<html><head></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; "><div><div>Begin forwarded message:</div><br class="Apple-interchange-newline"><blockquote type="cite"><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>From: </b></span><span style="font-family:'Helvetica'; font-size:medium;">"Dougherty, Matthew T" <<a href="mailto:matthewd@bcm.edu">matthewd@bcm.edu</a>></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Date: </b></span><span style="font-family:'Helvetica'; font-size:medium;">30 April 2012 23:54:51 GMT+01:00<br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>To: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Jason Swedlow <<a href="mailto:j.r.swedlow@dundee.ac.uk">j.r.swedlow@dundee.ac.uk</a>>, "<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a> (<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>)" <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Cc: </b></span><span style="font-family:'Helvetica'; font-size:medium;">Carlos Oscar Sorzano <<a href="mailto:coss@cnb.csic.es">coss@cnb.csic.es</a>><br></span></div><div style="margin-top: 0px; margin-right: 0px; margin-bottom: 0px; margin-left: 0px;"><span style="font-family:'Helvetica'; font-size:medium; color:rgba(127, 127, 127, 1.0);"><b>Subject: </b></span><span style="font-family:'Helvetica'; font-size:medium;"><b>RE: Feedback on the use of OME in MATLAB/MRC/CCP4 format</b><br></span></div><br><br>Hi-<br><br>I have some familiarity with the MRC format. The current specification by the EM Databank is located here.<br><br><a href="http://emdatabank.org/mapformat.html">http://emdatabank.org/mapformat.html</a><br>ftp://ftp.wwpdb.org/pub/emdb/doc/map_format/EMDB_mapFormat_v1.0.pdf<br><br>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.<br><br>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.<br><br>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.<br><br>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.<br><br>To differentiate as to whether a file represents a cube or 2D planes the following was decided:<br><br>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).<span class="Apple-tab-span" style="white-space:pre"> </span><br>For 3D volumes of single particle or tomogram entries, ISPG=1 and NSYMBT=0. For image planes ISPG=0 and NSYMBT=0.<br><br><br>Matthew Dougherty<br>National Center for Macromolecular Imaging<br>Baylor College of Medicine<br>________________________________________<br>From: ome-users-bounces@lists.openmicroscopy.org.uk [ome-users-bounces@lists.openmicroscopy.org.uk] On Behalf Of Jason Swedlow [j.r.swedlow@dundee.ac.uk]<br>Sent: Monday, April 30, 2012 5:17 PM<br>To: ome-users@lists.openmicroscopy.org.uk (ome-users@lists.openmicroscopy.org.uk)<br>Cc: Carlos Oscar Sorzano<br>Subject: [ome-users] FW: Feedback on the use of OME in MATLAB<br><br>Hi-<br><br>Some feedback on Bio-Formats & Matlab from Carlos.<br><br>Carlos, you might just want to sign up for the mailing lists, or post further comments on the OME Forums.<br><br>Cheers,<br><br>Jason<br><br>-----Original Message-----<br>From: Carlos Oscar Sorzano [mailto:coss@cnb.csic.es]<br>Sent: Monday, April 30, 2012 10:17 PM<br>To: jason@lifesci.dundee.ac.uk<br>Subject: Feedback on the use of OME in MATLAB<br><br>Dear Jason,<br><br>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.<br><br>function V=bfOpenEMVolume(filename)<br> V=bfopen(filename);<br> Vaux{1}=zeros([size(V{1},1),size(V{1}{1})]);<br> for k=1:size(Vaux{1},1)<br> Vaux{1}(:,:,k)=V{1}{k};<br> end<br> Vaux{2}=filename;<br> V{1}=Vaux;<br>end<br><br>I hope it helps.<br><br>Also, I would like to suggest a number of standard file extensions in EM<br><br>SPIDER: .xmp (Spider image), .vol (Spider volume), .stk (Spider stack)<br>MRC: .st (MRC stack)<br><br>Finally, if at all possible, a nomenclature that is becoming standard in EM is<br><br>filename.whicheverExtension:spi (disregard the file extension and consider it to be Spider) number@stack.mrc (open only the image <number> (first image is number 1), from the given stack)<br><br>Kind regards, Carlos Oscar<br><br>--<br>------------------------------------------------------------------------<br>Carlos Oscar Sánchez Sorzano e-mail: coss@cnb.csic.es<br>Biocomputing unit http://biocomp.cnb.csic.es<br>National Center of Biotechnology (CSIC)<br>c/Darwin, 3<br>Campus Universidad Autónoma (Cantoblanco) Tlf: 34-91-585 4510<br>28049 MADRID (SPAIN) Fax: 34-91-585 4506<br>------------------------------------------------------------------------<br><br><br><br>The University of Dundee is a registered Scottish Charity, No: SC015096<br><br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br><br><br></blockquote></div><br></body></html>