Hi,
I have IHC staining on 2-3 serial FFPE tissue sections. I did my best to take pictures of the same regions on a brightfield microscope but I'd like to be able to align each section into a single overlay/stack (kind of like a z-stack) at the resolution of hematoxylin-stained nucleiii. Does anyone have any tips on how to do this somewhat easily in Image J/Fiji? Thank you in advance for your help!
Best
Adam
Have you tried using Cell profiler?, it has a module for automatic Align of pictures assuming that some features can correspond to each other...
You can try CombineZP software for a 'quasi'-stack. It is software which you can download for FREE.
Peter
Dear Adam,
you should try the StackReg plugin (http://bigwww.epfl.ch/thevenaz/stackreg/) I do thing that is what you are looking for.
Best Soenke
Hi Adam,
Were you ever able to solve this issue? I'm attempting to do the same thing myself and I came across your question.
Matt
This is one of the things you can do quickly with the ImageJ plugin TrakEM2 in Fiji. You can overlay layers using different color channels and then use an interactive tool to warp one image to fit the other using as many control points as you want to spend. If the images look reasonably similar, you could also let TrakEM2 do the alignment for you.
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