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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