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

Type of publication Not peer-reviewed
Publikationsform Contribution to book (non peer-reviewed)
Author Baroux Célia, Schubert Veit,
Project Mechanisms and role of linker histones dynamics in plant reproduction
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Contribution to book (non peer-reviewed)

Book Methods in molecular biology (Clifton, N.J.)
Editor , Bemer Marian; , Baroux Célia
Publisher Springer, NY
Volume (Issue) 1675
Page(s) 537 - 589
ISBN 978-1-4939-7318-7
Title of proceedings Methods in molecular biology (Clifton, N.J.)
DOI 10.1007/978-1-4939-7318-7_31


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.