Spatially pooling photon information enables photon-efficient quantitative imaging

Quantitative fluorescence imaging techniques such as fluorescence lifetime imaging microscopy and hyperspectral imaging infer molecular contrast from photons distributed across spatial pixels and temporal or spectral channels. In the few-photon regime, however, conventional pixel-wise analysis discards the spatial relationships imposed across neighboring pixels by the microscope point-spread function (PSF). Here we show that this spatially distributed information can be recovered without prior knowledge of emitter positions, spatial support or component assignments. We introduce SPOOL (Spatially Pooled Optical Observation Likelihood), a training-free Poisson inverse framework that jointly recovers source-space amplitudes and quantitative contrast by combining the PSF with temporal-decay or spectral-response dictionaries. For an isolated source, the attainable precision gain is governed by a dimensionless optical quantity: the PSF width expressed in detector pixels. The predicted gain therefore scales with optical sampling rather than with the physical origin of the contrast. The model predicts that lifetime-precision gain scales approximately linearly with the number of pixels spanning the PSF full width at half maximum, a scaling reproduced by Monte Carlo simulations. At one detected photon per foreground pixel, the reconstruction reduces lifetime dispersion sixfold in fluorescent-bead experiments and decreases the lifetime root-mean-square error relative to a high-photon reference from 1.19 to 0.45 ns in dual-labeled cells. The same framework transfers unchanged to hyperspectral imaging, recovering spectral contrast from generic emission bands without prior fluorophore spectra.