Framework for Accurate Single-Molecule Spectroscopic Imaging Analyses Using Monte Carlo Simulation and Deep Learning

Accurate single-molecule spectral imaging denoising and analysis are essential for advancing high-throughput single-molecule spectroscopy and spectrally resolved super-resolution microscopy. However, a standardized framework for guiding the accurate analysis of single-molecule spectral data remains unavailable. To address this, we developed an analysis framework that generates ground truth (GT) single-molecule spectral imaging data using Monte Carlo simulations, enabling the first supervised learning-based imaging denoising method (referred to as SpecUNet) for single-molecule spectral images. Within this framework, we established eight comprehensive evaluation metrics to systematically compare the performance of SpecUNet against existing imaging analytics using synthetic GT data. We further validated SpecUNet's performance experimentally and demonstrated its capability in accurately characterizing the single-molecule fluorescence spectral heterogeneity of Janelia Fluors. Additionally, we explored its ability to decode the spectral responses of the polarity-sensitive probe Nile Red under varying nanoscale chemical polarities and heterogeneities.