I want to correlate a DAPI stain and a IHC-signal with a TEM-image. Therefore, I used TrakEM2 to manually align the single images. It works, but the alignment is bad. Is it possible to perform a nice automated elastic alignment with adapted parameters too? Has anyone experience with this approach? My coarse alignment is ok, but some DAPI-nuclei are jumping in respect to the TEM-nuclei.