Počet záznamů: 1
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
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SYSNO ASEP 0566546 Druh ASEP J - Článek v odborném periodiku Zařazení RIV J - Článek v odborném periodiku Poddruh J Článek ve WOS Název Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes Tvůrce(i) Randall, R. S. (CH)
Jourdain, C. (DE)
Nowicka, Anna (UEB-Q) ORCID
Kaduchová, Kateřina (UEB-Q) ORCID
Kubová, M. (CZ)
Ayoub, M. A. (DE)
Schubert, V. (DE)
Tatout, C. (FR)
Colas, I. (FR)
Kalyanikrishna, A. (DE)
Desset, S. (FR)
Mermet, S. (FR)
Boulaflous-Stevens, A. (FR)
Kubalová, I. (CZ)
Mandáková, T. (CZ)
Heckmann, S. (DE)
Lysák, M. A. (CZ)
Panatta, M. (CH)
Santoro, R. (DE)
Schubert, D. (DE)
Pečinka, Aleš (UEB-Q) ORCID, RID
Routh, D. (CH)
Baroux, C. (CH)Celkový počet autorů 23 Zdroj.dok. Nucleus. - : Taylor & Francis - ISSN 1949-1034
Roč. 13, č. 1 (2022), s. 277-299Poč.str. 23 s. Jazyk dok. eng - angličtina Země vyd. US - Spojené státy americké Klíč. slova 3D organization ; chromatin ; chromosome ; crossovers ; image analysis ; meiosis ; metaphase ; mitosis ; nuclear bodies ; nuclear speckles ; Nucleus ; oligo FISH ; pachytene ; quantification ; RNA Pol II ; segmentation ; sim ; spatial distribution ; STED imaging ; transcription factories Obor OECD Cell biology CEP EF16_019/0000827 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy LM2018129 GA MŠMT - Ministerstvo školství, mládeže a tělovýchovy GA21-02929S GA ČR - Grantová agentura ČR Způsob publikování Open access Institucionální podpora UEB-Q - RVO:61389030 UT WOS 000898422400001 EID SCOPUS 85143064143 DOI 10.1080/19491034.2022.2144013 Anotace 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. Abbreviations: 3D FISH: three-dimensional fluorescence in situ hybridization, 3D: three-dimensional, ASY1: ASYNAPTIC 1, CC: chromocenters, CO: Crossover, DAPI: 4',6-diamidino-2-phenylindole, DMC1: DNA MEIOTIC RECOMBINASE 1, DSB: Double-Strand Break, FISH: fluorescence in situ hybridization, GFP: GREEN FLUORESCENT PROTEIN, HEI10: HUMAN ENHANCER OF INVASION 10, NCO: Non-Crossover, NE: Nuclear Envelope, Oligo-FISH: oligonucleotide fluorescence in situ hybridization, RNPII: RNA Polymerase II, SC: Synaptonemal Complex, SIM: structured illumination microscopy, ZMM (ZIP: MSH4: MSH5 and MER3 proteins), ZYP1: ZIPPER-LIKE PROTEIN 1. Pracoviště Ústav experimentální botaniky Kontakt David Klier, knihovna@ueb.cas.cz, Tel.: 220 390 469 Rok sběru 2023 Elektronická adresa https://doi.org/10.1080/19491034.2022.2144013
Počet záznamů: 1