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

ABSTRACT: 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.

SUBMITTER: Barho F

PROVIDER: S-EPMC10445908 | biostudies-literature | 2022

REPOSITORIES: biostudies-literature

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

Barho Franziska F Fiche Jean-Bernard JB Bardou Marion M Messina Olivier O Martiniere Alexandre A Houbron Christophe C Nollmann Marcelo M

Open research Europe 20220719

Multiplexed sequential and combinatorial imaging enables the simultaneous detection of multiple biological molecules, <i>e.g.</i> 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 ...[more]

PMID: 37645324

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