Self-Assembled (Aza)BODIPY Dyes for Biomedical in Vivo Imaging

4,4-difluoro-4-bora-3a,4a-diaza-s-indacenes (BODIPYs) and their N-containing analogs (aza-BODIPYs) are highly versatile organic dyes that combine excellent photophysical, electronic, and supramolecular properties with high chemical stability. These features have enabled their use in diverse applications such as bioimaging, targeted drug delivery, and functional self-assembled materials. Their broad structural modularity allows different stacking modes with controlled exciton coupling during self-assembly, resulting in supramolecular materials with tunable spectroscopic and morphological properties. This is particularly relevant in aqueous media, where tunable near-infrared (NIR) absorption and emission are essential for advanced contrast agents (CAs) in biomedical imaging. Besides meso-heteroatom modification, J-aggregation stands out as especially advantageous for achieving red-shifted absorption and emission, thereby improving tissue penetration and reducing autofluorescence and light scattering. Of particular promise is the concept of pathway complexity, whereby a single (aza)BODIPY scaffold can access multiple aggregated states with distinct photophysical signatures, enabling stimuli-responsive and multifunctional imaging behavior. Hence, understanding the interplay between (aza)BODIPY molecular design, exciton coupling in aqueous media and their resulting supramolecular and bioimaging properties is of utmost importance. This minireview discusses recent advances in (aza)BODIPY-based self-assembled structures used as CA platforms for in vivo biomedical imaging and highlights the structure-property relationships that govern their performance.