[OpenSPIM] [OpenSpim] 4D imaging, slicing

[Pavel Tomancak]

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Pavel Tomancak, Ph.D.

Group Leader
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstr. 108
D-01307 Dresden				Tel.: +49 351 210 2670
Germany						Fax: +49 351 210 2020
email: tomancak at mpi-cbg.de
homepage: http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html
twitter: @PavelTomancak
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Dear Stephanie,

You can use the BigDataViewer right now. Simply launch the Fiji updater, go to advanced mode and select the update site called BigDataViewer. Restart Fiji and you should have a new item in the plugin menu.

You need to save your stacks, SPIM or otherwise, in the HDF5 format. The Export plugins under the BigDataViewer should be self explanatory (for now, documentation is coming).

Once you have your data saved as HDF5, open the newly created xml file (in the directory where your HDF5 database sits) using the OpenXML/HDF5 plugin in the BigDataViewer submenu.

Once in the viewer press F1 or 'h' to get the help menu that explains the keyboard shortcuts.

We know that the documentation is inadequate (a nice way of saying that there is no documentation). We are sorry about it and in fact Tobias is actively working on it and we hope to have it on the Fiji wiki soon.

Hopefully this email will help you in the interim. Don't hesitate to ask if you encounter problems.

And use the BigDataViewer. It is an awesome piece of software.

All the best

Pavel



On Mar 20, 2014, at 6:52 PM, Johannes Schindelin <Johannes.Schindelin at gmx.de> wrote:

> Hi Stephanie,
> 
> On Thu, 20 Mar 2014, Dr S. Hoehn wrote:
> 
>> I am sorry that you where not the right person to address my questions to.
> 
> No worries. The BigDataViewer was developed in the Tomancak lab, the same
> one which is responsible for the hardware part of "OpenSPIM 1.0".
> 
>> I simply thought that one of the programers associated with the openspim
>> platform is working on this new plugin, that is specifically designed
>> for spim data.
> 
> Tobias Pietzsch indeed designed it for SPIM data, but as far as I can
> tell, he is not on the OpenSPIM mailing list.
> 
> Ciao,
> Johannes
> 
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