FIELD: medicine.SUBSTANCE: group of inventions relates to detection of microorganisms. Assembly for preparing a specimen for determining the presence of at least one microorganism species in the specimen, the assembly comprising a pipette configured to collect a specimen from a sample, wherein the pipette comprises an inlet, a sampling chamber and a shaft located therebetween; as well as an imaging cartridge configured to connect to the pipette so as to form a biologically isolated system. Imaging cartridge comprises a pipette dock, configured to(a) at least partially hold the pipette shaft and (b) connect with the pipette so as to form a fluid seal through (I) a threaded connection, (II) a snap connection, (III) a fit, (IV) a toothed mechanism, (V) a retaining washer and retainer or (Vi) clamping washers in the shape of a "star". Imaging cartridge for sample preparation is also disclosed, as well as a sample preparation method for determining the presence of at least one type of microorganism in the sample.E
