Disclosed is a system using a large area flat panel imager which is specifically adapted for rare cell detection methods. The system generally includes an imager having a sample receiving surface which can provide a digital or electronic image of a sample deposited on the surface. The system also includes a selectively positionable microscope and/or camera which are used to obtain high resolution images of the deposited samples. An electronic controller can also be used in conjunction with the imager, microscope, and/or camera to selectively position at least one of those components to focus on desired regions of the deposited sample. The noted system is particularly adapted for use with chemiluminescence or other tagging technologies.