Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61389030%3A_____%2F22%3A00566546" target="_blank" >RIV/61389030:_____/22:00566546 - isvavai.cz</a>
Alternative codes found
RIV/00216224:14740/22:00128557
Result on the web
<a href="https://doi.org/10.1080/19491034.2022.2144013" target="_blank" >https://doi.org/10.1080/19491034.2022.2144013</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1080/19491034.2022.2144013" target="_blank" >10.1080/19491034.2022.2144013</a>
Alternative languages
Result language
angličtina
Original language name
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Original language 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. 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.
Czech name
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Czech description
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Classification
Type
J<sub>imp</sub> - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10601 - Cell biology
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Others
Publication year
2022
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Nucleus
ISSN
1949-1034
e-ISSN
1949-1042
Volume of the periodical
13
Issue of the periodical within the volume
1
Country of publishing house
US - UNITED STATES
Number of pages
23
Pages from-to
277-299
UT code for WoS article
000898422400001
EID of the result in the Scopus database
2-s2.0-85143064143