Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
Résumé
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.
Mots clés
optical microscopy
multiplexed imaging
chromosome organization
transcription Author roles: Barho F: Conceptualization
Investigation
Methodology
Resources
Software
Validation
Visualization
Writing -Original Draft Preparation
Writing -Review & Editing Fiche JB: Conceptualization
Formal Analysis
Supervision
Writing -Review & Editing Bardou M: Validation Messina O: Validation Martiniere A: Validation Houbron C: Validation NOLLMANN M: Conceptualization
Funding Acquisition
Project Administration
Writing -Review & Editing
Fiche JB: Conceptualization
Bardou M: Validation
Messina O: Validation
Martiniere A: Validation
Houbron C: Validation
NOLLMANN M: Conceptualization
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