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<li><a class="reference internal" href="#"><strong>Multiscale_Coords.ijm documentation</strong></a><ul>
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<li><a class="reference internal" href="#introduction-purpose"><strong>Introduction & Purpose</strong></a></li>
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<li><a class="reference internal" href="#instructions-of-use"><strong>Instructions of use</strong></a></li>
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<div class="section" id="multiscale-coords-ijm-documentation">
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<h1><strong>Multiscale_Coords.ijm documentation</strong><a class="headerlink" href="#multiscale-coords-ijm-documentation" title="Permalink to this headline">¶</a></h1>
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<div class="section" id="introduction-purpose">
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<h2><strong>Introduction & Purpose</strong><a class="headerlink" href="#introduction-purpose" title="Permalink to this headline">¶</a></h2>
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<p>In some experiments, low resolution (LowRes) scans are acquired in order to have a global overview of the sample (usually fits in the field of view), and then higher resolution (HighRes) scans are performed in small desired regions of interest (ROI) in order to have a look at finer structures (usually local tomography). Placing the motors into the correct position for the HighRes scan requires tedious, not straightforward and error-prone calculations that need many parameters to be taken into account.</p>
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<p>Multiscale_Coords.ijm is an ImageJ plugin to find the final/relative coordinates for moving the XX, ZZ and Y motors in a visual manner. The ROI size of the HighRes scan is shown according to the user-supplied parameters of LowRes and HighRes scans. The user can move the ROI interactively to the desired position, and the corresponding movements in um are given as the result. Start and end position values for stitched scans are also available.</p>
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<p><em>Created by hector.dejea@psi.ch in May 2017 extending and adapting localtomo_coords.txt from bernd.pinzer@psi.ch (August 2011)</em></p>
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<div class="section" id="instructions-of-use">
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<h2><strong>Instructions of use</strong><a class="headerlink" href="#instructions-of-use" title="Permalink to this headline">¶</a></h2>
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<ol class="arabic">
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<li><p class="first">Open your LowRes stack of images with ImageJ.</p>
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</li>
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<li><p class="first">Initialise the plugin:</p>
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<blockquote>
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<div><ul class="simple">
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<li><strong>Locally</strong>: ImageJ -> Plugins -> Macros -> Run -> Browse script</li>
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<li><strong>Beamline</strong>: ImageJ -> Plugins -> TOMCAT -> Multiscale Coords</li>
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</ul>
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</div></blockquote>
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</li>
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<li><dl class="first docutils">
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<dt>A dialog asking for LowRes and HighRes acquisition parameters will appear. Fill up with the corresponding inputs:</dt>
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<dd><ul class="first last simple">
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<li><strong>LowRes imagePixelSize</strong>: pixel size (um) in your LowRes scan.</li>
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<li><strong>LowRes XX center</strong>: XX motor position in your LowRes scan.</li>
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<li><strong>LowRes ZZ center</strong>: ZZ motor position in your LowRes scan.</li>
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<li><strong>LowRes Y position</strong>: Y motor position in your LowRes scan.</li>
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<li><strong>HighRes FOV X</strong>: field of view in pixels in X (horizontal) of HighRes scan.</li>
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<li><strong>HighRes FOV Y</strong>: field of view in pixels in Y (vertical) of HighRes scan.</li>
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<li><strong>HighRes imagePixelSize</strong>: pixel size (um) in your HighRes scan.</li>
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<li><strong>Camera movement X</strong>: due to the use of both end stations or the change of magnification, camera realignment might be needed. Introduce here the camera movement in X.</li>
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<li><strong>Camera movement Y</strong>: Following previous explanation, introduce here the camera movement in Y.</li>
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<li><dl class="first docutils">
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<dt><strong>Stitched scan</strong>: check this box if you want to do a stitched scan and not just a single volume. If checked, a new dialog will pop up after pressing OK.</dt>
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<dd><ul class="first last">
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<li><strong>Overlap in X and Z (pixels)</strong>: amount of overlapping pixels in the X and Z directions. Currently, it’s not possible to have a different value for each direction.</li>
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<li><strong>Overlap in Y (pixels)</strong>: amount of overlapping slices in the Y directions.</li>
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<li><strong>Scans in X</strong>: size of the stitched scan grid in the X direction (the plugin assumes X to be vertical direction in reconstructed slices).</li>
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<li><strong>Scans in Z</strong>: size of the stitched scan grid in the Z direction (the plugin assumes Z to be horizontal direction in reconstructed slices).</li>
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<li><strong>Slices in Y</strong>: size in number of slices of the stitched scan.</li>
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<li><strong>Selected Y slice as</strong>: select the viewed slice to be the first (top) or the middle of the scan. It is recommended to use first.</li>
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</ul>
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</dd>
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</dl>
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</li>
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</ul>
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</dd>
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</dl>
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</li>
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</ol>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<ul class="last simple">
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<li>If <em>LowRes ZZ center, LowRes XX center, LowRes Y position,</em> and <em>Camera movements</em> are left to 0, only the relative movements will be given.</li>
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<li>If the value given to <em>Slices in Y</em> is smaller than the FOV Y in HighRes, the total FOV will be considered.</li>
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</ul>
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</div>
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<p>Once OK has been clicked, a circle (no stitched scan) or a rectangle (stitched scan) with the size of the area to be scanned given your inputs will appear in the image.</p>
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<a class="reference internal image-reference" href="_images/Dialog1.png"><img alt="_images/Dialog1.png" src="_images/Dialog1.png" style="height: 8cm;" /></a>
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<a class="reference internal image-reference" href="_images/DialogSt.png"><img alt="_images/DialogSt.png" src="_images/DialogSt.png" style="height: 8cm;" /></a>
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<ol class="arabic simple" start="4">
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<li>Move the ROI to the position in which you would like to perform the high resolution scans and press OK. If you selected stitched scan, the circles corresponding to each of the individual scans will be shown.</li>
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</ol>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">In case the size of the ROI shown is not adequate for your purposes, press Shift+OK and the stitched scan parameters dialog will pop up again. This applies both when stitched or not stitched scan have been selected in the first instance.</p>
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</div>
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<a class="reference internal image-reference" href="_images/single.png"><img alt="_images/single.png" src="_images/single.png" style="height: 9cm;" /></a>
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<a class="reference internal image-reference" href="_images/stitch.png"><img alt="_images/stitch.png" src="_images/stitch.png" style="height: 9cm;" /></a>
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<a class="reference internal image-reference" href="_images/stitchfin.png"><img alt="_images/stitchfin.png" class="align-center" src="_images/stitchfin.png" style="height: 9cm;" /></a>
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<ol class="arabic simple" start="5">
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<li>Finally, a dialog with the relative motor movements and absolute motor position values will pop up. In addition, a command line with the corresponding inputs will be generated. If, for any reason, you wish to restart the process, check the box and press okay, which will bring you directly back to step 3.</li>
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</ol>
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<div class="admonition note">
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<p class="first admonition-title">Note</p>
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<p class="last">Restarting the plugin using the checkbox instead of closing and opening again has the advantage that your last input values will appear as default in the new dialogs.</p>
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</div>
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<a class="reference internal image-reference" href="_images/finalsingle.png"><img alt="_images/finalsingle.png" class="align-center" src="_images/finalsingle.png" style="height: 8cm;" /></a>
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<a class="reference internal image-reference" href="_images/finalstitch.png"><img alt="_images/finalstitch.png" class="align-center" src="_images/finalstitch.png" style="height: 8cm;" /></a>
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