Tissue align with multiple IF Panels

Hi all,

I have serial tissue sections stained with different immunofluorescent marker combinations and I was wondering if there is a way of aligning the sections to visualise both panels at once? I have tried to use the tissue align feature without much luck. I am quite new to this and my programming skills are fairly basic.

Any tips would be highly appreciated!

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.

Random second thought. But if you have a DAPI or similar channel in each, and it is consistent, you might be able to detect cells in the image, convert the cells into points


and then align by points.

I have not tried this, just a thought.