A system and method for generating a digital image in fluorescence gel imaging is disclosed. The method includes providing a gel sample and placing the gel sample on a flat panel detector having array of photodiodes and transistors that collect light generated from the gel sample. The gel sample is illuminated using a light source integrated into the flat panel imaging system and light emitted by the gel sample responsive to an excitation of the gel sample by light provided by the light source is then collected, with the light emitted by the gel sample being collected by the array of photodiodes of the flat panel detector and converted to electric charges to generate light data. The light data is then processed to generate a digital image of the gel sample.