Alignment
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Ved Sharma
Jul 30, 2018, 12:18:17 PM7/30/18
to QuPath users
Hi,
I'm new to QuPath and still exploring its features. I was hoping if someone can guide me in the right direction.
I have two consecutive tissue sections, one stained with IHC and the other one with fluorescence. I was wondering if it is possible to align these two slides in QuPath, based on pairs of user-selected manual landmarks in the two slides.
Thanks,
Ved
micros...@gmail.com
Jul 30, 2018, 12:23:48 PM7/30/18
to QuPath users
That actually comes up quite a bit. The answer is not really. Further reading here: https://github.com/qupath/qupath/issues/178
Pete
Jul 30, 2018, 12:29:24 PM7/30/18
to QuPath users
Hi, I'm afraid not currently - this functionality would need to be created. Currently, you can only view the consecutive sections side-by-side, and potentially transfer annotations between them... although this is only likely to be very meaningful/useful if you have already registered the images in some other software, and written out whole slide images that are 'perfectly' aligned.
In the case that you have smaller images - or are willing to work with cropped regions from larger whole slide images - then some of the registration tools in Fiji might help.
Some places where this topic is discussed:
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