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Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging

Multiplexed sequential and combinatorial imaging enables the simultaneous detection of multiple biological molecules, e.g. proteins, DNA, or RNA, enabling single-cell spatial multi-omics measurements at sub-cellular resolution. Recently, we designed a multiplexed imaging approach (Hi-M) to study the...

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Detalles Bibliográficos
Autores principales: Barho, Franziska, Fiche, Jean-Bernard, Bardou, Marion, Messina, Olivier, Martiniere, Alexandre, Houbron, Christophe, Nollmann, Marcelo
Formato: Online Artículo Texto
Lenguaje:English
Publicado: F1000 Research Limited 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10445908/
https://www.ncbi.nlm.nih.gov/pubmed/37645324
http://dx.doi.org/10.12688/openreseurope.14641.2
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author Barho, Franziska
Fiche, Jean-Bernard
Bardou, Marion
Messina, Olivier
Martiniere, Alexandre
Houbron, Christophe
Nollmann, Marcelo
author_facet Barho, Franziska
Fiche, Jean-Bernard
Bardou, Marion
Messina, Olivier
Martiniere, Alexandre
Houbron, Christophe
Nollmann, Marcelo
author_sort Barho, Franziska
collection PubMed
description Multiplexed sequential and combinatorial imaging enables the simultaneous detection of multiple biological molecules, e.g. proteins, DNA, or RNA, enabling single-cell spatial multi-omics measurements at sub-cellular resolution. Recently, we designed a multiplexed imaging approach (Hi-M) to study the spatial organization of chromatin in single cells. In order to enable Hi-M sequential imaging on custom microscope setups, we developed Qudi-HiM, a modular software package written in Python 3. Qudi-HiM contains modules to automate the robust acquisition of thousands of three-dimensional multicolor microscopy images, the handling of microfluidics devices, and the remote monitoring of ongoing acquisitions and real-time analysis. In addition, Qudi-HiM can be used as a stand-alone tool for other imaging modalities.
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spelling pubmed-104459082023-08-29 Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging Barho, Franziska Fiche, Jean-Bernard Bardou, Marion Messina, Olivier Martiniere, Alexandre Houbron, Christophe Nollmann, Marcelo Open Res Eur Software Tool Article Multiplexed sequential and combinatorial imaging enables the simultaneous detection of multiple biological molecules, e.g. proteins, DNA, or RNA, enabling single-cell spatial multi-omics measurements at sub-cellular resolution. Recently, we designed a multiplexed imaging approach (Hi-M) to study the spatial organization of chromatin in single cells. In order to enable Hi-M sequential imaging on custom microscope setups, we developed Qudi-HiM, a modular software package written in Python 3. Qudi-HiM contains modules to automate the robust acquisition of thousands of three-dimensional multicolor microscopy images, the handling of microfluidics devices, and the remote monitoring of ongoing acquisitions and real-time analysis. In addition, Qudi-HiM can be used as a stand-alone tool for other imaging modalities. F1000 Research Limited 2022-07-19 /pmc/articles/PMC10445908/ /pubmed/37645324 http://dx.doi.org/10.12688/openreseurope.14641.2 Text en Copyright: © 2022 Barho F et al. https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Software Tool Article
Barho, Franziska
Fiche, Jean-Bernard
Bardou, Marion
Messina, Olivier
Martiniere, Alexandre
Houbron, Christophe
Nollmann, Marcelo
Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
title Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
title_full Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
title_fullStr Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
title_full_unstemmed Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
title_short Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
title_sort qudi-him: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
topic Software Tool Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10445908/
https://www.ncbi.nlm.nih.gov/pubmed/37645324
http://dx.doi.org/10.12688/openreseurope.14641.2
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