http://imagej.273.s1.nabble.com/TIFF-batch-LZW-compression-via-a-macro-tp5012892p5012903.html
You're right. When the target file name does not exist yet, the result
I am using Fiji. Is there any difference in using ImageJ1 instead of
> Hi Guenter,
>
>> The image is loaded via the script, and it is subsequently saved, but
>> with an increased file size (1.0 MB expanded to 1.7 MB)
> If the file already exists, then Bio-Formats tries to append additional
> data. Make sure you are saving to a file which does not already exist.
>
>> I receive the error message: "OME-XML java library not found"
> Hmm, not sure why that would be the case! Are you using Fiji? Or plain
> ImageJ1?
>
> Regards,
> Curtis
>
> On Wed, May 20, 2015 at 3:35 PM, Guenter Giese <
>
[hidden email]> wrote:
>
>> Dear ImageJ users,
>>
>> I try to set up a macro for batch LZW compression of multiple TIFF 16bit
>> grayscale image files.
>>
>> I started with macro recording. When I opened a TIFF file from the ImageJ
>> GUI and exported it with the BioFormats exporter as a LZW compressed TIFF,
>> I ended up with a TIFF image with a reduced file size (1.0 MB reduced to
>> 0.7 MB):
>> open("D:\\temp2\\test3\\d1_cropxyz_z0000.tif");
>> run("Bio-Formats Exporter",
>> "save=D:\\temp2\\test3\\macro_recorder.ome.tif compression=LZW");
>>
>>
>> Now I tried to include the recorded sequence for TIFF export and LZW
>> compression in an ImageJ macro:
>>
>> run("Bio-Formats Exporter", "save="+path+" compression=LZW"); //(path is
>> defined during loading, can also be specified like above)
>>
>> The image is loaded via the script, and it is subsequently saved, but with
>> an increased file size (1.0 MB expanded to 1.7 MB), and I receive the error
>> message: "OME-XML java library not found"
>>
>> What is the cause for the difference between manual conversion via the
>> GUI, and the loading and saving via a macro? It seems that the path to the
>> OME-XML java library is found when using the GI, but not from inside the
>> macro.
>>
>> Is there any path variable to be set before running the LZW compression
>> macro, or to be included in the macro code?
>>
>>
>> Thanks for any suggestion,
>>
>> Guenter
>>
>>
>> --
>> Dr. Guenter Giese
>> Light Microscopy Facility Manager
>> Dept. of Biomedical Optics
>> MPI fuer Medizinische Forschung
>> D-69120 Heidelberg, Germany
>> phone xx49 or 0 -6221-486-360 fax -325
>> e-mail:
[hidden email]
>>
>> --
>> ImageJ mailing list:
http://imagej.nih.gov/ij/list.html>>
> --
> ImageJ mailing list:
http://imagej.nih.gov/ij/list.htmlDr. Guenter Giese
Dept. of Biomedical Optics
MPI fuer Medizinische Forschung Jahnstr. 29