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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Here is what I have found to work with our Z1 data:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">The newest version of Bioformats can read and open the .CZI file off the microscope. As Bioformats opens the file, it opens each view as a separate stack and
gives you the option of which ones you want to open. As long as your system has enough RAM, you can open individual, or all views, and then convert to .tif using Fiji. If any of the views exceed your RAM, you will have to open them as a virtual stack, convert
to .tif and downsample before running the registration/fusion plugins.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If your data was subsetted in ZEN by anything other than time (channel/view/etc) during acquisition, it will not open in Bioformats.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Bioformats still seems to have problems reading certain multi-channel files. I have sent them some test data sets, but haven’t heard back yet.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">When all-else fails, the following protocol seems to work:<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">1)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">Subset your original file into individual .czi files for channel and view (don’t worry about time point). Do this using the Processing<Copy<File
Subset command in ZEN, NOT File<New File Browser.<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">2)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">You can then batch convert these .CZI files to .tif files using Fiji.<o:p></o:p></span></p>
<p class="MsoListParagraph" style="text-indent:-.25in;mso-list:l0 level1 lfo1"><![if !supportLists]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><span style="mso-list:Ignore">3)<span style="font:7.0pt "Times New Roman"">
</span></span></span><![endif]><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">These files can then be registered/fused/deconvolved<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">If anyone has other/better suggestions, I’d be happy to hear them.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D">-Doug<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">From:</span></b><span style="font-size:10.0pt;font-family:"Tahoma","sans-serif""> openspim-bounces@openspim.org [mailto:openspim-bounces@openspim.org]
<b>On Behalf Of </b>Selchow, Olaf<br>
<b>Sent:</b> Sunday, June 15, 2014 12:35 PM<br>
<b>To:</b> Kieran Short; Shugi@gmx.de<br>
<b>Cc:</b> openspim@openspim.org<br>
<b>Subject:</b> Re: [OpenSPIM] Input data for SPIM Registration PlugIn<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Arial","sans-serif"">Dear Kieran and Ricarda,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE" style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span 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 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 style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span 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 style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span 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 style="font-size:10.0pt;font-family:"Arial","sans-serif""><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">With best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:10.0pt;font-family:"Arial","sans-serif"">Olaf<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="DE" 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 lang="DE" 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 lang="DE" style="font-size:9.0pt;font-family:"Calibri","sans-serif";color:black"><br>
</span><span lang="DE" 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 lang="DE" 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 lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif";color:black"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">Von:</span></b><span lang="DE" style="font-size:10.0pt;font-family:"Tahoma","sans-serif"">
<a href="mailto:openspim-bounces@openspim.org">openspim-bounces@openspim.org</a> [<a href="mailto:openspim-bounces@openspim.org">mailto:openspim-bounces@openspim.org</a>]
<b>Im Auftrag von </b>Kieran Short<br>
<b>Gesendet:</b> Dienstag, 27. Mai 2014 23:19<br>
<b>An:</b> <a href="mailto:Shugi@gmx.de">Shugi@gmx.de</a><br>
<b>Cc:</b> <a href="mailto:openspim@openspim.org">openspim@openspim.org</a><br>
<b>Betreff:</b> Re: [OpenSPIM] Input data for SPIM Registration PlugIn<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="DE">Richard,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="DE">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></span></p>
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<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="DE">fyi: <a href="http://en.wikipedia.org/wiki/Endianness">http://en.wikipedia.org/wiki/Endianness</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="DE">cheers,<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE">Kieran<o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><span lang="DE"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="DE">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></span></p>
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<p class="MsoNormal"><span lang="DE" 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 lang="DE" style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE" 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 lang="DE" style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE" 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 lang="DE" style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE" 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 lang="DE" 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 lang="DE" style="font-size:9.0pt;font-family:"Verdana","sans-serif""> <o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE" 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 lang="DE" 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"><span lang="DE"><br>
_______________________________________________<br>
OpenSPIM mailing list<br>
<a href="mailto:OpenSPIM@openspim.org">OpenSPIM@openspim.org</a><br>
<a href="http://openspim.org/mailman/listinfo/openspim" target="_blank">http://openspim.org/mailman/listinfo/openspim</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="DE"><o:p> </o:p></span></p>
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