Oh, wait. The posted image is the result of your model, not the reconstructed pictures using the patches?
If so, I misunderstood this particular issue.



 banikr:

or shall I try overlapping patches and do intensity averaging in overlapping regions?


That would be a reasonable approach. The original UNet paper also used overlapping windows with good segmentation results. This is of course different to your approach, but I would assume it should smooth the image better.