[3dem] Registration and 3-D Reconstruction

Joachim Frank jf2192 at columbia.edu
Tue Jul 7 08:45:19 PDT 2009

Thanks, Steve, for mentioning my book (Oxford U. Press 2006).

I'd like to add the book on Electron Tomography I edited for  
Springer-- it contains the mathematical foundations of 3D  
reconstruction in great detail, expounded by experts in the field.

Our own software, SPIDER, has been described in J. Struct. Biol. 1996  
along with several other software systems.

A step-by-step protocol on how to do a single-particle reconstruction  
is contained in Shaikh et al., Nature Protocols 2008.

--Joachim Frank.

Quoting Steven Ludtke <sludtke at bcm.edu>:

> It's a very active field of research. The question is which
> methodology you are interested in, each has its own specialties:
> - single particle reconstruction - sets of very noisy images of
> individual ~identical nanoscale objects -> 3D reconstruction
> - 2D crystallography - 3D reconstructions from crystals, like x-ray
> crystallography, but with 2-D rather than 3-D crystals
> - helical reconstruction - reconstruction using packed arrays with
> helical symmetry
> - tomography - VERY noisy 3D reconstructions of possibly unique
> objects, if the objects are ~identical then 3D registration and
> averaging can proceed
> I would suggest starting out with Joachim Frank's introductory book :
> "Three-dimensional Electron Microscopy", then perhaps looking at the
> special issue of
> JSB from a couple of years ago. The one containing this:
> Tang, G., Peng, L., Baldwin, P.R., Mann, D.S., Jiang, W., Rees, I. &
> Ludtke, S.J., 2007, EMAN2: an extensible image processing suite for
> electron microscopy, Journal of structural biology, 157(1), pp. 38-46.
> It has articles on many of the current software packages. My group
> develops one of them (EMAN). There is some raw data available from our
> website
> http://ncmi.bcm.edu
> ----------------------------------------------------------------------------
> Steven Ludtke, Ph.D.
> Associate Professor
> Co-Director National Center For Macromolecular Imaging
> Dept of Biochemistry and Mol. Biol.
> Baylor College of Medicine
> sludtke at bcm.edu
> stevel at alumni.caltech.edu
> http://ncmi.bcm.edu/~stevel
> On Jul 7, 2009, at 4:53 AM, Arthur Goshtasby wrote:
>> Hello everyone,
>> I am a new member and my interest is in image registration and 3-D   
>>  reconstruction. My background is actually computer vision but have  
>>   recently become interested in microscopic image analysis. I have   
>>  found such image fascinating. I am wondering if anyone else is    
>> interested in or currently working on the problem. I have some    
>> methodologies worked out for registration and 3-D reconstruction   
>> and  would like to try them on different data sets. If you are   
>> working  with microscopic image sets and don't mind sharing a set   
>> or two with  me, I promise to share the obtained results and the   
>> methodology that  is employed to obtain them with you? I can be   
>> reached via phone  (937-775-5170) or e-mail    
>> (arthur.goshtasby at wright.edu).
>> Thank you,
>> Arthur Goshtasby _______________________________________________
>> 3dem mailing list
>> 3dem at ncmir.ucsd.edu
>> https://mail.ncmir.ucsd.edu/mailman/listinfo/3dem

Joachim Frank, Ph.D.
Howard Hughes Medical Institute Investigator,
Professor, Department of Biochemistry and Molecular Biophysics,
and Department of Biology, Columbia University,
650 West 168th Street, P&S Black 2-221
New York, NY 10032
(T) 212 305-9510  (F) 212 305-9500  Admin Asst: Tornubari Barinee 212 305-9512
(E) jf2192 at columbia.edu

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