Long-Term Imaging of Endoplasmic Reticulum Morphology in Embryos During Seed Germination

Part of the Methods in Molecular Biology book series (MIMB, volume 1691)


Imaging plant embryos at the cellular level over time is technically challenging, since the embryo, once its protective seed coat is removed, must be kept viable and unstressed on a microscope slide for the duration of the experiment. Here we describe a procedure and suitable apparatus for the visualization, over several days, of changes in endoplasmic reticulum (ER) morphology associated with the process of germination in Arabidopsis thaliana seeds. Moreover, we also present a user-friendly image analysis tool which enables subtle perturbations in the ER network to be measured.

Key words

Confocal microscopy Imaging chamber Embryo Germination 


  1. 1.
    Bewley JD (1997) Seed germination and dormancy. Plant Cell 9:1055–1066CrossRefPubMedPubMedCentralGoogle Scholar
  2. 2.
    Finch-Savage WE, Leubner-Metzger G (2006) Seed dormancy and the control of germination. New Phytol 171:501–523CrossRefPubMedGoogle Scholar
  3. 3.
    Holdsworth MJ, Bentsink L, Soppe WJJ (2008) Molecular networks regulating Arabidopsis seed maturation, after-ripening, dormancy and germination. New Phytol 179:33–54CrossRefPubMedGoogle Scholar
  4. 4.
    Boevink P, Cruz S, Hawes C, Harris N (1996) Virus-mediated delivery of the green fluorescent protein to the endoplasmic reticulum of plant cells. Plant J 10:935–941CrossRefGoogle Scholar
  5. 5.
    Schindelin J, Arganda-Carreras I, Frise E et al (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676–682CrossRefPubMedGoogle Scholar
  6. 6.
    Linkert M, Rueden CT, Allan C et al (2010) Metadata matters: access to image data in the real world. J Cell Biol 189:777–782CrossRefPubMedPubMedCentralGoogle Scholar
  7. 7.
    Arganda-Carreras I, Kaynig V, Rueden C et al (2017) Trainable Weka Segmentation: a machine learning tool for microscopy pixel classification. Bioinformatics. doi: 10.1093/bioinformatics/btx180
  8. 8.
    Arganda-Carreras I, Kaynig V, Rueden C et al Trainable_Segmentation: release v3.1.2 [data set]. Zenodo. doi: 10.5281/zenodo.59290
  9. 9.
    Pichette B (2012) Color pixel counter. Available at

Copyright information

© Springer Science+Business Media LLC 2018

Authors and Affiliations

  1. 1.School of Life SciencesUniversity of WarwickCoventryUK

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