[OpenSPIM] Zebra fish SPIM imaging

[Pavel Tomancak]

Hi Edgar,

Ok, I thought its something like that. Definitely use more beads and smaller diameter.

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 Oct 25, 2013, at 9:35 AM, edgar.escobar.nieto at ipt.fraunhofer.de wrote:

> Dear Pavel,
> 
> The data is a tiling across a large field of view, for the stitching I used the Grid/Collection Stitching plugin from
> Fiji, it works perfectly. So I will buy the 0.5 um beads that are recommended in the OpenSPIM wiki and have a greater concentration. This image was only a test with the beads that we have already available. Thanks a lot for your update.
> 
> Kind regards,
> Edgar
> 
> 
> _________________________________________________________________________
> 
> Fraunhofer-Institut für Produktionstechnologie IPT 
> Edgar Escobar Nieto 
> 
> 
> 
> 
> Steinbachstraße 17 
> 52074 Aachen 
> 
> edgar.escobar.nieto at ipt.fraunhofer.de 
> http://www.ipt.fraunhofer.de 
> _________________________________________________________________________ 
> 
> 
> 
> 
> 
> -----Pavel Tomancak <tomancak at mpi-cbg.de> schrieb: -----
> An: edgar.escobar.nieto at ipt.fraunhofer.de
> Von: Pavel Tomancak <tomancak at mpi-cbg.de>
> Datum: 24.10.2013 20:04
> Kopie: "openspim at openspim.org" <openspim at openspim.org>
> Betreff: Re: [OpenSPIM] Zebra fish SPIM imaging
> 
> Dear Edgar,
> 
> I am not sure I understand what you did. How did you stitch them together? Is this multi-view (angle) data or a tiling across a large field of view?
> 
> In any case you most likely do not have enough beads in there. I would say you need ten times more.
> 
> Your beads are gigantic, 2um, we use much smaller beads typically.
> 
> Let me know more details and I am sure we can work it out.
> 
> 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 Oct 24, 2013, at 5:38 PM, edgar.escobar.nieto at ipt.fraunhofer.de wrote:
> 
>> Hi dear All,
>> 
>> I have made some imaging of a zebra fish that expresses GFP fluorescence with a heat shock, I have gotten 25 stacks (5x5) and stitched it together.
>> 2 µm green beads were embedded  to the agarose and I think that the beads signal is good in contrast to the signal of the fish. 
>> 
>> I would like to know if with the concentration of beads that could be appreciated in the Z projection and the video of the scanning of the resulting stack
>> is enough to perform multiview fusion.
>> 
>> https://www.dropbox.com/s/sooicfk68iszq3m/Fused_linear%20blending_18fps.avi 
>> https://www.dropbox.com/s/q98akotaynltbvc/Fused_linear%20blending_z%20projection.tif
>> 
>> Thanks in advance for your comments.
>> 
>> Kind regards,
>> Edgar
>> _________________________________________________________________________
>> 
>> Fraunhofer-Institut für Produktionstechnologie IPT 
>> Edgar Escobar Nieto 
>> 
>> 
>> 
>> 
>> Steinbachstraße 17 
>> 52074 Aachen 
>> 
>> edgar.escobar.nieto at ipt.fraunhofer.de 
>> http://www.ipt.fraunhofer.de 
>> _________________________________________________________________________ 
>> 
>> 
>> 
>> _______________________________________________
>> OpenSPIM mailing list
>> OpenSPIM at openspim.org 
>> http://openspim.org/mailman/listinfo/openspim
> 

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