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Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations

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Plant Chromatin Dynamics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1675))

Abstract

In situ nucleus and chromatin analyses rely on microscopy imaging that benefits from versatile, efficient fluorescent probes and proteins for static or live imaging. Yet the broad choice in imaging instruments offered to the user poses orientation problems. Which imaging instrument should be used for which purpose? What are the main caveats and what are the considerations to best exploit each instrument’s ability to obtain informative and high-quality images? How to infer quantitative information on chromatin or nuclear organization from microscopy images? In this review, we present an overview of common, fluorescence-based microscopy systems and discuss recently developed super-resolution microscopy systems, which are able to bridge the resolution gap between common fluorescence microscopy and electron microscopy. We briefly present their basic principles and discuss their possible applications in the field, while providing experience-based recommendations to guide the user toward best-possible imaging. In addition to raw data acquisition methods, we discuss commercial and noncommercial processing tools required for optimal image presentation and signal evaluation in two and three dimensions.

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Acknowledgments

CB is funded by the Swiss National Science Foundation (SNSF), the University of Zürich and SystemsX.ch. CB acknowledges the expert assistance and training provided by the Microscopy Facility of the University of Zürich particularly in TEM, LSM and SRM imaging (ZMB, Prof. Urs Ziegler, Jana Doehner, Dominik Haenni, Moritz Kirschmann, Andreas Kaech), Mariamawit Ashenafi for the 3D image file used in Fig. 3c3. We thank Jörg Fuchs for flow sorting of nuclei, Martina Kühne and Andrea Kunze for slide preparation, Andreas Houben, Gerhard Wanner and Klaus Weisshart for critical reading of the manuscript, Marian Bemer for critical reading and suggestions.

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  1. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zollikerstrasse 107, 8008, Zürich, Switzerland

    Célia Baroux

  2. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) Gatersleben, 06466, Seeland, Germany

    Veit Schubert

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  1. Célia Baroux
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Correspondence to Célia Baroux .

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  1. Department of Molecular Biology, Wageningen University & Research, Wageningen, The Netherlands

    Marian Bemer

  2. Department of Plant and Microbial Biology, Zürich-Basel Plant Science Center, University of Zürich, Zürich, Switzerland

    Célia Baroux

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Baroux, C., Schubert, V. (2018). Technical Review: Microscopy and Image Processing Tools to Analyze Plant Chromatin: Practical Considerations. In: Bemer, M., Baroux, C. (eds) Plant Chromatin Dynamics. Methods in Molecular Biology, vol 1675. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7318-7_31

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