<html><head><meta http-equiv="Content-Type" content="text/html charset=us-ascii"><base href="x-msg://50/"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">There is no Chimera command to run Segger so you would need to use Python code to automate it on a set of volumes. The Segger Python code is very messy so this will be difficult. If you are an experienced Python programmer then your aim would be to write a Python script that runs within Chimera opens the first map, creates a Segmentation instance from the class defined in<div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>chimera/share/Segger/regions.py</div><div><br></div><div>calls the smooth_and_group(steps, sdev) method, and writes out the resulting segmentation with the write_segmentation() routine in</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>chimera/share/Segger/segfile.py</div><div><br></div><div>or the writing could be done with the Chimera "segment" command to export a mask file</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/segment.html">http://www.cgl.ucsf.edu/chimera/docs/UsersGuide/midas/segment.html</a></div><div><br></div><div>The Segger code is complicated with lots of code that was testing experimental features, so if you are not an experienced Python programmer I'm afraid it will not be possible to automate processing using it.</div><div><br></div><div>It would be nice if the Chimera segment command let you run the Segger algorithm -- then your processing of many maps would be much easier. We will keep that in mind for the next generation of Chimera which we are currently working on.</div><div><br></div><div><span class="Apple-tab-span" style="white-space:pre"> </span>Tom</div><div><br></div><div><br><div><div>On Jan 23, 2014, at 5:04 AM, wrote:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div lang="EN-GB" link="blue" vlink="purple" style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; "><div class="WordSection1" style="page: WordSection1; "><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Hi,<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">I would like to automate watershed segmentation (Segger) on a set of volumes. Given that I have the details on the volume threshold, number of smoothing steps and minimum voxels in each region, is there a way to automate segmentation with different parameter inputs?<o:p></o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; "><o:p> </o:p></div><div style="margin: 0cm 0cm 0.0001pt; font-size: 11pt; font-family: Calibri, sans-serif; ">Many Thanks.<o:p></o:p></div></div><br><p>--<span class="Apple-converted-space"> </span><br>Scanned by iCritical.</p><br>_______________________________________________<br>Chimera-users mailing list<br><a href="mailto:Chimera-users@cgl.ucsf.edu" style="color: purple; text-decoration: underline; ">Chimera-users@cgl.ucsf.edu</a><br><a href="http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users" style="color: purple; text-decoration: underline; ">http://plato.cgl.ucsf.edu/mailman/listinfo/chimera-users</a><br></div></blockquote></div><br></div></body></html>