Čeština
EnglishImage analysis workflows to reveal the spatial organization of cell nuclei and chromosomes
Randall R.S., Jourdain C., Nowicka A., Kaduchová K., Kubová M., Ayoub,M.A., Schubert V., Tatout Ch., Colas I., Kalyanikrishna, Desset S., Mermet S., Boulaflous-Stevens A., Kubalová I., Mandáková T., Heckmann S., Lysak M.A., Panatta M., Santoro R., Schubert D., Pečinka A., Routh D., Baroux C.
NUCLEUS 13: 277-299, 2022
Keywords: Nucleus; chromatin; 3D organization; spatial distribution; image analysis; segmentation; quantification; mitosis; meiosis; chromosome; metaphase; pachytene; crossovers; nuclear speckles; nuclear bodies; RNA Pol II; transcription factories; oligo FISH; STED imaging; SIM
Abstract: 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.
DOI: 10.1080/19491034.2022.2144013
Fulltext: contact IEB authors
IEB authors: Kateřina Lahnerová, Anna Nowicka, Aleš Pečinka
NUCLEUS 13: 277-299, 2022
Keywords: Nucleus; chromatin; 3D organization; spatial distribution; image analysis; segmentation; quantification; mitosis; meiosis; chromosome; metaphase; pachytene; crossovers; nuclear speckles; nuclear bodies; RNA Pol II; transcription factories; oligo FISH; STED imaging; SIM
Abstract: 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.
DOI: 10.1080/19491034.2022.2144013
Fulltext: contact IEB authors
IEB authors: Kateřina Lahnerová, Anna Nowicka, Aleš Pečinka