TrakEM2; CLEM alignment


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.

Hi @CaDi,

I know one group that has had a good experience in using Bigwarp for manual CLEM alignment. Perhaps consider giving it a try.


PS. Iā€™m the author of Bigwarp, so please post back if you have any questions / issues.


You might also want to check out ec-CLEM, a plugin for Icy.

Align multidimensional images in 2D or 3D, rigidly or with warping, whatever the difference in scale. Provide also a set of tools for Correlative Light Electron Microscopy, but can be used for registration/alignement of any correlative imaging.



thank you for your answers, I started some alignments using Bigwarp and eC-CLEM.

Best regards,