BEEP Learning: Multi-View Image Decomposition for Massively Multiplexed Biological Fluorescence Microscopy

Fluorescence imaging with spectrally variant fluorophores allows the spatial mapping of biological structures with exquisite cellular and molecular specificity. However, the ability to robustly discriminate multiple fluorophores in any single imaging experiment is greatly hindered by the broad emission spectra of bio-compatible fluorophores and the large contribution of noise in low-energy regime fluorescence microscopy. In this study, we propose a novel machine learning framework, Bleaching-Excitation-Emission Photodynamics (BEEP) learning, that exploits multiple discriminatory features of fluorescent dyes to greatly expand the number of distinguishable objects in an image by integrating emission spectra, excitation variability, and bleaching dynamics into a unified multi-view, fluorescence unmixing approach. Our method is built upon a rank-one-tensor-based generalized linear model and leverages two biophysically grounded assumptions: consistent spectral and bleaching behaviors under fixed excitation, and invariant fluorophore abundances across excitations. We first extract excitation-specific spectral and bleaching signatures from reference images, and then use them to estimate abundances in complex mixtures. Experimental results on both simulated and real images of microbial populations demonstrate that our approach significantly outperforms conventional and partially multi-view methods, offering improved robustness and accuracy in highly multiplexed fluorescence imaging.