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. Finally, we provide a step-by-step guide to conduct a complete Hi-M acquisition using our open-source software package, Qudi-HiM, which controls the robotic microscope handling the entire acquisition procedure.

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, 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.

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-1. A clear red shift of the plasmon resonance as well as the enhancement of an absorption line are presented for 2 nm thin adlayers in simulations. We experimentally confirm the high sensitivity of the InAsSb grating by measurements of the wavelength shift induced by a 200 nm thin polymethylmethacrylate layer and demonstrate an enhancement of vibrational signals. A comparison to a gold grating with equivalent optical properties in the mid-infrared is performed. Our simulations and experimental results underline the interest in the alternative plasmonic material InAsSb for highly sensitive biosensors for the mid-infrared spectral range.

Fano-like resonances sustained by Si doped InAsSb plasmonic resonators integrated in GaSb matrix.

By using metal-free plasmonics, we report on the excitation of Fano-like resonances in the mid-infrared where the Fano asymmetric parameter, q, varies when the dielectric environment of the plasmonic resonator changes. We use silicon doped InAsSb alloy deposited by molecular beam epitaxy on GaSb substrate to realize the plasmonic resonators exclusively based on semiconductors. We first demonstrate the possibility to realize high quality samples of embedded InAsSb plasmonic resonators into GaSb host using regrowth technique. The high crystalline quality of the deposited structure is confirmed by scanning transmission electron microscopy (STEM) observation. Second, we report Fano-like resonances associated to localized surface plasmons in both cases: uncovered and covered plasmonic resonators, demonstrating a strong line shape modification. The optical properties of the embedded structures correspond to those modeled by finite-difference time-domain (FDTD) method and by a model based on Fano-like line shape. Our results show that all-semiconductor plasmonics gives the opportunity to build new plasmonic structures with embedded resonators of highly doped semiconductor in a matrix of un-doped semiconductor for mid-IR applications.