Posted by
Johannes Schindelin on
URL: http://confocal-microscopy-list.275.s1.nabble.com/Aligning-large-stacks-tp7581843p7581845.html
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Hi TF,
On Wed, 2 Apr 2014, Feinstein, Timothy wrote:
> Elements has an alignment feature built in but it does not produce great
> results from very large images (e.g. 4096 ^2 and up). I have tried the
> registration plugins menu in Fiji and my current favorite, StackReg, can
> produce solid results. Rigid body registration seems to do the job most
> of the time. On the other hand its progress bar is not very helpful and
> some alignments can take overnight to all weekend, if they work.
>
> So I thought it would help to throw this out to those of you who do this
> more often – do you have a favorite workflow for big-job registrations?
> Do you have a favorite freeware, Matlab plugin or paid option for these
> big jobs? Should I stop stitching the images and let the coded stage
> handle alignment on its own?
I had some very good experiences with "Linear Stack Alignment with SIFT"
in Fiji a little over a year ago. My problem was small enough to run
completely in computer RAM, though. And the parameters had to be adjusted
to the images of course.
I also heard that XuvTools (
http://www.xuvtools.org/) is supposed to work
quite well, but I never tried (I wanted to, and since it claims to be Open
Source, I wanted to inspect how it does it in true scientific fashion, but
you have to ask for permission to see the source code -- which is actually
not Open source -- so I did not). Your mileage may vary.
Hope this helps!
Johannes