A camera system uses a highly sensitive camera such as an intensified charge-coupled-device camera to acquire images. An image acquisition and processing tool can place the camera in a low-sensitivity mode and a high-sensitivity mode. In the low-sensitivity mode, a reference image may be acquired of a target that is illuminated by a light-emitting-diode. In the high sensitivity mode, low-photon-flux image data frames are acquired using a charge-coupled-device image sensor in the camera. The image acquisition and processing tool displays the acquired image data frames on top of the reference image in real time, so that a user is provided with immediate visual feedback. The image acquisition and processing tool has image preprocessing filters for enhancing image quality such as a sensor noise threshold filter, a cosmic ray filter, and a photon shape optimization filter. Pipeline filters may be used to further process acquired image data frames.