Most squaraines are encumbered by nucleophilic attack of the central four membered ring, which is highly electron deficient.
They are currently used as sensors for ions and have recently, with the advent of protected squaraine derivatives, been exploited in biomedical imaging.
For instance, squaraine dyes are also formed via reaction of squaric acid or its derivatives with so-called "methylene bases" like 2-methyl-indolenines, 2-methyl-benzthiazoles or 2-methyl-benzo-selenazoles.
Indolenine-based squaraines combine good photostability including high quantum yields when bound to proteins and reactive versions of these dyes are commonly used as fluorescent probes and labels for biomedical applications.
Encapsulation increases chemical and thermal stability of squarylium molecules; it also allows their isolation and individual characterization.