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 a Celia BAROUX. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. Nucleus. 2022, roč. 13, č. 1, s. 277-299. ISSN 1949-1034. Dostupné z: https://dx.doi.org/10.1080/19491034.2022.2144013. |
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@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 a Celia BAROUX. Image analysis workflows to reveal the spatial organization of cell nuclei and chromosomes. \textit{Nucleus}. 2022, roč.~13, č.~1, s.~277-299. ISSN~1949-1034. Dostupné z: https://dx.doi.org/10.1080/19491034.2022.2144013.
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