The Millipore Smartflare kits use Cy3 and Cy5 as fluorescent tags and thus Cy3 can be analyzed on a Muse for those Users without access to a Yellow-Green (561nm) laser. There are over 50 different mRNA biologically specific kits available. The technology employs a gold nanoparticle taht when unbound to it's target quenches the Cy3 (or Cy5) conjugated to the gold particle, see figure below.
Excitation & Emission of Smartflares
Muse Kit Results