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Organic fluorescent dyes active in the near infrared (NIR) region have attracted ongoing attention because of their diverse applications in biomedicine, materials, and related fields. The advantages include minimal interfering absorption and fluorescence from biological samples, inexpensive laser diode excitation, reduced scattering, and enhanced tissue penetration depth. Great efforts have been made in the design, synthesis, and application of organic NIR fluorophores. So far, several classes of NIR dyes, including bay-substituted perylene or naphthalene bisimides, cyanine dyes, 4,4-difluoro-4-bora-3a,4a-diaza-s-indacene (BODIPY) derivatives, 1,4-diketo-3,6-diphenylpyrrole[3,4-c]pyrrole (DPP) derivatives, and porphyrin analogues, have been developed and intensively researched. However, most organic NIR fluorophores, which commonly have a large conjugation system, suffer from low stability. Although structural modification of existing fluorophores could enhance stability to some extent, attention has increasingly been focused on the fabrication of NIR dye-based nanomaterials with better stability and performance than free dyes. Various kinds of nanoparticles based on different substrates that encapsulate or dope NIR dyes (and therapeutic agents), some of which are surface modified by functional groups, have been derived for biological application. Moreover, fluorophores with very bright fluorescence in the aggregated form, also known as aggregation-induced emission (AIE) derivatives, have recently become a brand new research field. AIE derivatives with NIR fluorescence have exhibited excellent performance in in vivo bioimaging. This chapter focuses on recent progress in this area, including major NIR organic chromophores, luminescent principles, and construction methods, as well as applications in biomedicine and challenges.

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