Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

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Authors

RANDALL Ricardo S JOURDAIN Claire NOWICKA Anna KADUCHOVA Kateina KUBOVÁ Michaela AYOUB Mohammad A SCHUBERT Veit TATOUT Christophe COLAS Isabelle KALYANIKRISHNA K. DESSET Sophie MERMET Sarah BOULAFLOUS-STEVENS Aurelia KUBALOVA Ivona MALÍK MANDÁKOVÁ Terezie HECKMANN Stefan LYSÁK Martin PANATTA Martina SANTORO Raffaella SCHUBERT Daniel PECINKA Ales ROUTH Devin BAROUX Celia

Year of publication 2022
Type Article in Periodical
Magazine / Source Nucleus
MU Faculty or unit

Central European Institute of Technology

Citation
Web https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2144013
Doi http://dx.doi.org/10.1080/19491034.2022.2144013
Keywords Nucleus; chromatin; 3D organization; spatial distribution; image analysis; segmentation; quantification; mitosis; meiosis; chromosome; metaphase; pachytene; crossovers; nuclear speckles; nuclear bodies
Description Nucleus, chromatin, and chromosome organization studies heavily rely on fluorescence microscopy imaging to elucidate the distribution and abundance of structural and regulatory components. Three-dimensional (3D) image stacks are a source of quantitative data on signal intensity level and distribution and on the type and shape of distribution patterns in space. Their analysis can lead to novel insights that are otherwise missed in qualitative-only analyses. Quantitative image analysis requires specific software and workflows for image rendering, processing, segmentation, setting measurement points and reference frames and exporting target data before further numerical processing and plotting. These tasks often call for the development of customized computational scripts and require an expertise that is not broadly available to the community of experimental biologists. Yet, the increasing accessibility of high- and super-resolution imaging methods fuels the demand for user-friendly image analysis workflows. Here, we provide a compendium of strategies developed by participants of a training school from the COST action INDEPTH to analyze the spatial distribution of nuclear and chromosomal signals from 3D image stacks, acquired by diffraction-limited confocal microscopy and super-resolution microscopy methods (SIM and STED). While the examples make use of one specific commercial software package, the workflows can easily be adapted to concurrent commercial and open-source software. The aim is to encourage biologists lacking custom-script-based expertise to venture into quantitative image analysis and to better exploit the discovery potential of their images.
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