TrakEM2: Globally optimized registration

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TrakEM2: Globally optimized registration

André Pereira
Hi everyone,

In order to save computational time, I'm trying to do two levels of image stitching: intra- and inter-region.

The intra-region stitching correction patterns are consistent in all regions, however the alignment between regions is not.
I was wondering if, after obtaining all the pair corrections, there is a scripting function that performs the globally optimized registration with the least squares method, as described in Preibisch et al., Bioinformatics 2009?

Thank you for your help, in advance.

All my best,
Andre Pereira

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Re: TrakEM2: Globally optimized registration

Stephan Preibisch
Hi Andre,

not really, but it is relatively straight forward to implement it using the mpicbg module available on github: https://github.com/axtimwalde/mpicbg <https://github.com/axtimwalde/mpicbg>

Just orient yourself on the code that is used in the Stitching: https://github.com/fiji/Stitching/blob/master/src/main/java/mpicbg/stitching/GlobalOptimization.java <https://github.com/fiji/Stitching/blob/master/src/main/java/mpicbg/stitching/GlobalOptimization.java>

Hope this helps,
Stephan
---

Dr. Stephan Preibisch
HFSP Fellow
Robert H. Singer / Eugene Myers lab

Albert Einstein College of Medicine / HHMI Janelia Farm / MPI-CBG

email: [hidden email] <mailto:[hidden email]> / [hidden email] <mailto:[hidden email]> / [hidden email] <mailto:[hidden email]>
web: http://www.preibisch.net/ <http://fly.mpi-cbg.de/preibisch>

> On Apr 6, 2015, at 14:19 , Andre Pereira <[hidden email]> wrote:
>
> Hi everyone,
>
> In order to save computational time, I'm trying to do two levels of image stitching: intra- and inter-region.
>
> The intra-region stitching correction patterns are consistent in all regions, however the alignment between regions is not.
> I was wondering if, after obtaining all the pair corrections, there is a scripting function that performs the globally optimized registration with the least squares method, as described in Preibisch et al., Bioinformatics 2009?
>
> Thank you for your help, in advance.
>
> All my best,
> Andre Pereira
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html


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