[ome-users] FW: Feedback on the use of OME in MATLAB

[Jason Swedlow]

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

--
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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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