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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Dear all,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Thank you all for your answers! The command:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">tif2mrc name*.tif name.mrc worked for me to solve my last problem.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">After that I ran the newstack command to create the *.st file.
<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">NEW PROBLEM:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">However, since there is no original header with the Saxton tilt angles (the images are completely computer generated tiff:s), I created the com scripts
in the terminal in the following way:<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">copytomocoms -angles -70.0000,-69.3432,-68.2310,-67.0623,-65.8346,-64.5457,-63.1933,-61.7750,-60.2886,-58.7320,-57.1031,-55.4001,-53.6213,-51.7652,-49.8305,-47.8165,-45.7226,-43.5487,-41.2952,-38.9630,-36.5535,-34.0687,-31.5114,-28.8849,-26.1933,-23.4410,-20.6336,-17.7770,-14.8777,-11.9427,-8.9795,-5.9959,-3.0000,0,3.0000,5.9959,8.9795,11.9427,14.8777,17.7770,20.6336,23.4410,26.1933,28.8849,31.5114,34.0687,36.5535,38.9630,41.2952,43.5487,45.7226,47.8165,49.8305,51.7652,53.6213,55.4001,57.1031,58.7320,60.2886,61.7750,63.1933,64.5457,65.8346,67.0623,68.2310,69.3432,70.0000
-name Output_imod.st -pixel 1.438 -rotation 0 -x 200 -y 207 -go 0<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">I got no error message, but when I go along the etomo workflow, it complains about a non-existing *.preali file.<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">How to I produce this file?<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Best regards,<o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Charlotte<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">Från: </span>
</b><span style="font-family:Calibri;color:black">3dem <3dem-bounces@ncmir.ucsd.edu> på uppdrag av Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist@chalmers.se></span><span style="font-family:PMingLiU;color:black"><br>
</span><b><span style="font-family:Calibri;color:black">Datum: </span></b><span style="font-family:Calibri;color:black">fredag 7 april 2017 14:46<br>
<b>Till: </b>"3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Ämne: </b>Re: [3dem] How to merge tif-files into an *.mrc-file<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Hello again,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">I have some questions about the tf2mrc command which is a part of the iMOD package. The specifications say this:
</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">NAME</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> tif2mrc - Make a MRC file from TIFF image files.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">SYNOPSIS</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> tif2mrc [options] TIFF_input_files... MRC_output_file</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">DESCRIPTION</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> tif2mrc takes a series of TIFF files and converts them into an MRC</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> stack. tif2mrc can also convert a single multi-page TIFF file to an</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">
</span><span style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">MRC stack.</span><o:p></o:p></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">
</span><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">….</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">I have 67 files named: seriesname_001.tif to seriesname_067.tif. How do I write for creating the mrc file? I tried writing in the file names of all
the files at the “TIFF_input_files... ”-position, but it only seem to accept one name at the position. I also tried using the “cat” command for creating a tiff-stack of the images and then the mrc-file, but the resulting mrc-file is very small and doesn’t
open in inspect3D.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Does this ring a bell?</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Best,</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Charlotte</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">Från: </span>
</b><span style="font-family:Calibri;color:black">3dem <3dem-bounces@ncmir.ucsd.edu> på uppdrag av Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist@chalmers.se></span><span style="font-family:PMingLiU;color:black"><br>
</span><b><span style="font-family:Calibri;color:black">Datum: </span></b><span style="font-family:Calibri;color:black">fredag 7 april 2017 11:01<br>
<b>Till: </b>Sacha De Carlo <sachadecarlo@yahoo.com>, "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Ämne: </b>Re: [3dem] How to merge tif-files into an *.mrc-file in Inspect3D</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Sounds like a good idea.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">I will try the tif2mrc command.</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">Thanks!</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US">/Charlotte</span><o:p></o:p></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:11.0pt;font-family:Calibri;mso-fareast-language:EN-US"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span style="font-family:Calibri;color:black">Från: </span>
</b><span style="font-family:Calibri;color:black">Sacha De Carlo <sachadecarlo@yahoo.com><br>
<b>Datum: </b>fredag 7 april 2017 10:57<br>
<b>Till: </b>Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist@chalmers.se>, "3dem@ncmir.ucsd.edu" <3dem@ncmir.ucsd.edu><br>
<b>Ämne: </b>Re: [3dem] How to merge tif-files into an *.mrc-file in Inspect3D</span><o:p></o:p></p>
</div>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Why not use imod or em2em to convert your tif files into an MRC stack that can then be imported into inspect 3D?
<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Best<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Sacha<br>
<br>
<br>
<a href="https://yho.com/footer0">Sent from Yahoo Mail for iPhone</a><o:p></o:p></p>
<p class="yahoo-quoted-begin" style="margin-top:0cm"><span style="font-size:11.5pt;color:#715FFA">On Friday, April 7, 2017, 10:41 AM, Charlotte Hamngren Blomqvist <charlotte.hamngren.blomqvist@chalmers.se> wrote:</span><o:p></o:p></p>
<blockquote style="border:none;border-left:solid #715FFA 1.0pt;padding:0cm 0cm 0cm 6.0pt;margin-left:0cm;margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt">Dear Hivemind,</span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt">I want to use computer-generated projections in order to quantify our ET method. Now I want to load the projected images (tif) into the software using the
concert/merge files option. I get the error message: "Operation failed Reason: Error reading file". What do I need to change in order for this to work? My version is v. 3.0.0.3494REL of Inspect3D.</span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt">Best regards</span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt">Charlotte Hamngren Blomqvist</span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:11.0pt"> </span><o:p></o:p></p>
<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;color:black">_______________________</span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;color:black">Charlotte Hamngren Blomqvist, PhD</span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;color:black">Researcher</span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;color:black"> </span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;color:black">Department of Physics</span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;color:black">Eva Olsson group</span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span lang="EN-US" style="font-size:10.5pt;color:black">Chalmers University of Technology</span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span style="font-size:10.5pt;color:black">SE-41296 Gothenburg, Sweden</span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span style="font-size:10.5pt;color:black">Tel
<a href="tel:+46-31%20772%2051%2080">+46-(0)31 772 51 80</a></span><o:p></o:p></p>
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<div>
<p class="yiv8191876247msonormal" style="background:white"><span style="font-size:10.5pt;color:black"><a href="http://www.chalmers.se/" target="_blank">www.chalmers.se</a></span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span style="font-size:10.5pt;color:black">E-mail: <a href="mailto:charlotte.hamngren@chalmers.se" target="_blank">charlotte.hamngren.blomqvist@chalmers.se</a></span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span style="font-size:10.5pt;color:black"> </span><o:p></o:p></p>
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<p class="yiv8191876247msonormal" style="background:white"><span style="font-size:10.5pt;color:black">Visiting address: Fysikgränd 3, room F4417b</span><o:p></o:p></p>
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<p class="MsoNormal" style="background:white">_______________________________________________<br>
3dem mailing list<br>
<a href="mailto:3dem@ncmir.ucsd.edu">3dem@ncmir.ucsd.edu</a><br>
<a href="https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem" target="_blank">https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem</a><o:p></o:p></p>
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