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<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Dear Kieran and Ricarda,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif"">To my knowledge, the export of .czi data from the ZEISS Lightsheet Z.1 should be not necessary any more.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif"">The .czi data can be read directly by Bioformats reader into Fiji …<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif"">Kevin Eliceiri and Stephan Preibisch are the experts in this …
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif"">Pls let me know if I can help in that data from ZEISS microscopes can be opened in the software where you need it.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif"">With best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif"">Olaf<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:black">__________________________<br>
<br>
Carl Zeiss Microscopy GmbH<br>
Geschäftsbereich BioSciences / BioSciences Division<br>
Produktmanager / Product Manager<br>
<br>
D r. O l a f S e l c h o w<br>
<br>
Carl-Zeiss-Promenade 10, 07745 Jena<br>
Telefon/Phone: +49 3641 64-2089<br>
Cell Phone: +49 151 4615 8629<br>
Fax: +49 3641 64-3144<br>
</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><a href="mailto:olaf.selchow@zeiss.com" target="_blank"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:purple">mailto:olaf.selchow@zeiss.com</span></a></span><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:black"><br>
</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><a href="http://www.zeiss.com/microscopy" target="_blank"><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:purple">http://www.zeiss.com/microscopy</span></a></span><span style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:black"><br>
<br>
__________________________<br>
<br>
Carl Zeiss Microscopy GmbH<br>
Vorsitzender des Aufsichtsrates: Dr. Michael Kaschke <br>
Geschäftsführung: Dr. Ulrich Simon, Wilhelm Nörthemann, Dr. Frank Stietz<br>
Sitz der Gesellschaft: 07740 Jena, Deutschland <br>
Amtsgericht Jena, HRB 210.536, USt-IdNr: DE 814 503 774</span><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> openspim-bounces@openspim.org [mailto:openspim-bounces@openspim.org]
<b>Im Auftrag von </b>Kieran Short<br>
<b>Gesendet:</b> Dienstag, 27. Mai 2014 23:19<br>
<b>An:</b> Shugi@gmx.de<br>
<b>Cc:</b> openspim@openspim.org<br>
<b>Betreff:</b> Re: [OpenSPIM] Input data for SPIM Registration PlugIn<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Richard,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">The endianness of the TIFF data might be wrong (wrong byte order). Try switching to intel-byte order (or if it already is, switch it to big endian).<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">fyi: <a href="http://en.wikipedia.org/wiki/Endianness">http://en.wikipedia.org/wiki/Endianness</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">cheers,<o:p></o:p></p>
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<p class="MsoNormal">Kieran<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><o:p> </o:p></p>
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<p class="MsoNormal">On Tue, May 27, 2014 at 8:19 PM, <<a href="mailto:Shugi@gmx.de" target="_blank">Shugi@gmx.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Hello,<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">I read about your tool for registration and fusion of multiple view images. It is the topic of my intership to find a way doing this with our data and I would like to try
your tool. But it seems to have a problem with our data. The original data from a Z1 are present as czi file. I extract them as ome.tif file with the ZEN2012 Software. Like in the tutorial the extension was changed from ome.tif to tif. I was following the
tutorial and when to interactivlly choosing the threshold for the beads and click "Done" the following Messages occure in the Log:<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Opening first image to determine z-stretching.<br>
Cannot open fie: ...<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">The path and the filename are correct. Maybe it is something about the formate? Do you need special tags in the tiff file or does the bit depth has influence?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Hope you can help me, because your tool seems to be very promising.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Kind regardas<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Verdana","sans-serif"">Ricarda Bräuniger<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><br>
_______________________________________________<br>
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<a href="http://openspim.org/mailman/listinfo/openspim" target="_blank">http://openspim.org/mailman/listinfo/openspim</a><o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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