Brightness demixing for simultaneous multi-target imaging in 3D single-molecule localization microscopy

Abstract Single-Molecule Localization Microscopy (SMLM) has revolutionized high-resolution imaging, but the simultaneous detection of multiple fluorophores traditionally relies on spectral-based separation, which is inherently constrained by spectral overlap. Here, we introduce Brightness Demixing, a novel method for fluorophore discrimination that exploits brightness, which directly depends on the fluorophores extinction coefficient and quantum yield. By oversampling blinking events, we precisely quantify photon flux as a proxy for brightness, enabling robust differentiation of fluorophores independent of their spectral properties, without requiring additional spectral separation. Brightness Demixing operates within a single detection channel, eliminating the need for additional spectral filters or cameras. We demonstrate this approach with simultaneous two- and three-target imaging in both 2D and 3D configurations. By maintaining single-wavelength excitation and minimizing chromatic aberrations, this method significantly enhances multiplexing in SMLM while remaining fully compatible with existing setups. Brightness Demixing thus offers a simple yet powerful approach for expanding multi-target imaging capabilities in super-resolution microscopy.