1. A method for using an image acquisition and processing tool implemented on a computer system to analyze a target in a camera system that has a light-tight enclosure surrounding the target, a reference light source, and a camera, the method comprising: turning the reference light source on to illuminate the target with the reference light source; using the image acquisition and processing tool to place the camera in a low-sensitivity mode; while the camera is in the low-sensitivity mode and while the target is illuminated with the reference light source, acquiring a reference image of the target; using the image acquisition and processing tool to place the camera in a high-sensitivity mode; turning the reference light source off; while the camera is in the high-sensitivity mode and while the reference light source is off, acquiring low-photon-flux image data frames with the camera that contain photons received from the target and that contain noise signals, wherein the image data frames are acquired with the camera at a frame rate that is sufficiently fast to ensure that the photons are individually resolved within each acquired image data frame; processing the acquired image data frames to remove the noise signals while retaining the individually resolved photons; and displaying the processed acquired image data frames in real time in combination with the acquired reference image.