[ome-devel] Issue happened while using bfConverter

[Parvathy Pillai]

Hi All

I have seen a code like below
https://www.openmicroscopy.org/community/viewtopic.php?f=15&t=524

Kindly let me know how to use OME in c#.

Please send a sample.




FileStream stream = new FileStream("somefile.xml", FileMode.Open);
            XmlSerializer formatter = new XmlSerializer(typeof(OME));
            OME ome = (OME)formatter.Deserialize(stream);


From: Parvathy Pillai
Sent: Tuesday, 8 November 2016 3:56 PM
To: 'ome-devel at lists.openmicroscopy.org.uk'
Subject: RE: Issue happened while using bfConverter



Hi All


When I try to convert the file got the below exception.


Kindly help me on the same.



C:\Users\ParvathyP>C:\Downloads\bftools\bftools\bfconvert -bigtiff C:\OptiscanCo
nfocalImages\OME1\OME1.tiff C:\OptiscanConfocalImages\OME1\OME1.ome.tiff
C:\OptiscanConfocalImages\OME1\OME1.tiff
TiffDelegateReader initializing C:\OptiscanConfocalImages\OME1\OME1.tiff
Reading IFDs
Populating metadata
Checking comment style
Populating OME metadata
[Tagged Image File Format] -> C:\OptiscanConfocalImages\OME1\OME1.ome.tiff [OME-
TIFF]
Exception in thread "main" loci.formats.UnsupportedCompressionException: Sorry,
CCITT T.6 bi-level encoding (Group 4 Fax) compression mode is not supported
        at loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:276
)
        at loci.formats.tiff.TiffParser.getTile(TiffParser.java:743)
        at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:986)
        at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:783)
        at loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:29
9)
        at loci.formats.DelegateReader.openBytes(DelegateReader.java:227)
        at loci.formats.FormatReader.openBytes(FormatReader.java:890)
        at loci.formats.ImageReader.openBytes(ImageReader.java:437)
        at loci.formats.tools.ImageConverter.convertPlane(ImageConverter.java:63
4)
        at loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:559
)
        at loci.formats.tools.ImageConverter.main(ImageConverter.java:880)

Parvathy Pillai
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