<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><br><div apple-content-edited="true">
<div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div style="color: rgb(0, 0, 0); font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div style="font-size: 12px; ">-----------------------------------------------------------------------------------<br>Pavel Tomancak, Ph.D.<br><br>Group Leader<br>Max Planck Institute of Molecular Cell Biology and Genetics<br>Pfotenhauerstr. 108<br>D-01307 Dresden<span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span>Tel.: +49 351 210 2670<br>Germany<span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span><span class="Apple-tab-span" style="white-space: pre; "> </span>Fax: +49 351 210 2020<br>email: <a href="mailto:tomancak@mpi-cbg.de">tomancak@mpi-cbg.de</a><br>homepage: <a href="http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html">http://www.mpi-cbg.de/research/research-groups/pavel-tomancak.html</a></div><div style="font-size: 12px; ">twitter: @PavelTomancak<br>-----------------------------------------------------------------------------------</div></div><div><br></div></div><br class="Apple-interchange-newline"></div>Dear Stephanie,</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">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.</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">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).</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">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.</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">Once in the viewer press F1 or 'h' to get the help menu that explains the keyboard shortcuts.</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">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.</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">Hopefully this email will help you in the interim. Don't hesitate to ask if you encounter problems.</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">And use the BigDataViewer. It is an awesome piece of software.</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">All the best</div><div apple-content-edited="true"><br></div><div apple-content-edited="true">Pavel</div><div apple-content-edited="true"><br></div><div apple-content-edited="true"><br class="Apple-interchange-newline">
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<br><div><div>On Mar 20, 2014, at 6:52 PM, Johannes Schindelin <<a href="mailto:Johannes.Schindelin@gmx.de">Johannes.Schindelin@gmx.de</a>> wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite">Hi Stephanie,<br><br>On Thu, 20 Mar 2014, Dr S. Hoehn wrote:<br><br><blockquote type="cite">I am sorry that you where not the right person to address my questions to.<br></blockquote><br>No worries. The BigDataViewer was developed in the Tomancak lab, the same<br>one which is responsible for the hardware part of "OpenSPIM 1.0".<br><br><blockquote type="cite">I simply thought that one of the programers associated with the openspim<br>platform is working on this new plugin, that is specifically designed<br>for spim data.<br></blockquote><br>Tobias Pietzsch indeed designed it for SPIM data, but as far as I can<br>tell, he is not on the OpenSPIM mailing list.<br><br>Ciao,<br>Johannes<br><br>_______________________________________________<br>OpenSPIM mailing list<br><a href="mailto:OpenSPIM@openspim.org">OpenSPIM@openspim.org</a><br>http://openspim.org/mailman/listinfo/openspim<br></blockquote></div><br></body></html>