Nice coincidence, but I am planning on writing up a post soon about some of my thoughts on tissue align, and some use cases. I haven’t done anything with IF, though.
Could you explain in more detail what you have tried, and what problems you have run into, exactly? It’s hard to target anything to “without much luck” I am afraid. If you are able to provide any two IF images to align, I would be interested in taking a look, and potentially even using it as part of the post if there are problems specific to IF images.
There is a massive 100ish post thread on the topic here:
If using the automatic alignment, I would probably start with Points or Annotations you create in each image. Not sure how the alignment handles multichannel intensity.