<html><head></head><body><div style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div style="font-family:Helvetica Neue, Helvetica, Arial, sans-serif;font-size:16px;"><div><div>A relevant discussion is provided in Section 6.3.2</div><div>of the book Computational Methods for Three-Dimensional</div><div>Microscopy Reconstruction by Gabor T. Herman and</div><div>Joachim Frank, Birkhauser, 2014.<br></div><div><br></div><div class="ydp5c2a1140signature"><div style="font-size:16px;"><div>Gabor T. Herman, Ph.D.</div><div>Professor Emeritus<br></div><div>Ph.D. Computer Science Program<br></div><div>The Graduate Centerbook</div><div>City University of New York</div>Web-Page: <a href="http://gabor.ws.gc.cuny.edu/" rel="nofollow" target="_blank">http://gabor.ws.gc.cuny.edu/</a><br>.<br>========================================== <br>.<br>A new and improved version of<br>.<br>SNARK14 (a programming system for the reconstruction of 2D images from 1D projections)<br>is available for downloading from<br><a shape="rect" href="http://turing.iimas.unam.mx/SNARK14M" id="ydp2c81abefyui_3_16_0_1_1497385228514_8796" rel="nofollow" target="_blank">http://turing.iimas.unam.mx/SNARK14M</a><br>.</div></div></div>
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On Tuesday, July 24, 2018, 7:32:31 AM EDT, Ludtke, Steven J <sludtke@bcm.edu> wrote:
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Even centering class-averages is subject to these questions, but I'd hardly say that center of gravity is the only other possible definition of center. Indeed when humans look at images they tend to perceive objects as "centered" if there is a uniform border
around the outside "edge" of the particle, which is a very different sort of operation for many shapes. I absolutely agree with Marin's comment that even if there is no controversy over what "center" means, applying it to raw particles raises additional problems
(noise and filtration of the particles). However, if they are icosahedral viruses, for example, you can do a pretty good job, and the various criteria will come very close to agreeing. So it is very problem-dependent.
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<font class="ydpc62c4768yiv0969646897" face="Courier"><span class="ydpc62c4768yiv0969646897" style="font-size:14px;">--------------------------------------------------------------------------------------<br class="ydpc62c4768yiv0969646897" clear="none">
Steven Ludtke, Ph.D. <<a shape="rect" class="ydpc62c4768yiv0969646897" href="mailto:sludtke@bcm.edu" rel="nofollow" target="_blank">sludtke@bcm.edu</a>> Baylor College of Medicine <br class="ydpc62c4768yiv0969646897" clear="none">
Charles C. Bell Jr., Professor of Structural Biology<br class="ydpc62c4768yiv0969646897" clear="none">
Dept. of Biochemistry and Molecular Biology (<a shape="rect" class="ydpc62c4768yiv0969646897" href="http://www.bcm.edu/biochem" rel="nofollow" target="_blank">www.bcm.edu/biochem</a>)<br class="ydpc62c4768yiv0969646897" clear="none">
Academic Director, CryoEM Core (<a shape="rect" class="ydpc62c4768yiv0969646897" href="http://cryoem.bcm.edu" rel="nofollow" target="_blank">cryoem.bcm.edu</a>)<br class="ydpc62c4768yiv0969646897" clear="none">
Co-Director CIBR Center (<a shape="rect" class="ydpc62c4768yiv0969646897" href="http://www.bcm.edu/research/cibr" rel="nofollow" target="_blank">www.bcm.edu/research/cibr</a>)<br class="ydpc62c4768yiv0969646897" clear="none">
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<div class="ydpc62c4768yiv0969646897">On Jul 24, 2018, at 5:59 AM, Philip Koeck <<a shape="rect" class="ydpc62c4768yiv0969646897" href="mailto:Philip.Koeck@ki.se" rel="nofollow" target="_blank">Philip.Koeck@ki.se</a>> wrote:</div>
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<div class="ydpc62c4768yiv0969646897">Hi.<br class="ydpc62c4768yiv0969646897" clear="none">
<br class="ydpc62c4768yiv0969646897" clear="none">
Another question you might want to think about is what you actually mean by center of geometry, but maybe you have already.<br class="ydpc62c4768yiv0969646897" clear="none">
Most views even of symmetric particles will not be symmetric so the only center you can define is the center of gravity, which is very sensitive to noise. If the views are symmetric you can use that symmetry to find the position of the symmetry axis.<br class="ydpc62c4768yiv0969646897" clear="none">
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All the best,<br class="ydpc62c4768yiv0969646897" clear="none">
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Philip<br class="ydpc62c4768yiv0969646897" clear="none">
<br class="ydpc62c4768yiv0969646897" clear="none">
-----Ursprungligt meddelande-----<br class="ydpc62c4768yiv0969646897" clear="none">
Från: 3dem [<a shape="rect" class="ydpc62c4768yiv0969646897" href="mailto:3dem-bounces@ncmir.ucsd.edu" rel="nofollow" target="_blank">mailto:3dem-bounces@ncmir.ucsd.edu</a>] För Marin van Heel<br class="ydpc62c4768yiv0969646897" clear="none">
Skickat: den 24 juli 2018 12:34<br class="ydpc62c4768yiv0969646897" clear="none">
Till: Wang, Steven; <a shape="rect" class="ydpc62c4768yiv0969646897" href="mailto:CCPEM@JISCMAIL.AC.UK" rel="nofollow" target="_blank">CCPEM@JISCMAIL.AC.UK</a><br class="ydpc62c4768yiv0969646897" clear="none">
Kopia: <a shape="rect" class="ydpc62c4768yiv0969646897" href="mailto:3dem@ncmir.ucsd.edu" rel="nofollow" target="_blank">3dem@ncmir.ucsd.edu</a><br class="ydpc62c4768yiv0969646897" clear="none">
Ämne: Re: [3dem] [ccpem] 2D centering of particle images<br class="ydpc62c4768yiv0969646897" clear="none">
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Dear Steven Wang,<br class="ydpc62c4768yiv0969646897" clear="none">
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Alignment is more of a statistical issue affecting the whole data set than something that should be done on an individual (noisy) particle-by-particle basis.<br class="ydpc62c4768yiv0969646897" clear="none">
See, for example, our: "Alignment By Classification" (ABC) paper: <br class="ydpc62c4768yiv0969646897" clear="none">
<a shape="rect" class="ydpc62c4768yiv0969646897" href="https://urldefense.proofpoint.com/v2/url?u=http-3A__journals.iucr.org_m_issues_2017_05_00_kf5002_index.html&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=M-Hg3PKoluhJPx97zStbNrb4WzU7gDV3T_Edr906gUQ&s=haWrV6mzUD0U15PfOzX25oRMCe5iIMbSPj6sbVrjl6w&e=" rel="nofollow" target="_blank">https://urldefense.proofpoint.com/v2/url?u=http-3A__journals.iucr.org_m_issues_2017_05_00_kf5002_index.html&d=DwIGaQ&c=ZQs-KZ8oxEw0p81sqgiaRA&r=GWA2IF6nkq8sZMXHpp1Xpg&m=M-Hg3PKoluhJPx97zStbNrb4WzU7gDV3T_Edr906gUQ&s=haWrV6mzUD0U15PfOzX25oRMCe5iIMbSPj6sbVrjl6w&e=</a><br class="ydpc62c4768yiv0969646897" clear="none">
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But our IMAGIC-4D software does of course have various options to do it particle-by-particle if that is what you insist you need for testing.<br class="ydpc62c4768yiv0969646897" clear="none">
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Cheers<br class="ydpc62c4768yiv0969646897" clear="none">
<br class="ydpc62c4768yiv0969646897" clear="none">
Marin van Heel<br class="ydpc62c4768yiv0969646897" clear="none">
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On 23/07/2018 19:29, Wang, Steven wrote:<br class="ydpc62c4768yiv0969646897" clear="none">
<blockquote class="ydpc62c4768yiv0969646897" type="cite">Dear all,<br class="ydpc62c4768yiv0969646897" clear="none">
<br class="ydpc62c4768yiv0969646897" clear="none">
Do you know any software available for aligning the center of geometry of each selected particle to the center of the particle-selection box? I need this centering for testing some algorithms, not for the regular cryo-EM map construction workflows. Thanks.<br class="ydpc62c4768yiv0969646897" clear="none">
<br class="ydpc62c4768yiv0969646897" clear="none">
Steven Wang<br class="ydpc62c4768yiv0969646897" clear="none">
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==============================================================<br class="ydpc62c4768yiv0969646897" clear="none">
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Prof Dr Ir Marin van Heel<br class="ydpc62c4768yiv0969646897" clear="none">
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Laboratório Nacional de Nanotecnologia - LNNano<br class="ydpc62c4768yiv0969646897" clear="none">
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