Subject: Re: Request to review a paper From: Ulf Skoglund <Ulf.Skoglund@cmb.ki.se> Date: Tue, 09 Jan 2001 12:41:27 +0100 To: fox@csit.fsu.edu Dear Geoffrey Fox, I'm willing to review the paper referred to below and these are my comments in a general way; I think it is good that researchers are beginning to develop various approaches to the problem of high speed 3D reconstruction from 2D projection data. In particular it is nice that algorithms for asymmetric data are being developed since they have a very broad application area. The paper has some fundamental flaws if it is supposed to compete with work in the field of 3D reconstruction in general; certainly the audience interested in this kind of software development is also found in the area of medical applications, from PET SPECT and NMR to the more similar CT procedures. The work presented here is of the type non-iterative 3D reconstruction algorithm, which has been the most used procedure in biological research, but which nowadays are rather far from what is achieved with methods used in the medical application areas by iterative methods of various kinds (including maximum likelihood techniques). Even in a virus icosahedral reconstruction application a maximum entropy algorithm has been developed and shown in practice to perform well. These methods are not so well parallelized yet, but the current paper doesn't even discuss these methods and/or if the presented algorithm with increased speed will be a survivor in the longer perspective in spite of the lower qualitative and quantitive performance (compared to iterative procedures). A second flaw is the lack of discussion of prior art: it is well known that a parallel implementation of the filtered backprojection algorithm, used for asymmetric objects, is up and running since some years at the supercomputer center in San Diego. At least a minimal discussion must be present were the work is compared with the papers from collaborators around Dr. Mark Ellismans group at NCMIR in San Diego. A technical remark is that the discrepancies between the icosahedrally averaged center of the non-icosahedral region in the slices shown in figs 5&6 are not discussed in detail, but nontheless very interesting (the symmetry seen here is a generated artefact) because it means that the two reconstruction methods really gives different results, not only a speed-up factor for the presented algorithm. The interpolation algorithm used to place the 2D DFT into the 3D space have not been evaluated or more analytically commented upon. The paper has its strength in the analysis of the number of operations used at different steps in the algorithm, but unless the critique above is met, the paper is more like a technical report and shouldn't be published in a scientific journal. Stockholm, January 9 2001 Best regards Ulf Skoglund > I am editor for a journal which is from January 1, 2001 called > Concurrency and Computation:Practice and Experience. Lennart Johnsson > suggested I could contact you. > > I thought you might be able to provide me a referee report by February 15 2001 > on the paper > C493: Space-Time Tradeoffs for Parallel 3D Reconstruction Algorithms for Virus > Structure Determination > The PDF Text of the paper can be found at URL > http://aspen.csit.fsu.edu/CCPEwebresource/C493marinescu/c493paper.pdf > > I am switching the journal to completely electronic form and hope you could > email > me a report. Please send a short email if you can or cannot do this > > Please do this in "free form" mentioning paper metadata above > Alternatively use form appended. > Note you can find the form and some other information at: > http://aspen.csit.fsu.edu/CandCPandE/index.html > > Thank you > Geoffrey > > --------------------------------------------------------------------------- > > CandC:PandE Referee Report Form -- Electronic Transimission to > fox@csit.fsu.edu strongly preferred > Referees Web Page: http://aspen.csit.fsu.edu/CandCPandE/ > Email fox@csit.fsu.edu for URL of full paper to be reviewed > > WILEY Journal Home Page > http://www3.interscience.wiley.com/cgi-bin/jtoc?ID=5361 > > John Wiley and Sons, Ltd. > Baffins Lane, Chichester > West Sussex, PO19 1UD, England > Telephone: (01243) 779777 > Fax: (01243) 770379 > > REFEREE'S REPORT > > Concurrency and Computation:Practice and Experience > > --------------------------------------------------------------------------- > > A: General Information > > Please return to: > Geoffrey C. 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