AFAIK if you use Mask R-CNN or Faster R-CNN to detect the small objects, the big images will internally automatically be resized. I saw some min_size(=800) and max_size(=1333) parameters down in the base classes that will make the decision when to scale the image. Unfortunately I did not find a way to change these min_size and max_size parameters without duplicating half of the PyTorch code.
Therefore I think the best way would be to split your image into slightly overlapping patches.
You might be able to speed this up by skipping empty patches with very little pixel contrast (std() of pixels very low).
Since I am very new here I think some pro’s should confirm my advise…