The present invention relates to methods and systems for labeling, isolating, detecting, and/or enumerating a statistically significant number of biological cells, or other biological analytes of interest, present in a complex matrix sample. The isolation of a biological target of interest from a sample mixture is done by immunomagnetic separation. Upon introduction of the sample within an imaging chamber, the capture complex (biological target-magnetic capture agent) will be attracted by the magnetic field and will lay on the surface of the chamber in the focal plane of the imaging system.