<div dir="ltr">Hello Chimera Developers,<div><br></div><div> There is this repeated procedure that I have to do to get a Segmented map from my soft x-ray tomography maps. Here is what I want do:</div><div><br></div><div>







<p class="gmail-p1"><span class="gmail-s1">1. open<span class="gmail-Apple-converted-space">  </span>*mrc </span></p><p class="gmail-p1">put the map to Level 0.011 <span class="gmail-Apple-converted-space">  </span></p><p class="gmail-p1">2. <b>vop<span class="gmail-Apple-converted-space">  </span>gaussian<span class="gmail-Apple-converted-space">  </span>#0 sd 0.005</b></p><p class="gmail-p2"><span class="gmail-s1"></span></p>
<p class="gmail-p1"><span class="gmail-s1">put Gaussian to 0.011</span></p>
<p class="gmail-p3">3. Go to: Tools --> Volume Data --> Segment Map<br><span class="gmail-s1"></span></p>
<p class="gmail-p1"><span class="gmail-s1">Segment the gaussian map</span></p>
<p class="gmail-p1"><span class="gmail-s1">Smoothing step: 1</span></p>
<p class="gmail-p1"><span class="gmail-s1">Step size: 500 voxels</span></p>
<p class="gmail-p1"><span class="gmail-s1">Keep only regions at lease: 100 voxels</span></p>
<p class="gmail-p1"><span class="gmail-s1">Save segments as an .mrc file</span></p>
<p class="gmail-p1"><span class="gmail-s1">Go to: File (Segment Map) --> Save all regions to .mrc</span></p>
<p class="gmail-p1"><span class="gmail-s1">Set Segment map to 0.011</span></p>
<p class="gmail-p3">4. Type: <b>vop subtract #3 #0<br><span class="gmail-s1"></span></b></p>
<p class="gmail-p1"><span class="gmail-s1">#3 Corresponds with ID# of the segmented .mrc file</span></p>
<p class="gmail-p1"><span class="gmail-s1">#0 Corresponds with ID# of the original file</span></p>
<p class="gmail-p3">5. <b>sop split #0<span class="gmail-Apple-converted-space"> </span></b><br></p>
<p class="gmail-p1"><span class="gmail-s1">#0 Corresponds with ID# of the original file</span></p>
<ul>
<li class="gmail-li1"><span class="gmail-s2"></span><span class="gmail-s1">Splits surface into disconnected parts</span></li>
</ul><div>The steps in <b>bold </b>are in command line. Is there anyway to have everything in a script format? Setting the levels, opening segmentation and setting values to specific Voxel values every time is quite time consuming. I would appreciate your help. Thanks</div><div><br></div><div>Best,</div><div class="gmail_signature"><div dir="ltr"><div><div dir="ltr">Soumya Govinda Remesh, Ph.D.<div><span style="font-size:12.8px">Postdoctoral Fellow at Advanced Light Source</span></div><div>SIBYLS group: <a href="http://sibyls.als.lbl.gov/" target="_blank">http://sibyls.als.lbl.gov/</a> <br style="font-size:12.8px"><span style="font-size:12.8px">Lawrence Berkeley National Laboratory</span><br style="font-size:12.8px"><br style="font-size:12.8px"><span style="font-size:12.8px">1 Cyclotron Road   MS 6R2100</span><br style="font-size:12.8px"><span style="font-size:12.8px">Berkeley, CA 94720</span><br style="font-size:12.8px"><span style="font-size:12.8px">(phone) </span><a href="tel:510-495-8179" value="+15104958179" style="color:rgb(17,85,204);font-size:12.8px" target="_blank">510-495-8179</a><br style="font-size:12.8px"><span style="font-size:12.8px">(cell) 804-402-8730</span></div><div><br style="font-size:12.8px"><a href="mailto:sgremesh@lbl.gov" target="_blank">sgremesh@lbl.gov</a><br><div><br></div></div></div></div></div></div>
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