Our team is happy to share a whole slide image registration workflow that can reach cellular resolution over a large area (an area that typically requires more than an affine transformation). We bridge QuPath, Fiji (in particular BigWarp) and elastix, in an attempt to merge these 3 worlds.
Briefly, a Project is defined in QuPath, and can be opened in Fiji to be registered either automatically, manually (BigWarp), or semi-automatically (BigWarp is used to correct the result of the automated registration). The resulting transformation is saved in a QuPath Project folder as a JSON transformation file, which QuPath can then retrieve and use to transfer and transform PathObjects (annotations and detections) from one image to another, in one direction or the other.
The full documentation of the workflow can be found here, as well as some video tutorials:
It’s still quite experimental and the UI lacks polishing, but things should work. If you find this useful, we’re happy to get your feedback and issues on the forum,