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The plant endoplasmic reticulum forms a network of tubules connected by three-way junctions or sheet-like cisternae. Although the network is three-dimensional, in many plant cells, it is constrained to a thin volume sandwiched between the vacuole and plasma membrane, effectively restricting it to a 2-D planar network. The structure of the network, and the morphology of the tubules and cisternae can be automatically extracted following intensity-independent edge-enhancement and various segmentation techniques to give an initial pixel-based skeleton, which is then converted to a graph representation. Collectively, this approach yields a wealth of quantitative metrics for ER structure and can be used to describe the effects of pharmacological treatments or genetic manipulation. The software is publicly available.

Original publication




Journal article


Methods Mol Biol

Publication Date





43 - 66


Confocal imaging, ER cisternae, ER tubule morphology, Endoplasmic reticulum, Network analysis, Phase congruency, Reticulon, Endoplasmic Reticulum, Gene Expression, Genes, Reporter, Image Processing, Computer-Assisted, Microscopy, Confocal, Oxidation-Reduction, Plant Cells, Software, Workflow