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

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Barho, Franziska | Fiche, Jean-Bernard | Bardou, Marion | Messina, Olivier | Martinière, Alexandre | Houbron, Christophe | Nollmann, Marcelo

Edité par CCSD ; F1000 Research Limited on behalf of the European Commission -

International audience. 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 HiM 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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