This two-volume set LNCS 15829-15830 constitutes the proceedings of the 29th International Conference on Information Processing in Medical Imaging, IPMI 2025, held on Kos, Greece, during May 25-30, 2025. The 51 full papers presented in this volume were carefully reviewed and selected from 143 submissions. They were organized in topical sections as follows: Part I: Classification/Detection; Registration; Reconstruction; Image synthesis; Image enhancement; and Segmentation. Part II: Computer-aided diagnosis/surgery; Brain; Diffusion models; Self-supervised learning; Vision-language models; Shape analysis; and Time-series image analysis.