A MEMS-based cell sorting system is disclosed, which uses a novel combination of features to accomplish the cell sorting in the microfabricated channels housed in a disposable cartridge. The MEMS-based cell sorting system may include a microfabricated cell sorting valve that is responsive to an applied magnetic field. The MEMS-based cell sorting system may further include an electromagnet that generates a magnetic field to actuate the microfabricated cell sorting valve. The electromagnet may have a design which allows it to create a very localized magnetic field while having adequate thermal properties to operate reliably.