[OpenSPIM] stitching of OpenSPIM data

[Monika Pawłowska]

Thanks, I didn't realize that stitching is possible with SPIM plugins as  
well.

It turns out that the problem was the ome.tiff format - Fiji was reading  
all the files and starting the calculation, but never getting the right  
result, after conversion to .tif my test images worked.

Regards,
Monika

W dniu .02.2015 o 12:28 Pavel Tomancak <tomancak at mpi-cbg.de> pisze:

> 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
> --------------------------------------------------------------------------------------------------
> 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
> --------------------------------------------------------------------------------------------------
>
>
> 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
>> http://openspim.org/mailman/listinfo/openspim
>



-- 
Monika Pawłowska
Nencki Institute
Laboratory of Neurobiology
3, Pasteur Street
02-093 Warsaw, Poland
phone: (+48) 22 5892 382
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