Hi-M: A Multiplex Oligopaint FISH Method to Capture Chromatin Conformations In Situ and Accompanying Open-Source Acquisition Software.

The simultaneous observation of three-dimensional (3D) chromatin structure and transcription in single cells is critical to understand how DNA is organized inside cells and how this organization influences or is affected by other processes, such as transcription. We have recently introduced an innovative technology known as Hi-M, which enables the sequential tagging, 3D visualization, and precise localization of multiple genomic DNA regions alongside RNA expression within individual cells. In this chapter, we present a comprehensive guide outlining the creation of probes, as well as sample preparation and labeling.

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

Multiplexed sequential and combinatorial imaging enables the simultaneous detection of multiple biological molecules, 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.

All-semiconductor plasmonic gratings for biosensing applications in the mid-infrared spectral range.

We propose 1D periodic, highly doped InAsSb gratings on GaSb substrates as biosensing platforms applicable for surface plasmon resonance and surface enhanced infrared absorption spectroscopies. Based on finite-difference time-domain simulations, the electric field enhancement and the sensitivity on refractive index variations are investigated for different grating geometries. The proposed, optimized system achieves sensitivities of 900 nm RIU.