The invention provides a version of fluorescent in situ hybridization (FISH) in which all the steps are performed at physiological temperatures, i.e., body temperature, to detect and identify pathogenic bacteria in clinical samples. Methods of the invention use species-specific fluorescent probes to label clinically important infectious bacteria. A sample such as a urine sample is loaded into a cartridge, fluorescently labeled, and imaged with a microscope. Labelled bacteria are pulled down onto an imaging surface and a dye cushion is used to keep unbound probes off of the imaging surface. A microscopic image of the surface shows whether and in what quantities the infectious bacteria are present in the clinical sample.

A reagent cartridge includes a cartridge body configured to store a solid reagent, the cartridge body having a reagent well accessible through an access port. A seal plate is proximate the access port, the seal plate extends away from the access port to a seal plate edge remote from the access port. The reagent cartridge includes an isolation envelope surrounding the reagent well. The isolation envelope includes a seal membrane covering the access port, at least one isolation wall, and at least one isolation cavity interposed between the isolation wall and the well sidewall. One or more reagent cartridges are received in a cartridge magazine. The cartridge magazine includes at least one complementary profile seat configured to receive the one or more reagent cartridges having a corresponding cartridge profile.