In situ optical analysis of bacterial endospores can be inhibited when the endospores are present within an optically active carrier medium. To help isolate the endospores from the carrier medium, in some examples, the carrier medium is passed through a hydrophobic material that captures the endospores via hydrophobic attraction. Subsequently, a germination fluid and lanthanide source, such as terbium, can be added to the bacterial endospores captured on the hydrophobic material to form a lanthanide-dipicolinic acid complex in the germination fluid. The germination fluid can then be optically analyzed by measuring the fluorometric response of the lanthanide-dipicolinic acid complex to determine a concentration of the bacterial endospores in the carrier medium.