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

J 2022

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

RANDALL, Ricardo S, Claire JOURDAIN, Anna NOWICKA, Kateina KADUCHOVA, Michaela KUBOVÁ et. al.

Basic information

Original name

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

Authors

RANDALL, Ricardo S, Claire JOURDAIN, Anna NOWICKA, Kateina KADUCHOVA, Michaela KUBOVÁ (203 Czech Republic, belonging to the institution), Mohammad A AYOUB, Veit SCHUBERT, Christophe TATOUT, Isabelle COLAS, K. KALYANIKRISHNA, Sophie DESSET, Sarah MERMET, Aurelia BOULAFLOUS-STEVENS, Ivona KUBALOVA, Terezie MALÍK MANDÁKOVÁ (203 Czech Republic, belonging to the institution), Stefan HECKMANN, Martin LYSÁK (203 Czech Republic, guarantor, belonging to the institution), Martina PANATTA, Raffaella SANTORO, Daniel SCHUBERT, Ales PECINKA, Devin ROUTH and Celia BAROUX

Edition

Nucleus, 2022, 1949-1034

Other information

Language

English

Type of outcome

Článek v odborném periodiku

Field of Study

10601 Cell biology

Country of publisher

United States of America

Confidentiality degree

není předmětem státního či obchodního tajemství

References:

URL

Impact factor

Impact factor: 3.700

RIV identification code

RIV/00216224:14740/22:00128557

Organization unit

Central European Institute of Technology

DOI

http://dx.doi.org/10.1080/19491034.2022.2144013

UT WoS

000898422400001

Keywords in English

Nucleus; chromatin; 3D organization; spatial distribution; image analysis; segmentation; quantification; mitosis; meiosis; chromosome; metaphase; pachytene; crossovers; nuclear speckles; nuclear bodies

Abstract

V originále

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.

Links

EF19_073/0016943, research and development project

Name: Interní grantová agentura Masarykovy univerzity

GA18-20134S, research and development project

Name: Organizace interfázních chromosomů a časné meiotické párování chromosomů u brukvovitých

Investor: Czech Science Foundation

90129, large research infrastructures

Name: Czech-BioImaging II

Citovat

RANDALL, Ricardo S, Claire JOURDAIN, Anna NOWICKA, Kateina KADUCHOVA, Michaela KUBOVÁ, Mohammad A AYOUB, Veit SCHUBERT, Christophe TATOUT, Isabelle COLAS, K. KALYANIKRISHNA, Sophie DESSET, Sarah MERMET, Aurelia BOULAFLOUS-STEVENS, Ivona KUBALOVA, Terezie MALÍK MANDÁKOVÁ, Stefan HECKMANN, Martin LYSÁK, Martina PANATTA, Raffaella SANTORO, Daniel SCHUBERT, Ales PECINKA, Devin ROUTH and Celia BAROUX. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus. 2022, vol. 13, No 1, p. 277-299. ISSN 1949-1034. Available from: https://dx.doi.org/10.1080/19491034.2022.2144013.

@article{2252799,
   author = {Randall, Ricardo S and Jourdain, Claire and Nowicka, Anna and Kaduchova, Kateina and Kubová, Michaela and Ayoub, Mohammad A and Schubert, Veit and Tatout, Christophe and Colas, Isabelle and Kalyanikrishna, K. and Desset, Sophie and Mermet, Sarah and BoulaflousandStevens, Aurelia and Kubalova, Ivona and Malík Mandáková, Terezie and Heckmann, Stefan and Lysák, Martin and Panatta, Martina and Santoro, Raffaella and Schubert, Daniel and Pecinka, Ales and Routh, Devin and Baroux, Celia},
   article_number = {1},
   doi = {http://dx.doi.org/10.1080/19491034.2022.2144013},
   keywords = {Nucleus; chromatin; 3D organization; spatial distribution; image analysis; segmentation; quantification; mitosis; meiosis; chromosome; metaphase; pachytene; crossovers; nuclear speckles; nuclear bodies},
   language = {eng},
   issn = {1949-1034},
   journal = {Nucleus},
   title = {Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes},
   url = {https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2144013},
   volume = {13},
   year = {2022}
}

TY  - JOUR
ID  - 2252799
AU  - Randall, Ricardo S - Jourdain, Claire - Nowicka, Anna - Kaduchova, Kateina - Kubová, Michaela - Ayoub, Mohammad A - Schubert, Veit - Tatout, Christophe - Colas, Isabelle - Kalyanikrishna, K. - Desset, Sophie - Mermet, Sarah - Boulaflous-Stevens, Aurelia - Kubalova, Ivona - Malík Mandáková, Terezie - Heckmann, Stefan - Lysák, Martin - Panatta, Martina - Santoro, Raffaella - Schubert, Daniel - Pecinka, Ales - Routh, Devin - Baroux, Celia
PY  - 2022
TI  - Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
JF  - Nucleus
VL  - 13
IS  - 1
SP  - 277-299
EP  - 277-299
SN  - 19491034
KW  - Nucleus
KW  - chromatin
KW  - 3D organization
KW  - spatial distribution
KW  - image analysis
KW  - segmentation
KW  - quantification
KW  - mitosis
KW  - meiosis
KW  - chromosome
KW  - metaphase
KW  - pachytene
KW  - crossovers
KW  - nuclear speckles
KW  - nuclear bodies
UR  - https://www.tandfonline.com/doi/full/10.1080/19491034.2022.2144013
N2  - 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.
ER  -

RANDALL, Ricardo S, Claire JOURDAIN, Anna NOWICKA, Kateina KADUCHOVA, Michaela KUBOVÁ, Mohammad A AYOUB, Veit SCHUBERT, Christophe TATOUT, Isabelle COLAS, K. KALYANIKRISHNA, Sophie DESSET, Sarah MERMET, Aurelia BOULAFLOUS-STEVENS, Ivona KUBALOVA, Terezie MALÍK MANDÁKOVÁ, Stefan HECKMANN, Martin LYSÁK, Martina PANATTA, Raffaella SANTORO, Daniel SCHUBERT, Ales PECINKA, Devin ROUTH and Celia BAROUX. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. \textit{Nucleus}. 2022, vol.~13, No~1, p.~277-299. ISSN~1949-1034. Available from: https://dx.doi.org/10.1080/19491034.2022.2144013.

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