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

[Melissa Linkert]

Hi Matthew,

> > 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
> > 
*snip*
> > 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.
>

Thank you for the additional information.  I have filed a ticket on our
issue tracking system to have Bio-Formats correctly record this piece of
metadata:

http://trac.openmicroscopy.org.uk/ome/ticket/8688

Regards,
-Melissa

On Tue, May 01, 2012 at 09:19:53AM +0100, Chris Allan wrote:
> 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
> > ------------------------------------------------------------------------
> > 
> > 
> > 
> > The University of Dundee is a registered Scottish Charity, No: SC015096
> > 
> > _______________________________________________
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> > ome-users at lists.openmicroscopy.org.uk
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> > 
> > 
> 

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