This paper introduces a library of borondipyrromethene (BODIPY) derivatives for spectroscopic single-molecule imaging, demonstrating the ability to distinguish individual molecules with different substituents using deep learning. I was involved in the acquisition of single-molecule fluorescence data and the development of the deep learning algorithms critical for classification of spectrally similar fluorophores.

This paper introduces an improved dual-wedge prism-based monolithic imaging spectrometer for spectroscopic single-molecule localization microscopy (sSMLM). I was involved in the experimental design, validation, and data analysis of the new imaging system, which demonstrated improved spatial and spectral precisions compared to grating-based sSMLM.

This protocol provides essential information for researchers to implement spectroscopic single-molecule localization microscopy (sSMLM) in a laboratory setting. We describe the assembly and alignment of a 3D dual-wedge prism (DWP)-based sSMLM instrument, spectral and axial calibration, and the reconstruction of super-resolution 3D images using RainbowSTORM v2. I was involved in the development of the MATLAB package, which provides a easy way to reconstruct super-resolution 3D images, as well as the optimization of the calibration procedures.

This paper demonstrates the feasibility of swept-source visible-light optical coherence tomography (SS-vis-OCT) using a fanout periodically poled lithium niobate (PPLN) crystal for second harmonic generation (SHG) to convert a commercial near-infrared swept-source (NIR-SS) laser into a visible-light SS laser. I was involved in the initial design and experimental optimization of the SS-vis-OCT system.

This paper introduces a sparse vimentin-SunTag labeling strategy to unambiguously visualize individual filament dynamics, revealing extensive bidirectional motion within the perinuclear vimentin network. We also present high-resolution electron microscopy volumes of a vitreously frozen cell to reconstruct VIFs and microtubules within a ∼50 µm3 window, demonstrating minimal local co-alignment between VIFs and microtubules. I was involved in the image analysis and interpretation of the single-particle tracking data.

This paper investigates the dynamic nature of chromosomes in relation to nuclear organelles across the cell cycle using photoconvertible GFP H3-Dendra2 in PC3M cells. I was involved in the analysis of chromosome dynamics in living cells.

This paper demonstrates the use of visible-light optical coherence tomography (vis-OCT) with temporal speckle averaging to visualize and track vitreal hyperreflective foci (VHRFs) in a mouse model of acute optic nerve damage. I was involved in the analysis of the vis-OCT images, which revealed a significant increase in VHRF density following optic nerve crush injury.

This paper combines spectroscopic single-molecule localization microscopy (SMLM) with a Monte Carlo (MC) simulation to effectively model the imaging process with a dual-wedge prism (DWP), enabling us to better optimize our experimental setups for improved spectroscopic performance. I was involved in the development of the MC model, the optimization of the DWP system parameters, and the validation of the simulation results.

This paper combines single-molecule localization microscopy (SMLM) with a Monte Carlo (MC) simulation to effectively model the labeling uncertainties of the nuclear pore complex (NPC), enhancing the interpretation of SMLM images and deepening our understanding of cellular substructures. I was involved in the development of the MC model, the optimization of the clustering algorithm, and the generation of synthetic SMLM images.

This paper introduces a dual-wedge prism-based monolithic imaging spectrometer for spectroscopic single-molecule localization microscopy (sSMLM), which offers improved performance and feasibility compared to traditional grating-based methods. I was involved in the experimental validation of the dual-wedge prism, which demonstrated improved spatial and spectral precisions compared to grating-based sSMLM.