Trouble with Fine Image Rotation After Export


I’m having some trouble finding a way to rotate my image so that my image remains rotated after exporting. Oftentimes, certain brain images on our slides are off by maybe ~15 degrees, and it would be great if there were a way in QuPath to rotate specific portions of the entire image without needing another program. Thank you so much!

Aligning the data is going to be more accurate, in general, than aligning the slice due to the “square grid” nature of pixels. If you rotate an image 15 degrees, you have a lot of weird pixel overlap to resolve back into that grid that can be presented on screen. Resolving this issue is the work of many papers and different methods.

Meanwhile, rotating the annotation can be a relatively simple affine transformation.

As you have probably already seen, you can visually overlap two of the brains with a 15 degree angle and take a viewer snapshot of that, if desired, but exporting an image with a non-90 degree rotation is likely to be a bit more involved!