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The annotation and analysis of complex 3D plant organs using 3DCoordX.

ABSTRACT: A fundamental question in biology concerns how molecular and cellular processes become integrated during morphogenesis. In plants, characterization of 3D digital representations of organs at single-cell resolution represents a promising approach to addressing this problem. A major challenge is to provide organ-centric spatial context to cells of an organ. We developed several general rules for the annotation of cell position and embodied them in 3DCoordX, a user-interactive computer toolbox implemented in the open-source software MorphoGraphX. 3DCoordX enables rapid spatial annotation of cells even in highly curved biological shapes. Using 3DCoordX, we analyzed cellular growth patterns in organs of several species. For example, the data indicated the presence of a basal cell proliferation zone in the ovule primordium of Arabidopsis (Arabidopsis thaliana). Proof-of-concept analyses suggested a preferential increase in cell length associated with neck elongation in the archegonium of Marchantia (Marchantia polymorpha) and variations in cell volume linked to central morphogenetic features of a trap of the carnivorous plant Utricularia (Utricularia gibba). Our work demonstrates the broad applicability of the developed strategies as they provide organ-centric spatial context to cellular features in plant organs of diverse shape complexity.

SUBMITTER: Vijayan A

PROVIDER: S-EPMC9237718 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundLaserscanning recently has become a powerful and common method for plant parameterization and plant growth observation on nearly every scale range. However, 3D measurements with high accuracy, spatial resolution and speed result in a multitude of points that require processing and analysis. The primary objective of this research has been to establish a reliable and fast technique for high throughput phenotyping using differentiation, segmentation and classification of single plants by a fully automated system. In this report, we introduce a technique for automated classification of point clouds of plants and present the applicability for plant parameterization.ResultsA surface feature histogram based approach from the field of robotics was adapted to close-up laserscans of plants. Local geometric point features describe class characteristics, which were used to distinguish among different plant organs. This approach has been proven and tested on several plant species. Grapevine stems and leaves were classified with an accuracy of up to 98%. The proposed method was successfully transferred to 3D-laserscans of wheat plants for yield estimation. Wheat ears were separated with an accuracy of 96% from other plant organs. Subsequently, the ear volume was calculated and correlated to the ear weight, the kernel weights and the number of kernels. Furthermore the impact of the data resolution was evaluated considering point to point distances between 0.3 and 4.0 mm with respect to the classification accuracy.ConclusionWe introduced an approach using surface feature histograms for automated plant organ parameterization. Highly reliable classification results of about 96% for the separation of grapevine and wheat organs have been obtained. This approach was found to be independent of the point to point distance and applicable to multiple plant species. Its reliability, flexibility and its high order of automation make this method well suited for the demands of high throughput phenotyping.Highlights• Automatic classification of plant organs using geometrical surface information• Transfer of analysis methods for low resolution point clouds to close-up laser measurements of plants• Analysis of 3D-data requirements for automated plant organ classification.

Project description:Macromolecular visualization as well as automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards the understanding of molecular systems and processes. For example, three dimensional (3D) models help in exploring protein active sites and functional hot spots that can be targeted in drug design. Automated annotation and visualization pipelines can also reveal other functionally important attributes of macromolecules. These goals are dependent on the availability of advanced tools that integrate better the existing databases, annotation servers and other resources with state-of-the-art rendering programs.We present a new tool for protein structure analysis, with the focus on annotation and visualization of protein complexes, which is an extension of our previously developed POLYVIEW web server. By integrating the web technology with state-of-the-art software for macromolecular visualization, such as the PyMol program, POLYVIEW-3D enables combining versatile structural and functional annotations with a simple web-based interface for creating publication quality structure rendering, as well as animated images for Powerpoint, web sites and other electronic resources. The service is platform independent and no plug-ins are required. Several examples of how POLYVIEW-3D can be used for structural and functional analysis in the context of protein-protein interactions are presented to illustrate the available annotation options.POLYVIEW-3D server features the PyMol image rendering that provides detailed and high quality presentation of macromolecular structures, with an easy to use web-based interface. POLYVIEW-3D also provides a wide array of options for automated structural and functional analysis of proteins and their complexes. Thus, the POLYVIEW-3D server may become an important resource for researches and educators in the fields of protein science and structural bioinformatics. The new server is available at http://polyview.cchmc.org/polyview3d.html.

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The annotation and analysis of complex 3D plant organs using 3DCoordX.

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