The pi system of cyanines is electron deficient, so it will not epoxidate easily. Cyanines are not very stable to nucleophiles like alkali, but they can be exposed to electrophilic reagents without problems.

In water-based conditions, olefins are not epoxidized by water unless some special reagent like peroxide is added. The dyes get degraded or excreted from the organism with time, but there is a lot of time to do imaging before it.