The cosine similarity matrix shows how unique the spectral signature is of one dye compared to another dye. Values range from 0 (no similarity) to 1 (identical spectra). It is used in spectral panel design to flag fluorochrome pairs with high similarity and predict them as more risky or likely to interfere with each other during unmixing.
The cosine similarity matrix is generated in the Make Unmixing Matrix task in OMIQ. To learn more on how to use the Make Unmixing Matrix task, please see our article Create and Apply a Spectral Unmixing Matrix.