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

[Melissa Linkert]

Hi Carlos,

> 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.

Thank you.  I have put a slightly modified version of this function up
to be reviewed for inclusion into the official version of Bio-Formats:

https://github.com/openmicroscopy/bioformats/pull/61

> 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)

To my knowledge, all of these are supported already.  If you have
encountered cases where files with these extensions do not open, then
please let us know.

> 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)

I'm afraid I don't fully understand.  Is the idea to be able to do this
(in MATLAB)?:

  image = bfopen('1 at stack.mrc');

Regards,
-Melissa

On Mon, Apr 30, 2012 at 10:17:23PM +0000, Jason Swedlow wrote:
> 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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