Abstract
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.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
van den Berg C, Willemsen V, Hage W, Weisbeek P, Scheres B (1995) Cell fate in the Arabidopsis root meristem determined by directional signalling. Nature 378:62–65
de Reuille PB, Routier-Kierzkowska AL, Kierzkowski D, Bassel GW, Schüpbach T, Tauriello G, Bajpai N, Strauss S, Weber A, Kiss A, Burian A et al (2015) MorphoGraphX: a platform for quantifying morphogenesis in 4D. Elife 4:5864
Truernit E, Bauby H, Dubreucq B, Grandjean O, Runions J, Barthélémy J, Palauqui JC (2008) High-resolution whole-mount imaging of three-dimensional tissue organization and gene expression enables the study of phloem development and structure in Arabidopsis. Plant Cell 20:1494–1503
Smith ZR, Long JA (2010) Control of Arabidopsis apical-basal embryo polarity by antagonistic transcription factors. Nature 464:423–426
Musielak TJ, Schenkel L, Kolb M, Henschen A, Bayer M (2015) A simple and versatile cell wall staining protocol to study plant reproduction. Plant Reprod 28:161–169
Schindelin J, Arganda-Carreras I, Frise E, Kaynig V, Longair M, Pietzsch T, Preibisch S, Rueden C, Saalfeld S, Schmid B, Tinevez JY, White DJ, Hartenstein V, Eliceiri K, Tomancak P, Cardona A (2012) Fiji: an open-source platform for biological-image analysis. Nat Methods 9:676
Montenegro-Johnson TD, Stamm P, Strauss S, Topham AT, Tsagris M, Wood AT, Smith RS, Bassel GW (2015) Digital single-cell analysis of plant organ development using 3D CellAtlas. Plant Cell 27:1018–1033
Stamm P, Strauss S, Montenegro-Johnson TD, Smith R, Bassel GW (2017) In silico methods for cell annotation, quantification of gene expression, and cell geometry at single-cell resolution using 3D Cell atlas. Methods Mol Biol 1497:99–123
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2020 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Kerstens, M., Strauss, S., Smith, R., Willemsen, V. (2020). From Stained Plant Tissues to Quantitative Cell Segmentation Analysis with MorphoGraphX. In: Bayer, M. (eds) Plant Embryogenesis. Methods in Molecular Biology, vol 2122. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-0342-0_6
Download citation
DOI: https://doi.org/10.1007/978-1-0716-0342-0_6
Published:
Publisher Name: Humana, New York, NY
Print ISBN: 978-1-0716-0341-3
Online ISBN: 978-1-0716-0342-0
eBook Packages: Springer Protocols