2022
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
RANDALL, Ricardo S, Claire JOURDAIN, Anna NOWICKA, Kateina KADUCHOVA, Michaela KUBOVÁ et. al.Základní údaje
Originální název
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Autoři
RANDALL, Ricardo S, Claire JOURDAIN, Anna NOWICKA, Kateina KADUCHOVA, Michaela KUBOVÁ (203 Česká republika, domácí), Mohammad A AYOUB, Veit SCHUBERT, Christophe TATOUT, Isabelle COLAS, K. KALYANIKRISHNA, Sophie DESSET, Sarah MERMET, Aurelia BOULAFLOUS-STEVENS, Ivona KUBALOVA, Terezie MALÍK MANDÁKOVÁ (203 Česká republika, domácí), Stefan HECKMANN, Martin LYSÁK (203 Česká republika, garant, domácí), Martina PANATTA, Raffaella SANTORO, Daniel SCHUBERT, Ales PECINKA, Devin ROUTH a Celia BAROUX
Vydání
Nucleus, 2022, 1949-1034
Další údaje
Jazyk
angličtina
Typ výsledku
Článek v odborném periodiku
Obor
10601 Cell biology
Stát vydavatele
Spojené státy
Utajení
není předmětem státního či obchodního tajemství
Odkazy
Impakt faktor
Impact factor: 3.700
Kód RIV
RIV/00216224:14740/22:00128557
Organizační jednotka
Středoevropský technologický institut
UT WoS
000898422400001
Klíčová slova anglicky
Nucleus; chromatin; 3D organization; spatial distribution; image analysis; segmentation; quantification; mitosis; meiosis; chromosome; metaphase; pachytene; crossovers; nuclear speckles; nuclear bodies
Příznaky
Mezinárodní význam, Recenzováno
Změněno: 8. 10. 2024 10:39, Ing. Martina Blahová
Anotace
V originále
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.
Návaznosti
EF19_073/0016943, projekt VaV |
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GA18-20134S, projekt VaV |
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90129, velká výzkumná infrastruktura |
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