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

[Titus M. Franzmann]

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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