Dataset Information

Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies.

ABSTRACT:

Premise of the study

Studies of plant cell and organ outline using shape analysis for taxonomic and morphological research have increased in the past decade. However, there are a limited number of available modern, intuitive, and easy software tools to conduct this work.

Methods

We developed a tool for shape outline extraction using MATLAB accompanied with R scripts to perform elliptic Fourier analysis. To demonstrate the shape tool, we applied the software and scripts for genera and species shape determinations of diatom (single cell) species with x-, y-, and x- + y-shape symmetries.

Results

Using the shape analysis tool, we were able to identify and distinguish different diatom taxa based on forms representing size diminutions associated with population changes.

Discussion

Independent of symmetry, species were successfully distinguished using supervised and unsupervised analyses. We hope that these shape analysis tools will be used to add another metric to plant science studies.

SUBMITTER: Wishkerman A

PROVIDER: S-EPMC6303154 | biostudies-literature | 2018 Dec

REPOSITORIES: biostudies-literature

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Publications

Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies.

Wishkerman Asher A Hamilton Paul B PB

Applications in plant sciences 20181221 12

<h4>Premise of the study</h4>Studies of plant cell and organ outline using shape analysis for taxonomic and morphological research have increased in the past decade. However, there are a limited number of available modern, intuitive, and easy software tools to conduct this work.<h4>Methods</h4>We developed a tool for shape outline extraction using MATLAB accompanied with R scripts to perform elliptic Fourier analysis. To demonstrate the shape tool, we applied the software and scripts for genera ...[more]

PMID: 30598862

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Project description:We present here a newly developed software package named Artifact GeoMorph Toolbox 3-D (AGMT3-D). It is intended to provide archaeologists with a simple and easy-to-use tool for performing 3-D landmarks-based geometric morphometric shape analysis on 3-D digital models of archaeological artifacts. It requires no prior knowledge of programming or proficiency in statistics. AGMT3-D consists of a data-acquisition procedure for automatically positioning 3-D models in space and fitting them with grids of 3-D semi-landmarks. It also provides a number of analytical tools and procedures that allow the processing and statistical analysis of the data, including generalized Procrustes analysis, principal component analysis, a warp tool, automatic calculation of shape variabilities and statistical tests. It provides an output of quantitative, objective and reproducible results in numerical, textual and graphic formats. These can be used to answer archaeologically significant questions relating to morphologies and morphological variabilities in artifact assemblages. Following the presentation of the software and its functions, we apply it to a case study addressing the effects of different types of raw material on the morphologies and morphological variabilities present in an experimentally produced Acheulian handaxe assemblage. The results show that there are statistically significant differences between the mean shapes and shape variabilities of handaxes produced on flint and those produced on basalt. With AGMT3-D, users can analyze artifact assemblages and address questions that are deducible from the morphologies and morphological variabilities of material culture assemblages. These questions can relate to issues of, among others, relative chronology, cultural affinities, tool function and production technology. AGMT3-D is aimed at making 3-D landmarks-based geometric morphometric shape analysis more accessible to archaeologists, in the hope that this method will become a tool commonly used by archaeologists.

Project description:BACKGROUND:Triatoma dimidiata (Reduviidae: Triatominae) is an important vector of Chagas disease in various countries in the Americas. Phylogenetic studies have defined three lineages in Mexico and part of Central America. While there is a marked genetic differentiation, methods for identifying them using morphometric analyses with landmarks have not yet been fully resolutive. Elliptical Fourier descriptors (EFDs), which mathematically describe the shape of any closed two-dimensional contours, could be a potentially useful alternative method. Our objective was to validate the use of EFDs for the identification of three lineages of this species complex. METHOD:A total of 84 dorsal view images of individuals of the three lineages were used. Body contours were described with EFDs using between 5 and 30 harmonics. The number of obtained coefficients was reduced by a principal components analysis and the first axis scores were used as shape variables. A linear discriminant function analysis and an ordination plot of the discriminant analysis were performed using the shape variables. A confusion matrix of the ordination plot of the discriminant analysis was obtained to estimate the classification errors, the first five PC scores were statistically compared, and a neural network were then performed using the shape variables. RESULTS:The first principal component explained 50% of the variability, regardless the number of harmonics used. The results of discriminant analysis get improved by increasing the number of harmonics and components considered. With 25 harmonics and 30 components, the identification of haplogroups was achieved with an overall efficiency greater than 97%. The ordering diagram showed the correct discrimination of haplogroups, with only one error of discrimination corroborated by the confusion matrix. When comparing the first five PC scores, significant differences were found among at least two haplogroups. The 30 multilayer perceptron neural networks were also efficient in identification, reaching 91% efficiency with the validation data. CONCLUSIONS:The use of EFD is a simple and useful method for the identification of the main lineages of Triatoma dimidiata, with high values of correct identification.

Dataset Information

Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies.

Premise of the study

Methods

Results

Discussion

Publications

Shape outline extraction software (DiaOutline) for elliptic Fourier analysis application in morphometric studies.

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