[3dem] [ccpem] 2D centering of particle images

Gabor Herman gabortherman at yahoo.com
Tue Jul 24 06:30:36 PDT 2018


A relevant discussion is provided in Section 6.3.2of the book Computational Methods for Three-DimensionalMicroscopy Reconstruction by Gabor T. Herman andJoachim Frank, Birkhauser, 2014.

Gabor T. Herman, Ph.D.Professor Emeritus
Ph.D. Computer Science Program
The Graduate CenterbookCity University of New YorkWeb-Page: http://gabor.ws.gc.cuny.edu/
.
========================================== 
.
A new and improved version of
.
SNARK14 (a programming system for the reconstruction of 2D images from 1D projections)
is available for downloading from
http://turing.iimas.unam.mx/SNARK14M
. 

    On Tuesday, July 24, 2018, 7:32:31 AM EDT, Ludtke, Steven J <sludtke at bcm.edu> wrote:  
 
 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.

--------------------------------------------------------------------------------------
Steven Ludtke, Ph.D. <sludtke at bcm.edu>                      Baylor College of Medicine 
Charles C. Bell Jr., Professor of Structural Biology
Dept. of Biochemistry and Molecular Biology                      (www.bcm.edu/biochem)
Academic Director, CryoEM Core                                        (cryoem.bcm.edu)
Co-Director CIBR Center                                    (www.bcm.edu/research/cibr)




On Jul 24, 2018, at 5:59 AM, Philip Koeck <Philip.Koeck at ki.se> wrote:
Hi.

Another question you might want to think about is what you actually mean by center of geometry, but maybe you have already.
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.

All the best,

Philip

-----Ursprungligt meddelande-----
Från: 3dem [mailto:3dem-bounces at ncmir.ucsd.edu] För Marin van Heel
Skickat: den 24 juli 2018 12:34
Till: Wang, Steven; CCPEM at JISCMAIL.AC.UK
Kopia: 3dem at ncmir.ucsd.edu
Ämne: Re: [3dem] [ccpem] 2D centering of particle images



Dear Steven Wang,

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.
See, for example, our: "Alignment By Classification" (ABC) paper: 
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=

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.

Cheers

Marin van Heel



On 23/07/2018 19:29, Wang, Steven wrote:

Dear all,

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.

Steven Wang



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