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Since classical methods operate pixel-wise and rely on least-squares fitting, their performance degrades with increasingly overlapping emission spectra and higher levels of noise, suggesting that a data-driven approach that can learn and utilize a structural prior might lead to improved results. Learning-based approaches for spectral imaging do exist, but they are either not optimized for microscopy data or are developed for very specific cases that are not applicable to fluorescence microscopy settings. To address this, we propose {\\lambda}Split, a physics-informed deep generative model that learns a conditional distribution over concentration maps using a hierarchical Variational Autoencoder. 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