Quantitation of ER Morphology and Dynamics

• Published in: Methods in molecular biology (Clifton, N.J.) Vol. 2772; p. 49
• Main Authors: Fricker, Mark, Breeze, Emily, Pain, Charlotte, Kriechbaumer, Verena, Aguilar, Carlos, Ugalde, José M, Meyer, Andreas J
• Format: Journal Article
• Language: English
• Published: United States 2024
• Subjects: Benchmarking; Cell Membrane; Endoplasmic Reticulum; Food; Plant Cells; Endoplasmic reticulum morphology; Lunapark; Phase congruency; Network analysis; Persistency analysis; Reticulon; Endoplasmic reticulum dynamics; ER cisternae; Quantitative confocal imaging
• ISSN: 1940-6029
• DOI: 10.1007/978-1-0716-3710-4_5

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 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. ER dynamics can be determined using optical flow techniques from computer vision or persistency analysis. 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.