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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

DOI

10.1007/978-1-4939-7389-7_5

Type

Journal article

Journal

Methods Mol Biol

Publication Date

2018

Volume

1691

Pages

43 - 66

Keywords

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