Silica nanoparticles with dyes-encapsulated has been characterized by TEM and DLS, which were employed in biological applications with A. castellanii. Amoebae have pathogenic properties that can cause sight-threatening keratitis and granulomatous encephalitis. Phagocytosis of dye-covalently encapsulated in silica nanoparticles has shown promise in vitro and could be employed in vivo for detection. Time-dependent analysis of the SiNPs and A. castellanii displays micrographs of cellular components in the process of endocytosis and exocytosis. Alive and potentially deceased investigation of A. castellanii with SiNP uptake was evaluated to indicate detection with altered variables. Spectroscopic analyses were conducted on NIR dyes that will be essential for nanoparticle synthesis for in vivo and in vitro imaging.