Methods and cartridges for detecting targets are provided. A biological sample is introduced to a cartridge. Targets in the sample are photonically labeled with fluorescent particles in a first liquid layer in the cassette. Photonically-labeled targets are separated out of the sample into a second liquid layer within the cassette, detected, and counted to show presence of the targets in the subject. Cartridges include a receiving reservoir, a mixing well for introducing the sample to photonic labels and magnetic particles, and an imaging well for detecting and counting targets from the sample. The sample may be a human stool sample. A filter may be used to filter particulates out of the sample.