Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform

Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior performance for artifact suppression and high-fidelity reconstruction relative to other algorithms on various specimens and over a range of signal-to-noise level...

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Autores principales: Cao, Ruijie, Li, Yaning, Chen, Xin, Ge, Xichuan, Li, Meiqi, Guan, Meiling, Hou, Yiwei, Fu, Yunzhe, Xu, Xinzhu, Leterrier, Christophe, Jiang, Shan, Gao, Baoxiang, Xi, Peng
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group US 2023
Materias:
Brief Communication
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10406603/
https://www.ncbi.nlm.nih.gov/pubmed/37474809
http://dx.doi.org/10.1038/s41592-023-01958-0
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author Cao, Ruijie
Li, Yaning
Chen, Xin
Ge, Xichuan
Li, Meiqi
Guan, Meiling
Hou, Yiwei
Fu, Yunzhe
Xu, Xinzhu
Leterrier, Christophe
Jiang, Shan
Gao, Baoxiang
Xi, Peng
author_facet Cao, Ruijie
Li, Yaning
Chen, Xin
Ge, Xichuan
Li, Meiqi
Guan, Meiling
Hou, Yiwei
Fu, Yunzhe
Xu, Xinzhu
Leterrier, Christophe
Jiang, Shan
Gao, Baoxiang
Xi, Peng
author_sort Cao, Ruijie
collection PubMed
description Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior performance for artifact suppression and high-fidelity reconstruction relative to other algorithms on various specimens and over a range of signal-to-noise levels. Open-3DSIM also offers the capacity to extract dipole orientation, paving a new avenue for interpreting subcellular structures in six dimensions (xyzθλt). The platform is available as MATLAB code, a Fiji plugin and an Exe application to maximize user-friendliness.
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spelling pubmed-104066032023-08-09 Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform Cao, Ruijie Li, Yaning Chen, Xin Ge, Xichuan Li, Meiqi Guan, Meiling Hou, Yiwei Fu, Yunzhe Xu, Xinzhu Leterrier, Christophe Jiang, Shan Gao, Baoxiang Xi, Peng Nat Methods Brief Communication Open-3DSIM is an open-source reconstruction platform for three-dimensional structured illumination microscopy. We demonstrate its superior performance for artifact suppression and high-fidelity reconstruction relative to other algorithms on various specimens and over a range of signal-to-noise levels. Open-3DSIM also offers the capacity to extract dipole orientation, paving a new avenue for interpreting subcellular structures in six dimensions (xyzθλt). The platform is available as MATLAB code, a Fiji plugin and an Exe application to maximize user-friendliness. Nature Publishing Group US 2023-07-20 2023 /pmc/articles/PMC10406603/ /pubmed/37474809 http://dx.doi.org/10.1038/s41592-023-01958-0 Text en © The Author(s) 2023, corrected publication 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Brief Communication
Cao, Ruijie
Li, Yaning
Chen, Xin
Ge, Xichuan
Li, Meiqi
Guan, Meiling
Hou, Yiwei
Fu, Yunzhe
Xu, Xinzhu
Leterrier, Christophe
Jiang, Shan
Gao, Baoxiang
Xi, Peng
Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
title Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
title_full Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
title_fullStr Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
title_full_unstemmed Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
title_short Open-3DSIM: an open-source three-dimensional structured illumination microscopy reconstruction platform
title_sort open-3dsim: an open-source three-dimensional structured illumination microscopy reconstruction platform
topic Brief Communication
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10406603/
https://www.ncbi.nlm.nih.gov/pubmed/37474809
http://dx.doi.org/10.1038/s41592-023-01958-0
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