[OpenSPIM] Zebra fish SPIM imaging

[edgar.escobar.nieto at ipt.fraunhofer.de]

 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 
_________________________________________________________________________ 
 
  
 
 
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