Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes

  1. Randall, Ricardo ORCID logo
  2. Jourdain, Claire ORCID logo
  3. Nowicka, Anna ORCID logo
  4. Kaduchová, Kateřina ORCID logo
  5. Kubová, Michaela ORCID logo
  6. Ayoub, Mohammad ORCID logo
  7. Schubert, Veit ORCID logo
  8. TATOUT, Christophe ORCID logo
  9. Colas, Isabelle ORCID logo
  10. ., Kalyanikrishna ORCID logo
  11. Desset, Sophie ORCID logo
  12. MERMET, Sarah ORCID logo
  13. Boulaflous-Stevens, Aurélia
  14. Kubalová, Ivona ORCID logo
  15. Mandakova, Terezie ORCID logo
  16. Heckmann, Stefan ORCID logo
  17. Lysak, Martin ORCID logo
  18. Panatta, Martina ORCID logo
  19. Santoro, Raffaella ORCID logo
  20. Schubert, Daniel ORCID logo
  21. Pecinka, Ales ORCID logo
  22. Routh, Devin
  23. Baroux, Célia ORCID logo

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1000 Titel
  • Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
1000 Autor/in
  1. Randall, Ricardo |
  2. Jourdain, Claire |
  3. Nowicka, Anna |
  4. Kaduchová, Kateřina |
  5. Kubová, Michaela |
  6. Ayoub, Mohammad |
  7. Schubert, Veit |
  8. TATOUT, Christophe |
  9. Colas, Isabelle |
  10. ., Kalyanikrishna |
  11. Desset, Sophie |
  12. MERMET, Sarah |
  13. Boulaflous-Stevens, Aurélia |
  14. Kubalová, Ivona |
  15. Mandakova, Terezie |
  16. Heckmann, Stefan |
  17. Lysak, Martin |
  18. Panatta, Martina |
  19. Santoro, Raffaella |
  20. Schubert, Daniel |
  21. Pecinka, Ales |
  22. Routh, Devin |
  23. Baroux, Célia |
1000 Erscheinungsjahr 2022
1000 LeibnizOpen
1000 Publikationstyp
  1. Artikel |
1000 Online veröffentlicht
  • 2022-11-29
1000 Erschienen in
1000 Quellenangabe
  • 13(1):277-299
1000 FRL-Sammlung
1000 Copyrightjahr
  • 2022
1000 Lizenz
1000 Verlagsversion
  • https://dx.doi.org/10.1080/19491034.2022.2144013 |
  • https://pmc.ncbi.nlm.nih.gov/articles/PMC9754023/ |
1000 Publikationsstatus
1000 Begutachtungsstatus
1000 Sprache der Publikation
1000 Abstract/Summary
  • 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.
1000 Sacherschließung
lokal crossovers
lokal mitosis
lokal Nucleus
lokal oligo FISH
lokal pachytene
lokal 3D organization
lokal quantification
lokal spatial distribution
lokal chromosome
lokal meiosis
lokal RNA Pol II
lokal chromatin
lokal transcription factories
lokal SIM
lokal image analysis
lokal segmentation
lokal nuclear bodies
lokal nuclear speckles
lokal STED imaging
lokal metaphase
1000 Fächerklassifikation (DDC)
1000 Liste der Beteiligten
  1. https://orcid.org/0000-0002-2778-519X|https://orcid.org/0000-0002-3568-580X|https://orcid.org/0000-0002-5762-3482|https://orcid.org/0000-0001-9259-5942|https://orcid.org/0000-0003-3474-7324|https://orcid.org/0000-0001-9371-3277|https://orcid.org/0000-0002-3072-0485|https://orcid.org/0000-0001-5215-2338|https://orcid.org/0000-0001-6980-9906|https://orcid.org/0000-0002-8026-246X|https://orcid.org/0000-0002-4897-4977|https://orcid.org/0000-0001-6839-3224|https://frl.publisso.de/adhoc/uri/Qm91bGFmbG91cy1TdGV2ZW5zLCBBdXLDqWxpYQ==|https://orcid.org/0000-0002-5673-9715|https://orcid.org/0000-0001-6485-0563|https://orcid.org/0000-0002-0189-8428|https://orcid.org/0000-0003-0318-4194|https://orcid.org/0000-0002-8180-8380|https://orcid.org/0000-0001-9894-2896|https://orcid.org/0000-0003-2390-0733|https://orcid.org/0000-0001-9277-1766|https://frl.publisso.de/adhoc/uri/Um91dGgsIERldmlu|https://orcid.org/0000-0001-6307-2229
1000 Label
1000 Förderer
  1. Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung |
  2. Velux Stiftung |
  3. Ricola foundation |
  4. HORIZON EUROPE European Research Council |
  5. Biotechnology and Biological Sciences Research Council |
  6. Deutsche Forschungsgemeinschaft |
  7. Deutscher Akademischer Austauschdienst France |
  8. International Max Planck Research School for Biology and Computation |
  9. Grantová Agentura České Republiky |
  10. Masarykova Univerzita |
  11. Bundesministerium für Bildung und Forschung |
  12. H2020 European Research Council |
  13. Agence nationale de la recherche |
1000 Fördernummer
  1. 310030_185186;IZCOZ0_198171;310030_201268
  2. 1107
  3. -
  4. 669182
  5. BB/T008636/1
  6. Schu 762/11-1
  7. -
  8. IMPRS-BAC
  9. 18-20134Sto MAL;21-02929S
  10. CZ.02.2.69/0.0/0.0/19_073/0016943;CZ.02.1.01/0.0/0.0/16_019/0000827
  11. 031B0188
  12. ERC-AdG -787074-NucleolusChromatin
  13. 16-IDEX-0001 CAP 20-25 CIR1;CIR3
1000 Förderprogramm
  1. -
  2. -
  3. -
  4. -
  5. -
  6. -
  7. -
  8. -
  9. -
  10. -
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  12. -
  13. -
1000 Dateien
1000 Förderung
  1. 1000 joinedFunding-child
    1000 Förderer Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung |
    1000 Förderprogramm -
    1000 Fördernummer 310030_185186;IZCOZ0_198171;310030_201268
  2. 1000 joinedFunding-child
    1000 Förderer Velux Stiftung |
    1000 Förderprogramm -
    1000 Fördernummer 1107
  3. 1000 joinedFunding-child
    1000 Förderer Ricola foundation |
    1000 Förderprogramm -
    1000 Fördernummer -
  4. 1000 joinedFunding-child
    1000 Förderer HORIZON EUROPE European Research Council |
    1000 Förderprogramm -
    1000 Fördernummer 669182
  5. 1000 joinedFunding-child
    1000 Förderer Biotechnology and Biological Sciences Research Council |
    1000 Förderprogramm -
    1000 Fördernummer BB/T008636/1
  6. 1000 joinedFunding-child
    1000 Förderer Deutsche Forschungsgemeinschaft |
    1000 Förderprogramm -
    1000 Fördernummer Schu 762/11-1
  7. 1000 joinedFunding-child
    1000 Förderer Deutscher Akademischer Austauschdienst France |
    1000 Förderprogramm -
    1000 Fördernummer -
  8. 1000 joinedFunding-child
    1000 Förderer International Max Planck Research School for Biology and Computation |
    1000 Förderprogramm -
    1000 Fördernummer IMPRS-BAC
  9. 1000 joinedFunding-child
    1000 Förderer Grantová Agentura České Republiky |
    1000 Förderprogramm -
    1000 Fördernummer 18-20134Sto MAL;21-02929S
  10. 1000 joinedFunding-child
    1000 Förderer Masarykova Univerzita |
    1000 Förderprogramm -
    1000 Fördernummer CZ.02.2.69/0.0/0.0/19_073/0016943;CZ.02.1.01/0.0/0.0/16_019/0000827
  11. 1000 joinedFunding-child
    1000 Förderer Bundesministerium für Bildung und Forschung |
    1000 Förderprogramm -
    1000 Fördernummer 031B0188
  12. 1000 joinedFunding-child
    1000 Förderer H2020 European Research Council |
    1000 Förderprogramm -
    1000 Fördernummer ERC-AdG -787074-NucleolusChromatin
  13. 1000 joinedFunding-child
    1000 Förderer Agence nationale de la recherche |
    1000 Förderprogramm -
    1000 Fördernummer 16-IDEX-0001 CAP 20-25 CIR1;CIR3
1000 Objektart article
1000 Beschrieben durch
1000 @id frl:6511113.rdf
1000 Erstellt am 2025-04-17T11:08:27.007+0200
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