Plugin for conversion from MRC to TIFF

[Daniy]

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

[Albert Cardona-2]

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

[Daniy]

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]

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]
/*******************************************************/

[Daniy]

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]
/*******************************************************/

[ctrueden]

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]
> > /*******************************************************/
>

[dscho]

Hi,

On Mon, 31 Aug 2009, Curtis Rueden wrote:

> 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.

If you want to do it with a macro, this tutorial might be helpful:

http://pacific.mpi-cbg.de/wiki/index.php/How_to_apply_a_common_operation_to_a_complete_directory

Ciao,
Johannes