From stained plant tissues to quantitative cell segmentation analysis with MorphoGraphX

Merijn Kerstens, Soeren Strauss, Richard Smith, Viola Willemsen*

*Corresponding author for this work

Research output: Chapter in Book/Report/Conference proceedingChapterAcademicpeer-review

5 Citations (Scopus)


Development and growth of plant organs is determined by a myriad of molecular processes that occur in each individual cell. As a direct consequence of these processes, cells alter in size and shape. They therefore serve as excellent parameters to thoroughly understand gene function. However, conventional single-plane analyses fail to accurately capture cell metrics. Here, we present a comprehensive illustrated guide that demonstrates how SCRI Renaissance 2200 staining of Arabidopsis thaliana embryos and roots can be combined with the open-source application MorphoGraphX to quantify cell parameters in 3D. We compare this staining method with other common staining techniques and provide examples of embryo and root tissue segmentation. With our novel approach, subtle single-cell phenotypes can be identified in their native context, providing new possibilities to dissect gene networks.

Original languageEnglish
Title of host publicationPlant Embryogenesis
Subtitle of host publicationMethods and protocols
EditorsM. Bayer
Place of PublicationNew York
PublisherHumana Press
Number of pages21
ISBN (Electronic)9781071603420
ISBN (Print)9781071603413
Publication statusPublished - 24 Jan 2020

Publication series

NameMethods in Molecular Biology
ISSN (Print)1064-3745
ISSN (Electronic)1940-6029


  • 3D imaging
  • 3D segmentation
  • Cell volume
  • Embryos
  • Lateral roots
  • MorphoGraphX
  • Roots
  • SCRI Renaissance


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