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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thank you Stephan for your speedy response.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I do downsample x4 in xy when defining the beads… Does this downsampling continue through to the alignment and MV decon too? If so, would the output image be 2.56 um instead?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Assuming the above, should I only use downsampling when I’m checking that the alignment will work, but then start fresh without downsampling to attain the full resolution?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks again for your time.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Neil<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> Stephan.Preibisch@mdc-berlin.de [mailto:Stephan.Preibisch@mdc-berlin.de]
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<b>Sent:</b> Friday, August 05, 2016 4:47 AM<br>
<b>To:</b> openspim@openspim.org<br>
<b>Cc:</b> Pavel Tomancak <tomancak@mpi-cbg.de>; Anthony, Neil <nantho2@emory.edu><br>
<b>Subject:</b> Re: [OpenSPIM] Multiview deconvolution - output image scaling<o:p></o:p></span></p>
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<p class="MsoNormal">Hi, by default the resolution of the output image is equal to the highest resolved dimension, so in your case 0.64x0.64x0.64 um. If you, however, manually apply any scaling during the alignment process it can be different.
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<p class="MsoNormal">All the best,<o:p></o:p></p>
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<p class="MsoNormal">Stephan<o:p></o:p></p>
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<p class="MsoNormal"><span style="color:black">---<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Dr. Stephan Preibisch<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Group Leader<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Berlin Institute of Medical Systems Biology of the MDC<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">Building 89, 1.08b<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="color:black">email:<span class="apple-converted-space"> </span><a href="mailto:stephan.preibisch@mdc-berlin.de">stephan.preibisch@mdc-berlin.de</a><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:black">web: <a href="http://fly.mpi-cbg.de/preibisch">http://www.preibisch.net/</a><o:p></o:p></span></p>
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<p class="MsoNormal">On 05 Aug 2016, at 08:55, Pavel Tomancak <<a href="mailto:tomancak@mpi-cbg.de">tomancak@mpi-cbg.de</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">FYI<o:p></o:p></span></p>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">From: </span>
</b><span style="font-family:"Helvetica",sans-serif">"Anthony, Neil" <<a href="mailto:nantho2@emory.edu">nantho2@emory.edu</a>><br>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">Subject: [OpenSPIM] Multiview deconvolution - output image scaling</span></b><span style="font-family:"Helvetica",sans-serif"><br>
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</span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">Date: </span>
</b><span style="font-family:"Helvetica",sans-serif">August 4, 2016 5:06:15 PM GMT+02:00<br>
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<p class="MsoNormal"><b><span style="font-family:"Helvetica",sans-serif">To: </span>
</b><span style="font-family:"Helvetica",sans-serif">"<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>" <<a href="mailto:openspim@openspim.org">openspim@openspim.org</a>><br>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Hi guys, I hope the scope are treating you well.<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">I was wondering what the output image scaling is after the Multiview deconvolution. I provide the input image scaling of 0.64 x 0.64 x 3 um, and I’m assuming after the different
angles have been factored in the output would have a more isotropic scaling…?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Does anybody know where to find that information?<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Thanks<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">Neil<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> <o:p></o:p></span></p>
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