Quantitation of ER Structure and Function

  • Mark FrickerEmail author
  • Luke Heaton
  • Nick Jones
  • Boguslaw Obara
  • Stefanie J. Müller
  • Andreas J. Meyer
Part of the Methods in Molecular Biology book series (MIMB, volume 1691)


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.

Key words

Confocal imaging Endoplasmic reticulum Network analysis Phase congruency Reticulon ER tubule morphology ER cisternae 



Funding is gratefully acknowledged from the DFG in the framework of the priority program SPP1710 (A.M.), The Human Frontier Science Program (RGP0053/2012, M.D.F., L.L.H., N.J.), and the Leverhulme Foundation (RPG-2015-437, M.D.F., L.L.H., N.J.).


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Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  • Mark Fricker
    • 1
    Email author
  • Luke Heaton
    • 1
    • 2
  • Nick Jones
    • 2
  • Boguslaw Obara
    • 3
  • Stefanie J. Müller
    • 4
  • Andreas J. Meyer
    • 4
  1. 1.Department of Plant SciencesUniversity of OxfordOxfordUK
  2. 2.Mathematics DepartmentImperial CollegeLondonUK
  3. 3.School of Engineering and Computing SciencesUniversity of DurhamDurhamUK
  4. 4.INRES-Chemical SignallingUniversität BonnBonnGermany

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