[ome-users] .mrc file import into omero

[Daniel James White]

Hi Bjorn,

Well, the point is that bio-formats reads the electron microscopy  
format .mrc
but OMERO.import does not.

I dont know if its supposed to or not,
or if there is some way i can add support by turning it on on the  
server,
or by working out how to do it and submitting a patch.

Users don't want to convert gigabytes of .mrc files to tiff before  
they put them in OMERO
and lose all the meta data in the process!

Maybe its a more general question....
does OMERO.import aim to work for all data file types that bio-formats  
can read, or just a subset of those?

cheers

Dan



On Jul 10, 2009, at 11:57 AM, Björn Quast wrote:

> Hi Dan,
>
> I guess you mean .mrc files from imod (http://bio3d.colorado.edu/ 
> imod/). Perhaps you can save them as one multilayer tif-file with  
> imagej or export the layers as single tif-files by using the command  
> line, mrc2tif <mrc-file> <basename_for_tif-files>.
>
> You can reconvert the tifs to mrc with tif2mrc. But I am not sure if  
> this all helps you, if you want to keep your metadata with the mrc- 
> files.
>
> cheers
>
> Björn
>
>
>
>
>
>
>
> Am Freitag, 10. Juli 2009 11:26:20 schrieb Daniel James White:
> > Hi All,
> >
> > I see bio-formats reads .mrc files from electron microscopy,
> > but OMERO.import doesnt seem to like them?
> > They are not in the list of acceptable file types.
> >
> > Can i add .mrc somehow?
> >
> >
> > cheers
> >
> > Dan
> >
> > Dr. Daniel James White BSc. (Hons.) PhD
> > Senior Microscopist / Image Visualisation, Processing and Analysis
> > Light Microscopy and Image Processing Facilities
> > Max Planck Institute of Molecular Cell Biology and Genetics
> > Pfotenhauerstrasse 108
> > 01307 DRESDEN
> > Germany
> >
> > +49 (0)15114966933 (German Mobile)
> > +49 (0)351 210 2627 (Work phone at MPI-CBG)
> > +49 (0)351 210 1078 (Fax MPI-CBG LMF)
> >
> > http://www.bioimagexd.net BioImageXD
> > http://pacific.mpi-cbg.de Fiji Fiji is just ImageJ - Batteries  
> Included
> > http://www.chalkie.org.uk
> > dan at chalkie.org.uk
> > ( white at mpi-cbg.de )
> >
> >
> >
> >
> >
> >
> >
> >
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
> > http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
> -- 
> Dr. Björn Quast
> Universität Bonn
> Institut für Evolutionsbiologie und Ökologie
> 53121 Bonn
> Tel.: 0228/735758 email: bquast at evolution.uni-bonn.de
>

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Visualisation, Processing and Analysis
Light Microscopy and Image Processing Facilities
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net 	BioImageXD
http://pacific.mpi-cbg.de Fiji 	Fiji is just ImageJ - Batteries Included
http://www.chalkie.org.uk
dan at chalkie.org.uk
( white at mpi-cbg.de )