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Automated 3D Gene Position Analysis Using a Customized Imaris Plugin: XTFISHInsideNucleus

Type of publication Peer-reviewed
Publikationsform Contribution to book (peer-reviewed)
Author Ashenafi Mariam, Baroux Célia,
Project Mechanisms and role of linker histones dynamics in plant reproduction
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Contribution to book (peer-reviewed)

Book Methods in Molecular Biology - Plant Chromatin Dynamics
Editor , Bemer Marian; , Baroux Célia
Publisher Springer, New York
Page(s) 1
ISBN 978-1-4939-7318-7
Title of proceedings Methods in Molecular Biology - Plant Chromatin Dynamics
DOI 10.1007/978-1-4939-7318-7_32


Fluorescent in situ hybridization (FISH) is commonly used to visualize chromosomal regions or genomic loci within the nucleus, and can largely contribute to unraveling the link between structure and function in the nucleus. Three dimensional (3D) analyses are required to best capture the nucleus’ organizing principles, but the experimental setup and computational analyses are far from trivial. Here, we present a robust workflow for 3D FISH against repeats and single copy loci in embedded intact nuclei from Arabidopsis leaves. We then describe in detail the image acquisition, subsequent image deconvolution before 3D image processing, and the image reconstruction. We developed an automated batch image processing pipeline using a customized, open source plugin implemented in the Imaris environment.