[OpenSPIM] stitching of OpenSPIM data

[Pavel Tomancak]

Dear Monika,

If you have enough overlap between the tiles and enough memory on your computer you can probably just do it with the SPIM registration plugins. Potentially, better with the new pipeline which is less well documented http://fiji.sc/Multiview-Reconstruction.

Otherwise, register the multi view in one vertical position, fuse. Then do the same in the other vertical position and try stitching this in Fiji (with the Grid/Collection stitching). We did that with LZ1 data, it should work with OpenSPIM too. Note that stitching only makes sense when your images are shifted/translated only. It will not work if they are rotated.

All the best

PAvel
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Pavel Tomancak, Ph.D.

Research Group Leader
Max Planck Institute of Molecular Cell Biology and Genetics in Dresden
Pfotenhauerstr. 108
D-01307 Dresden							Tel.: +49 351 210 2670
Germany									Fax: +49 351 210 2020

tomancak at mpi-cbg.de
http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html
twitter: @PavelTomancak
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On Feb 17, 2015, at 12:01 PM, Monika Pawłowska <m.pawlowska at nencki.gov.pl> wrote:

> Hi,
> 
> I was wondering if anybody made some experience with stitching of OpenSPIM data? In the wiki only time lapses and angles are described, and I'm interested with stitching tiles at different XY positions. I made some attempts with the Grid/Collection stitching plugin of Fiji, but no success so far. Maybe my images are simply not good enough.
> 
> It would be cool to collect the experience about it and made a correspoding wiki page.
> 
> -- 
> Monika Pawłowska
> Nencki Institute
> Laboratory of Neurobiology
> 3, Pasteur Street
> 02-093 Warsaw, Poland
> phone: (+48) 22 5892 427
> 
> _______________________________________________
> OpenSPIM mailing list
> OpenSPIM at openspim.org
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