[ome-users] Fwd: Feedback on the use of OME in MATLAB/MRC/CCP4 format

[Chris Allan]

Begin forwarded message:

> From: "Dougherty, Matthew T" <matthewd at bcm.edu>
> Date: 30 April 2012 23:54:51 GMT+01:00
> To: Jason Swedlow <j.r.swedlow at dundee.ac.uk>, "ome-users at lists.openmicroscopy.org.uk (ome-users at lists.openmicroscopy.org.uk)" <ome-users at lists.openmicroscopy.org.uk>
> Cc: Carlos Oscar Sorzano <coss at cnb.csic.es>
> Subject: RE: Feedback on the use of OME in MATLAB/MRC/CCP4 format
> 
> 
> Hi-
> 
> I have some familiarity with the MRC format.  The current specification by the EM Databank is located here.
> 
> http://emdatabank.org/mapformat.html
> ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf
> 
> The history and evolution of MRC format goes back to the early 1980's.  It is a ad hoc format, that is users have wide leeway to modify the meaning of the header for whatever purpose.
> 
> A dejure spinoff by the crystallographic community was in the 1990's and is called the ccp4.  This format formalizes the metadata header, and introduces supplemental symmetry data for crystallography.
> 
> In 2000, the CCP4 standards committee working with Medical Research Council began negotiations to rejoin the formats, called MRC2000 by the EM community, which is part of the ccp4 standards minutes.
> 
> Later the EM Databank chose to use the CCP4 format as the primary data format for distribution.  Subsequently a survey was done of key people involved with the CCP4 and MRC formats who could explain every detail and convention used.
> 
> To differentiate as to whether a file represents a cube or 2D planes the following was decided:
> 
> The parameter ISPG, represents Space Group Numbers are defined by IUCr conventions (Table 12.3.4.1 Standard space-group symbols”, pages 824-831, International Tables for Crystallography, Volume A, fifth edition).	
> For 3D volumes of single particle or tomogram entries, ISPG=1 and NSYMBT=0.  For image planes ISPG=0 and NSYMBT=0.
> 
> 
> Matthew Dougherty
> National Center for Macromolecular Imaging
> Baylor College of Medicine
> ________________________________________
> From: ome-users-bounces at lists.openmicroscopy.org.uk [ome-users-bounces at lists.openmicroscopy.org.uk] On Behalf Of Jason Swedlow [j.r.swedlow at dundee.ac.uk]
> Sent: Monday, April 30, 2012 5:17 PM
> To: ome-users at lists.openmicroscopy.org.uk       (ome-users at lists.openmicroscopy.org.uk)
> Cc: Carlos Oscar Sorzano
> Subject: [ome-users] FW: Feedback on the use of OME in MATLAB
> 
> Hi-
> 
> Some feedback on Bio-Formats & Matlab from Carlos.
> 
> Carlos, you might just want to sign up for the mailing lists, or post further comments on the OME Forums.
> 
> Cheers,
> 
> Jason
> 
> -----Original Message-----
> From: Carlos Oscar Sorzano [mailto:coss at cnb.csic.es]
> Sent: Monday, April 30, 2012 10:17 PM
> To: jason at lifesci.dundee.ac.uk
> Subject: Feedback on the use of OME in MATLAB
> 
> Dear Jason,
> 
> I have tried to use bioformats in MATLAB for opening a MRC volume. It returns a set of planes. An EM developer would be expecting more something like a 3D volume. The following function is converting the set of planes into a MATLAB 3D volume.
> 
> function V=bfOpenEMVolume(filename)
>     V=bfopen(filename);
>     Vaux{1}=zeros([size(V{1},1),size(V{1}{1})]);
>     for k=1:size(Vaux{1},1)
>         Vaux{1}(:,:,k)=V{1}{k};
>     end
>     Vaux{2}=filename;
>     V{1}=Vaux;
> end
> 
> I hope it helps.
> 
> Also, I would like to suggest a number of standard file extensions in EM
> 
> SPIDER: .xmp (Spider image), .vol (Spider volume), .stk (Spider stack)
> MRC: .st (MRC stack)
> 
> Finally, if at all possible, a nomenclature that is becoming standard in EM is
> 
> filename.whicheverExtension:spi (disregard the file extension and consider it to be Spider) number at stack.mrc (open only the image <number> (first image is number 1), from the given stack)
> 
> Kind regards, Carlos Oscar
> 
> --
> ------------------------------------------------------------------------
> Carlos Oscar Sánchez Sorzano                  e-mail:   coss at cnb.csic.es
> Biocomputing unit                             http://biocomp.cnb.csic.es
> National Center of Biotechnology (CSIC)
> c/Darwin, 3
> Campus Universidad Autónoma (Cantoblanco)     Tlf: 34-91-585 4510
> 28049 MADRID (SPAIN)                          Fax: 34-91-585 4506
> ------------------------------------------------------------------------
> 
> 
> 
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