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The three-volume set LNCS 6361, 6362 and 6363 constitutes the refereed proceedings of the 13th International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2010, held in Beijing, China, in September 2010. Based on rigorous peer reviews, the program committee carefully selected 251 revised papers from 786 submissions for presentation in three volumes. The second volume includes 84 papers organized in topical sections on ultrasound imaging, neuroimage analysis, simulation of anatomical structures, endoscopic and microscopic imaging, and image registration.