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Try out m2stitch for general mosaic tile stitching #383
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Checking out m2stitch and https://github.com/labsyspharm/ashlar have long been on my to-do list. BTW, has stitching always been the default? I know I was adding FALSE programmatically, but I don't remember that behavior in |
Nope, The
Agree. I think there is room for a parameter that informs how to stitch and we can use it to switch between algs.
You could do this today if you wanted to now that we are storing the |
..but this would still be FYI, while playing with this I can confirm the LIF mosaics are still not correct—for my samples—see: #278 For the plugin, some more ideas maybe from here:
More from @VolkerH using dask: |
Gotcha. I don't really have time to dive deep into this right now. So anyone looking at this thread and wanting to take a stab at it, feel free. |
This would be super helpful. Many of the image data I work with have actually been stitched at the microscope on acquisition so the quick'n'dirty approach would be exactly what I need. |
This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions. |
Use Case
Please provide a use case to help us understand your request in context
We have a whole host of open issues about mosaics not being correct so going to use this single issue as a higher level "what can we do to solve a bunch of them."
Solution
Please describe your ideal solution
From napari conversation, m2stitch looks like a pretty good option. I got it almost working in ~30 minutes:
The compute time is much longer than ours because it is actually doing boundary checking / overlap, and which tile should overlap which other tile, and so on, where as in a lot of cases we are simply just shoving tiles one next to each other.
If we can offload tile stitching to a library that would be better imo, even if slower because that single libary may get faster with time.
Notes
While working on this, I realized that I think a part of the problem with our current workflow is that
AICSImage
defaults to stitching the mosaic image. I think in the future (in the v5 update??) it may be good to haveAICSImage
separate out the functionality from "default behavior" as to not confuse users as to "why is it taking so long to load this image".An example of this may be:
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