High-efficiency procedure to characterize, segment, and quantify complex multicellularity in raw micrographs in plants.

Abstract

Background The increasing number of novel approaches for large-scale, multi-dimensional imaging of cells has created an unprecedented opportunity to analyze plant morphogenesis. However, complex image processing, including identifying specific cells and quantitating parameters, and high running cost of some image analysis softwares remains challenging. Therefore, it is essential to develop an efficient method for identifying plant complex multicellularity in raw micrographs in plants. Results Here, we developed a high-efficiency procedure to characterize, segment, and quantify plant multicellularity in various raw images using the open-source software packages ImageJ and SR-Tesseler. This procedure allows for the rapid, accurate, automatic quantification of cell patterns and organization at different scales, from large tissues down to the cellular level. We validated our method using different images captured from Arabidopsis thaliana roots and seeds and Populus tremula stems, including fluorescently labeled images, Micro-CT scans, and dyed sections. Finally, we determined the area, centroid coordinate, perimeter, and Feret's diameter of the cells and harvested the cell distribution patterns from Voronoï diagrams by setting the threshold at localization density, mean distance, or area. Conclusions This procedure can be used to determine the character and organization of multicellular plant tissues at high efficiency, including precise parameter identification and polygon-based segmentation of plant cells.

Plant phenotyping relevance

植物画像から細胞形態・配置を自動抽出する画像解析手法を開発し、複数植物種・画像 modality で検証しており、表現型取得が研究の中心です。

Code and data availability

The paper describes an ImageJ/SR-Tesseler phenotyping workflow with supplementary datasets (Additional files 7–16) containing cell parameters and centroid data, but no public deposit URL or availability statement for these paper-specific datasets or any author code appears in the supplied blocks. All listed URLs are to

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