Qudi-HiM: an open-source acquisition software package for highly multiplexed sequential and combinatorial optical imaging
Franziska Barho, Jean-Bernard Fiche, Marion Bardou, Olivier Messina, Alexandre Martinière, Christophe Houbron, Marcelo Nöllmann
Abstract
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.