[ome-users] Bioformats Exporter - split channels and preserve OME-DATA

[Melissa Linkert]

Hi Titus,

> I am trying to split and save each channel of a dual color time-labs
> OME-TIFF using the Bioformats Exporter within FIJI.
> 
> When I export as .tif, the channels get split, but the OME time stamp for
> each frame is lost.
> 
> When I export as ome.tif, the OME time stamp is maintained but the channels
> are not split. The exporter creates two files, with same content as the
> original file. 
> 
> Does anyone have a solution how to split channels and preserve the channel
> specific OME data?

Exporting to OME-TIFF with channel splitting should result in one file
per channel, but by default opening any one of those files using
Bio-Formats will result in the entire dataset being opened.  If you select
the "Open files individually" option when opening one of the OME-TIFF
files, then only that channel will be opened.  The "Specify range for
each series" option may also help, if you wish to open more than one (but not
every) channel.

If neither of those options solves the problem, please let us know.

Regards,
-Melissa


On Thu, Sep 04, 2014 at 10:04:22AM +0200, Titus M. Franzmann wrote:
> Hi, 
> 
> I am trying to split and save each channel of a dual color time-labs
> OME-TIFF using the Bioformats Exporter within FIJI.
> 
> When I export as .tif, the channels get split, but the OME time stamp for
> each frame is lost.
> 
> When I export as ome.tif, the OME time stamp is maintained but the channels
> are not split. The exporter creates two files, with same content as the
> original file. 
> 
> Does anyone have a solution how to split channels and preserve the channel
> specific OME data?
> 
> Thanks for your support
> 
> Best Titus
> 
>  
> 
> (FIJI MACRO)
> 
> input = getDirectory("Choose Source Directory ");
> 
> output = input;
> 
> setBatchMode(true);
> 
> list = getFileList(input);
> 
> for (i = 0; i < list.length; i++)
> 
>     processFile(input, output, list[i]);
> 
>  
> 
> function processFile(input, output, filename)
> 
> {
> 
>                 a = input + filename;
> 
>                 run("Bio-Formats Importer", "open=a color_mode=Composite
> view=Hyperstack stack_order=XYCZT");  
> 
>                 name = getTitle;
> 
>                 b = output+name+'.tif'; //ome.tif
> 
>                 run("Bio-Formats Exporter", "save=["+b+"] write_each_channel
> compression=Uncompressed");
> 
>                 close();
> 
>                call("java.lang.System.gc");
> 
> }
> 
> call("java.lang.System.gc");
> 
> setBatchMode(false);
> 
>  
> 
>  
> 
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> 
> of Molecular Cell Biology
> 
> and Genetics 
> 
> Pfotenhauerstr. 108
> 
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> 
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> 
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> 
>  
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