Squaraine dyes are a class of organic dyes showing intense fluorescence, typically in the red and near infrared region (absorption maxima are found between 630 and 670 nm and their emission maxima are between 650–700 nm). They are characterized by their unique aromatic four membered ring system derived from squaric acid. Most squaraines are encumbered by nucleophilic attack of the central four membered ring, which is highly electron deficient. This encumbrance can be attenuated by the formation of a rotaxane around the dye to protect it from nucleophiles. They are currently used as sensors for ions and have recently, with the advent of protected squaraine derivatives, been exploited in biomedical imaging.