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.

Plant phenotyping relevance

植物器官の3Dデジタル表現から細胞位置を注釈し、細胞成長や形態特徴を解析する専用ツールを開発しており、表現型取得・抽出手法が研究の中心です。

Code and data availability

The paper deposits its phenotyping datasets (raw cell boundaries, PlantSeg predictions, segmented cells, annotated 3D cell meshes, and csv attribute files) in the BioStudies repository under accession S-BSST734, making the paper-specific 3D plant organ data publicly available.