An image processing system includes an interface to which an annotation result on a learning image captured inside a living body is input and a processor including hardware. The processor acquires metadata including difficulty information indicating difficulty of the annotation of the learning image itself, determines reliability information indicating reliability of the annotation result based on the metadata, and outputs a dataset in which the learning image, the annotation result, and the reliability information are associated with each other, as data used in generating a trained model used in inference based on deep learning on an inference target image captured inside a living body.