A system for image inpainting of in-vivo images includes at least one processor and at least one memory storing instructions. The instructions, when executed by the processor(s), cause the system to access an in-vivo image of a portion of a gastrointestinal tract where the in-vivo image includes image regions to be reconstructed, process the in-vivo image by a trained image inpainting deep learning model to provide a reconstructed in-vivo image, and provide the reconstructed in-vivo image to a device for viewing by a medical professional.