Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved]
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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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F1000 Research Ltd
2022-07-01
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| Series: | Open Research Europe |
| Subjects: | |
| Online Access: | https://open-research-europe.ec.europa.eu/articles/2-46/v2 |
| _version_ | 1811195679367757824 |
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| author | Alexandre Martiniere Olivier Messina Christophe Houbron Franziska Barho Marcelo NOLLMANN Marion Bardou Jean-Bernard Fiche |
| author_facet | Alexandre Martiniere Olivier Messina Christophe Houbron Franziska Barho Marcelo NOLLMANN Marion Bardou Jean-Bernard Fiche |
| author_sort | Alexandre Martiniere |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-04-12T00:47:05Z |
| format | Article |
| id | doaj.art-702c870faae746e6bdf45c6ef37809ed |
| institution | Directory Open Access Journal |
| issn | 2732-5121 |
| language | English |
| last_indexed | 2024-04-12T00:47:05Z |
| publishDate | 2022-07-01 |
| publisher | F1000 Research Ltd |
| record_format | Article |
| series | Open Research Europe |
| spelling | doaj.art-702c870faae746e6bdf45c6ef37809ed2022-12-22T03:54:50ZengF1000 Research LtdOpen Research Europe2732-51212022-07-01216171Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved]Alexandre Martiniere0Olivier Messina1https://orcid.org/0000-0001-7218-138XChristophe Houbron2Franziska Barho3https://orcid.org/0000-0003-4502-0702Marcelo NOLLMANN4https://orcid.org/0000-0003-3339-2349Marion Bardou5https://orcid.org/0000-0003-1882-6065Jean-Bernard Fiche6Institut Agro Montpellier, INRAE, Montpellier, 34000, FranceCentre de Biologie Structurale, Centre National de la Recherche Scientifique, UMR5048, Montpellier, 34090, FranceCentre de Biologie Structurale, Centre National de la Recherche Scientifique, UMR5048, Montpellier, 34090, FranceCentre de Biologie Structurale, Centre National de la Recherche Scientifique, UMR5048, Montpellier, 34090, FranceCentre de Biologie Structurale, Centre National de la Recherche Scientifique, UMR5048, Montpellier, 34090, FranceCentre de Biologie Structurale, Centre National de la Recherche Scientifique, UMR5048, Montpellier, 34090, FranceCentre de Biologie Structurale, Centre National de la Recherche Scientifique, UMR5048, Montpellier, 34090, FranceMultiplexed 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.https://open-research-europe.ec.europa.eu/articles/2-46/v2optical microscopy multiplexed imaging chromosome organization transcriptioneng |
| spellingShingle | Alexandre Martiniere Olivier Messina Christophe Houbron Franziska Barho Marcelo NOLLMANN Marion Bardou Jean-Bernard Fiche Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved] Open Research Europe optical microscopy multiplexed imaging chromosome organization transcription eng |
| title | Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved] |
| title_full | Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved] |
| title_fullStr | Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved] |
| title_full_unstemmed | Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved] |
| title_short | Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging [version 2; peer review: 2 approved] |
| title_sort | qudi him an open source acquisition software package for highly multiplexed sequential and combinatorial optical imaging version 2 peer review 2 approved |
| topic | optical microscopy multiplexed imaging chromosome organization transcription eng |
| url | https://open-research-europe.ec.europa.eu/articles/2-46/v2 |
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