Abstract
BackgroundMany organisms such as plants can be characterized as complex-shaped branching forms. The morphological quantification of the forms is a support for a number of areas such as the effects of environmental factors and species discrimination. To date, there is no software package suitable for our dataset representing the forms. We therefore formulate methods for extracting morphological measurements from images of the forms.ResultsAs a case study we analyze two-dimensional images of samples from four groups belonging to three species of thalloid liverworts, genus Riccardia. The images are pre-processed and converted into binary images, then skeletonized to obtain a skeleton image, in which features such as junctions and terminals are detected. Morphological measurements known to characterize and discriminate the species in the samples such as junction thickness, branch thickness, terminal thickness, branch length, branch angle, and terminal spacing are then quantified. The measurements are used to distinguish among the four groups of Riccardia and also between the two groups of Riccardia amazonica collected in different locations, Africa and South America. Canonical discriminant analysis results show that those measurements are able to discriminate among the four groups. Additionally, it is able to discriminate R. amazonica collected in Africa from those collected in South America.ConclusionsThis paper presents general automated methods implemented in our software for quantifying two-dimensional images of complex branching forms. The methods are used to compute a series of morphological measurements. We found significant results to distinguish Riccardia species by using the measurements. The methods are also applicable for analyzing other branching organisms. Our software is freely available under the GNU GPL.
Highlights
Many organisms such as plants can be characterized as complex-shaped branching forms
We used a dataset with 138 images from the four taxonomical groups of thalloid liverworts, which consist of 37 samples from R. amazonica collected from Africa, 26 samples of R. amazonica collected from South America, 25 samples of R. compacta collected from Africa, and 50 samples of Riccardia obtusa collected from Africa
From our samples, that R. amazonica from South America and Africa show the significant differences in their morphometric features, and we propose the hypothesis that they could belong to different species
Summary
Many organisms such as plants can be characterized as complex-shaped branching forms. We formulate methods for extracting morphological measurements from images of the forms. There are three well known morphometric approaches for form analysis: traditional, landmark-based, and outline-based. Konglerd et al BMC Res Notes (2017) 10:103 outlines of form structures. Both are more suitable for non-modular organisms, but less applicable for the analysis of indeterminate growth forms of modular organisms, which prefers traditional approach by measuring linear distances (width, length), angles, and ratios. Advances of 3D imaging techniques can theoretically quantify the characters more accurately, for some plant organisms such as liverworts, which are used in our study, their characteristic features are thin and flat; 2D imaging techniques are more suitable than 3D which are complicated in terms of procedures, implementation, and executing time. In case of field work, it is more practical for 2D image acquisition by using a camera or a microscope
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