Investigating uncertainties in single-molecule localization microscopy using experimentally informed Monte-Carlo simulation
Published in Nano Letters, 2023
Recommended citation: Wei-Hong Yeo, Yang Zhang, Amy E. Neely, Xiaomin Bao, Cheng Sun, and Hao F. Zhang (2023). Investigating uncertainties in single-molecule localization microscopy using experimentally informed Monte-Carlo simulation. Nano Letters, 23(16), 7253-7259. https://doi.org/10.1021/acs.nanolett.3c00852
Abstract
Single-molecule localization microscopy (SMLM) enables the visualization of cellular nanostructures in vitro with sub-20 nm resolution. While substructures can generally be imaged with SMLM, the structural understanding of the images remains elusive. To better understand the link between SMLM images and the underlying structure, we developed a Monte Carlo (MC) simulation based on experimental imaging parameters and geometric information to generate synthetic SMLM imag-es. We chose the nuclear pore complex (NPC), a nanosized channel on the nuclear membrane which gates nucleo-cytoplasmic transport of biomolecules, as a test geometry for testing our MC model. Using the MC model to simulate SMLM images, we first optimized our clustering algorithm to separate >10^6 molecular localizations of fluorescently labeled NPC proteins into hundreds of individual NPCs in each cell. We then illustrated using our MC model to generate cellular sub-structures with different angles of labeling to inform our structural understanding through SMLM images obtained.