The RatCAP has been designed and constructed to image the awake rat brain. In order to maximize system performance, offline digital coincidence data processing algorithms including offset delay correction and prompt and delayed coincidence detection have been developed and validated. With offset delay correction using a singular value decomposition (SVD) technique, overall time resolution was improved from 32.6 to 17.6 ns FWHM. The experimental results confirm that the ratio of prompts to randoms was improved because a narrower timing window could be used. 18 F-fluoride rat bone scan data were reconstructed using our fully 3-D ML-EM algorithm with a highly accurate detector response model created from Monte Carlo simulation.