Re: Plugin for conversion from MRC to TIFF

Posted by ctrueden on
URL: http://imagej.273.s1.nabble.com/Plugin-for-conversion-from-MRC-to-TIFF-tp3691335p3691340.html

Hi Daniyal,

You can use the "bfconvert" Bio-Formats command line tool to convert an MRC
file into a TIFF stack. See:

  http://www.loci.wisc.edu/ome/formats-tools.html
  http://www.farsight-toolkit.org/wiki/FARSIGHT_Tutorials/Bio-Formats

If you want to convert each image plane to a separate file, you would need
to use an ImageJ macro, or write some Java code.

-Curtis

On Fri, Aug 28, 2009 at 11:12 AM, Daniy <
[hidden email]> wrote:

> That's great. Thank you.
>
> Are there any possibilities to realize this via command line ...per
> instance
> , to insert a stack and to return the required image (in jpeg)
>
> Thomas Boudier wrote:
> >
> > Hi,
> >
> > MRC files are standard files with a header, normally size 1024 bytes,
> > and then you got the images, if you know the size of your images, you
> > can calculate your offset to get to the image you want, using
> > Import/Raw. You can also have a look to
> > http://u759.curie.u-psud.fr/softwaresu759.html for a MRC reader.
> >
> > Thomas
> >
> >
> > Daniy a écrit :
> >> Thank you a lot,
> >>
> >> but I'm curious, ...is it possible to get only one specific image out of
> >> the
> >> MRC image stack, and get it converted to an JPEG or (preferable) TIFF
> >> file,
> >> instead of extracting all images out of the stack and get them into a
> >> TIFF
> >> or JPEG ?
> >>
> >> Daniyal
> >>
> >>
> >> Albert Cardona-2 wrote:
> >>> Daniy wrote:
> >>>> Greetings,
> >>>>
> >>>> during our project we came to a point where we do need to convert or
> >>>> better
> >>>> said extract images out of a MRC stack file. The extracted images
> >>>> should
> >>>> be
> >>>> than be available in the TIFF or JPEG file format. Therefore what we
> >>>> need
> >>>> is
> >>>> some sort of "MRC to TIFF/JPEG converter". Are currently any sort of
> >>>> plugins
> >>>> available for ImageJ, that can realize this ?
> >>>>
> >>>> Best regards
> >>>>
> >>>> Daniyal
> >>>>
> >>>
> >>>
> >>> In Fiji there is an MRC importer, but I don't know how if it can handle
> >>> stacks. Most likely LOCI can.
> >>>
> >>> If so, just drag and drop your MRC file, then "File - Save as - Image
> >>> Sequence" and choose TIF or JPG for exporting each section as a single,
> >>> numbered image.
> >>>
> >>> Albert
> >>>
> >>> --
> >>> Albert Cardona
> >>> http://albert.rierol.net
> >>>
> >>>
> >>
> >
> > --
> >    /**********************************************************/
> >       Thomas Boudier, MCU Université Pierre et Marie Curie,
> >       IFR 83. Bat B 7ème étage, porte 709, Jussieu.
> >       Tel : [phone]  Fax : [phone]
> > /*******************************************************/
>