, areole area, and skeleton graph statistics, like the number of branching or ending points. For the determination of vein widths, a model-based vein edge estimation approach has been implemented. Validation was performed for the measurement of vein length, vein width, and vein density of Arabidopsis (Arabidopsis thaliana), proving the reliability of phenoVein. We demonstrate the power of phenoVein on a set of previously described vein structure mutants of Arabidopsis (hemivenata, ondulata3, and asymmetric leaves2-101) compared with wild-type accessions Columbia-0 and Landsberg erecta-0. phenoVein is freely available as open-source software.
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.) j.buehler@fz-juelich.de.
authors.forename: Jonas
authors.identifier: http://orcid.org/0000-0002-4463-2291
authors.initials: J
authors.lastname: Bühler
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Louai
authors.identifier: http://orcid.org/0000-0001-8819-3457
authors.initials: L
authors.lastname: Rishmawi
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Daniel
authors.initials: D
authors.lastname: Pflugfelder
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Gregor
authors.initials: G
authors.lastname: Huber
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Hanno
authors.initials: H
authors.lastname: Scharr
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Martin
authors.initials: M
authors.lastname: Hülskamp
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Maarten
authors.initials: M
authors.lastname: Koornneef
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Ulrich
authors.identifier: http://orcid.org/0000-0003-0369-8777
authors.initials: U
authors.lastname: Schurr
authors.affiliation: Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, 52425 Juelich, Germany (J.B., D.P., G.H., H.S., U.S., S.J.);Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), University of Cologne, Cologne Biocenter, 50674 Cologne, Germany (L.R., M.H); andMax Planck Institute for Plant Breeding Research, Cluster of Excellence on Plant Sciences (CEPLAS), 50829 Cologne, Germany (L.R., M.K.).
authors.forename: Siegfried
authors.initials: S
authors.lastname: Jahnke
mesh_terms: D017360:Arabidopsis / Q000033:anatomy & histology*; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D010641:Phenotype; D018515:Plant Leaves / Q000033:anatomy & histology; D058526:Plant Vascular Bundle / Q000033:anatomy & histology*; D015203:Reproducibility of Results; D012984:Software