The present invention provides methods and apparatuses for detecting, measuring, or locating cells or substances present in even very low concentrations in vivo in subjects, using targeted magnetic nanoparticles and special magnetic systems. The magnetic systems can comprise magnetizing subsystems and sensors subsystems, including as examples SQUID sensors and atomic magnetometers. The magnetic systems can detect, measure, or location particles preferentially internalized by cells due to the action of antibodies, proteins, macromolecules, or nutrients required for cellular metabolism. Example magnetic systems are capable of detecting sub-nanogram amounts of these nanoparticles.
