Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Identifikátory výsledku
Kód výsledku v 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>
Nalezeny alternativní kódy
RIV/00216224:14740/22:00128557
Výsledek na webu
<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>
Alternativní jazyky
Jazyk výsledku
angličtina
Název v původním jazyce
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Popis výsledku v původním jazyce
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.
Název v anglickém jazyce
Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Popis výsledku anglicky
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.
Klasifikace
Druh
J<sub>imp</sub> - Článek v periodiku v databázi Web of Science
CEP obor
—
OECD FORD obor
10601 - Cell biology
Návaznosti výsledku
Projekt
Výsledek vznikl pri realizaci vícero projektů. Více informací v záložce Projekty.
Návaznosti
I - Institucionalni podpora na dlouhodoby koncepcni rozvoj vyzkumne organizace
Ostatní
Rok uplatnění
2022
Kód důvěrnosti údajů
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Údaje specifické pro druh výsledku
Název periodika
Nucleus
ISSN
1949-1034
e-ISSN
1949-1042
Svazek periodika
13
Číslo periodika v rámci svazku
1
Stát vydavatele periodika
US - Spojené státy americké
Počet stran výsledku
23
Strana od-do
277-299
Kód UT WoS článku
000898422400001
EID výsledku v databázi Scopus
2-s2.0-85143064143