It's all about the number of labels, not the number of images. A proportion of the images should be close up, high resolution, but, quite possibly, a large number can be lower resolution, so I decided to include photographs of the seedlings in groups of 9 as below:

This reduces image processing times in that we get 9 labelled objects for one cropped photo and labeling itself is quicker as 'selecting image time' is reduced.
The new, lower resolution images can now be uploaded to DIGITS and we can test the deployment success on the actual seed beds as before and check for false positives etc.