Hi all,
I have some 20x images acquired with AxioScan 7 that are showing breaks in the overlap. The stitches are set at 20% at the moment.
What’s the best approach to improving the stitching? Is it reasonable to expect better raw images from our imaging centre, or is this normal and should be improved using post-hoc touch-ups and plug-ins?
Thanks in advance.
Looks like the red channel is somewhat diffuse staining, it could be that the low contrast leads to the stitching issues.
If I recall correctly the stitching is done on the first channel imaged (or the focus reference?), perhaps changing the acquisition order dapi>whatever is in red will already lead to better results (don’t quote me on this one), when using '“online” stitching (default).
There is also the ‘‘offline’’ and ‘‘fuse active’’ options under ‘online-processing’ that may improve the stitching results.
You can also restitch post-acquisition with zen, and then only select the channel with good/best contrast.
There is some additional info on post-acquisition stitching in the post below:
I’ll look into those options! And thank you for linking the thread that solved this issue earlier, I must have missed it when browsing the forum. I really appreciate it!
