LAMINA: a tool for rapid quantification of leaf size and shape parameters

Bylesjö, Max; Segura, Vincent; Soolanayakanahally, Raju; Rae, Anne M.; Trygg, Johan; Gustafsson, Petter; Jansson, Stefan; Street, Nathaniel R.

doi:10.1186/1471-2229-8-82

Cited by 188 publications

(157 citation statements)

References 26 publications

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“…These were batch processed using LAMINA software [12]. LAMINA is Leaf Shape Determination software [12]. It can handle batch processing, which makes it particularly worthwhile.…”

Section: Methodsmentioning

confidence: 99%

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Fluctuating Asymmetry of Plant Leaves: Batch Processing with LAMINA and Continuous Symmetry Measures

et al. 2015

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Unlike landmark methods for estimating object asymmetry, continuous symmetry measures (CSM) can be used to measure the symmetry distance (ds) of inconsistent objects, such as plant leaves. Inconsistent objects have no homologous landmarks, no consistent topology, no quantitative consistency, and sometimes no matching points. When CSM is used in conjugation with LAMINA Leaf Shape Determination software, one can quickly and efficiently process a large number of scanned leaves. LAMINA automatically generates equally-spaced points around the perimeter of each leaf and the resulting x-y coordinates are normalized to average centroid size prior to estimating ds using a fold, average, unfold algorithm. We estimated shape asymmetry of leaves of three species of flowering plants: Ligustrum sinense (Chinese Privet), Rubus cuneifolius (blackberry), and Perilla frutescens (Perilla), as well as individual leaves from a few species of oaks (Quercus) and maples (Acer). We found that 100 to 200 equally-spaced points worked well for all three of the main species. Measurement error accounted for a small proportion of the asymmetry variation. Nevertheless, measurement error was great enough to generate some negative size scaling after normalization to average centroid size. OPEN ACCESSSymmetry 2015, 7 256

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“…These were batch processed using LAMINA software [12]. LAMINA is Leaf Shape Determination software [12]. It can handle batch processing, which makes it particularly worthwhile.…”

Section: Methodsmentioning

confidence: 99%

“…The leaves were arranged on the scanner such that the apices of all the leaves were oriented in the same direction and pointing towards the top of the image ( Figure 2). These were batch processed using LAMINA software [12]. LAMINA is Leaf Shape Determination software [12].…”

Section: Methodsmentioning

confidence: 99%

Fluctuating Asymmetry of Plant Leaves: Batch Processing with LAMINA and Continuous Symmetry Measures

et al. 2015

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“…Despite the economic and scientific importance of this genus, the identification of different Populus species and hybrids can be problematic due to intraspecific morphological plasticity (e.g., Bylesjö et al 2008) and frequent natural hybridization between species, particularly among members of the sections Aigeiros Duby and Tacamahaca Spach. (Eckenwalder 1984;Floate 2004;Mahama et al 2011).…”

Section: Introductionmentioning

confidence: 99%

A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids

Isabel

Lamothe

Thompson

2012

Tree Genetics & Genomes

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Rapid identification of Populus L. species and hybrids can be achieved with relatively little effort through the use of primer extension-based single nucleotide polymorphism (SNP) genotyping assays. We present an optimized set of 36 SNP markers from 28 gene regions that diagnose eight poplar species (Populus angustifolia James, Populus balsamifera L., Populus deltoides Bartram, Populus fremontii Watson, Populus laurifolia Ledeb., Populus maximowiczii Henry, Populus nigra L., and Populus trichocarpa Torr. & Gray). A total of 700 DNA sequences from six Populus species (1-15 individuals per species) were used to construct the array. A set of flanking and probe oligonucleotides was developed and tested. The accuracy of the SNP assay was validated by genotyping 448 putatively "pure" individuals from 14 species of Populus. Overall, the SNP assay had a high success rate (97.6 %) and will prove useful for the identification of all Aigeiros Duby and Tacamahaca Spach. species and their early-generation hybrids within natural populations and breeding programs.Null alleles and intraspecific polymorphisms were detected for a few locus/species combinations in the Aigeiros and Tacamahaca sections. When we attempted to genotype aspens of the section Populus (Populus alba L., Populus grandidentata Michx., Populus tremula L., and Populus tremuloides Michx.), the success rate of the SNP array decreased by 13 %, demonstrating moderate crosssectional transferability.

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“…al. [16] suggested LAMINA as a tool for rapid quantification of leaf size and shape parameters. This tool used blade dimensions and area to study leaf shape and leaf serration traits.…”

Section: Introductionmentioning

confidence: 99%

A Novel Shape based Descriptor for Plant Identification

Asrani¹,

Jain²

2014

IJCA

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Content based image retrieval is one of the most challenging field in which widespread research is been carried out. In this paper, a modified and effective shape based leaf image retrieval system is presented for leaf identification. The method proposed is an extension of centroid distance method. The major drawbacks of the centroid distance approach are identified and resolved in our proposed approach. This approach, called Quad Centroid Distance Variation (QCDV) uses the concept of shape based image retrieval approach. Four values are computed and used as the feature vectors. The proposed approach effectively manages the size of the feature vectors, is computationally simple and affine invariant. Experiments were conducted on Swedish Leaf Image Database (SLID). The results justify the superior performance of the method even though the feature vector representing the image is very small.

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LAMINA: a tool for rapid quantification of leaf size and shape parameters

Cited by 188 publications

References 26 publications

Fluctuating Asymmetry of Plant Leaves: Batch Processing with LAMINA and Continuous Symmetry Measures

Fluctuating Asymmetry of Plant Leaves: Batch Processing with LAMINA and Continuous Symmetry Measures

A second-generation diagnostic single nucleotide polymorphism (SNP)-based assay, optimized to distinguish among eight poplar (Populus L.) species and their early hybrids

A Novel Shape based Descriptor for Plant Identification

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