A nuclear imaging system includes a crystal identification system which receives a flood image which includes a plurality of peaks, each peak responsive to radiation detected by a corresponding scintillator crystal. A crystal identification processor partitions the flood image into a plurality of candidate regions with a watershed segmentator implementing a watershed algorithm. The candidate regions are linked in an adjacency graph, and then classified as background or relevant, where relevant regions contain a peak within the watershed lines. The regions are then assigned to a crystal according to an objective function and an assignability score. A calibration processor maps the peaks to a rectangular grid.