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A list of all the posts and pages found on the site. For you robots out there is an XML version available for digesting as well.
Pages
About me
About me
Posts
preprints
Maximizing photon utilization in spectroscopic single-molecule localization microscopy using symmetrically dispersed dual-wedge prisms
Preprint available at BioRxiv, 2024
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.
Transport and Organization of Individual Vimentin Filaments Within Dense Networks Revealed by Single Particle Tracking and 3D FIB-SEM
Preprint available at BioXRiv, 2024
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.
Spectroscopic Single-Molecule Discrimination of BODIPY Fluorophores with Deep Learning
Preprint available at Chem, 2024
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.
Implementation and calibration of spectroscopic single-molecule localization microscopy
Preprint available at BioXRiv, 2024
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.
Swept-source visible-light optical coherence tomography
Preprint available at Optica Open, 2024
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.
publications
Monolithic dual-wedge prism-based spectroscopic single-molecule localization microscopy
Published in Nanophotonics, 2022
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.
Investigating uncertainties in single-molecule localization microscopy using experimentally informed Monte-Carlo simulation
Published in Nano Letters, 2023
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.
Physically informed Monte Carlo simulation of dual-wedge prism-based spectroscopic single-molecule localization microscopy
Published in Journal of Biomedical Optics, 2023
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.
Longitudinal imaging of vitreal hyperreflective foci in mice with acute optic nerve damage using visible-light optical coherence tomography
Published in Optics Letters, 2024
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.
Dynamic chromosome association with nuclear organelles in living cells
Published in Histochem Cell Biol, 2024
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.