MatLab Tif does not open

[ERIC]

Hi All,
I try to open matlab(2015) tif file and even with a new version of
Bio-Format it does not open (error message below).
However the file can be opened by Windows "Paint" and Photoshop.
Any advices ?

Moreover when I join the image my message is rejected by ImageJ list !!! :

Your  posting to  the IMAGEJ  list  has been  rejected because  it contains  an
attachment of type 'APPLICATION/APPLEFILE'.


Thank you




loci.formats.UnsupportedCompressionException: Sorry, CCITT Group 3
1-Dimensional Modified Huffman compression mode is not supported
     at
loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:276)
     at loci.formats.tiff.TiffParser.getTile(TiffParser.java:745)
     at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:990)
     at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:785)
     at
loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:299)
     at loci.formats.DelegateReader.openBytes(DelegateReader.java:227)
     at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
     at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:225)
     at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
     at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
     at
loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
     at
loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
     at
loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
     at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
     at
loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
     at
loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
     at
loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
     at loci.plugins.in.Importer.readPixels(Importer.java:146)
     at loci.plugins.in.Importer.run(Importer.java:85)
     at loci.plugins.LociImporter.run(LociImporter.java:78)
     at ij.IJ.runUserPlugIn(IJ.java:212)
     at ij.IJ.runPlugIn(IJ.java:176)
     at ij.Executer.runCommand(Executer.java:132)
     at ij.Executer.run(Executer.java:65)
     at java.lang.Thread.run(Thread.java:619)

--

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ERIC]

Hi All,

Here is the MetaData from the MatLab tif file that does not open in imageJ.
Any help is aprreciated !!!


Key Value
  BitsPerPixel 1
  DimensionOrder XYCZT
  IsInterleaved false
  IsRGB false
  LittleEndian true
  PixelType uint8
  Series 0 Name roiMask.tif
  SizeC 1
  SizeT 1
  SizeX 505
  SizeY 502
  SizeZ 1
BitsPerSample 1
Compression CCITT Group 3 1-Dimensional Modified Huffman
ImageLength 502
ImageWidth 505
Location C:\plusTipTracker\D3_Tyr\Video_Tyr\15_07_24_Tyr\mchTyr_01\roi_1\roiMask.tif
MetaDataPhotometricInterpretation Monochrome
MetaMorph no
NumberOfChannels 1
Orientation 1st row - top; 1st column - left
PhotometricInterpretation WhiteIsZero
PlanarConfiguration Chunky
ResolutionUnit Inch
SamplesPerPixel 1
XResolution 72
YResolution 72

Eric Denarier
Grenoble Institut des Neurosciences
Inserm U836
Chemin Fortuné Ferrini
38700 La Tronche
France


Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 18/09/2015 17:55, Eric Denarier a écrit :

> Hi All,
> I try to open matlab(2015) tif file and even with a new version of
> Bio-Format it does not open (error message below).
> However the file can be opened by Windows "Paint" and Photoshop.
> Any advices ?
>
> Moreover when I join the image my message is rejected by ImageJ list
> !!! :
>
> Your  posting to  the IMAGEJ  list  has been  rejected because  it
> contains  an
> attachment of type 'APPLICATION/APPLEFILE'.
>
>
> Thank you
>
>
>
>
> loci.formats.UnsupportedCompressionException: Sorry, CCITT Group 3
> 1-Dimensional Modified Huffman compression mode is not supported
>     at
> loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:276)
>     at loci.formats.tiff.TiffParser.getTile(TiffParser.java:745)
>     at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:990)
>     at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:785)
>     at
> loci.formats.in.MinimalTiffReader.openBytes(MinimalTiffReader.java:299)
>     at loci.formats.DelegateReader.openBytes(DelegateReader.java:227)
>     at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
>     at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:225)
>     at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
>     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>     at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
>     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>     at
> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
>     at
> loci.plugins.in.ImagePlusReader.readProcessors(ImagePlusReader.java:416)
>     at
> loci.plugins.in.ImagePlusReader.readPlanes(ImagePlusReader.java:380)
>     at
> loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
>     at
> loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:238)
>     at
> loci.plugins.in.ImagePlusReader.readImages(ImagePlusReader.java:216)
>     at
> loci.plugins.in.ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
>     at loci.plugins.in.Importer.readPixels(Importer.java:146)
>     at loci.plugins.in.Importer.run(Importer.java:85)
>     at loci.plugins.LociImporter.run(LociImporter.java:78)
>     at ij.IJ.runUserPlugIn(IJ.java:212)
>     at ij.IJ.runPlugIn(IJ.java:176)
>     at ij.Executer.runCommand(Executer.java:132)
>     at ij.Executer.run(Executer.java:65)
>     at java.lang.Thread.run(Thread.java:619)
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ctrueden]

Hi Eric,

Apologies for the very long delay in reply.

> I try to open matlab(2015) tif file and even with a new version of
> Bio-Format it does not open (error message below).
...
> loci.formats.UnsupportedCompressionException: Sorry, CCITT Group 3
> 1-Dimensional Modified Huffman compression mode is not supported

The error says it all: Bio-Formats does not support the compression scheme
that MATLAB used.

There is a (very old!) issue for it in the Bio-Formats issue tracker:
    http://trac.openmicroscopy.org/ome/ticket/4117

You could contact the Bio-Formats development team [1] to renew the request
for support, if you like. Or if you have development chops available
locally, I'm sure a patch would be very welcome [2].

On the flip side: it is almost certainly possible to tell MATLAB to write
the TIFF file with a different (or no) compression scheme, to avoid this
limitation altogether.

Regards,
Curtis

[1] https://www.openmicroscopy.org/site/community
[2] https://github.com/openmicroscopy/bioformats/blob/v5.1.6/CONTRIBUTING.md

On Fri, Sep 18, 2015 at 10:55 AM, Eric Denarier <
[hidden email]> wrote:

> Hi All,
> I try to open matlab(2015) tif file and even with a new version of
> Bio-Format it does not open (error message below).
> However the file can be opened by Windows "Paint" and Photoshop.
> Any advices ?
>
> Moreover when I join the image my message is rejected by ImageJ list !!! :
>
> Your  posting to  the IMAGEJ  list  has been  rejected because  it
> contains  an
> attachment of type 'APPLICATION/APPLEFILE'.
>
>
> Thank you
>
>
>
>
> loci.formats.UnsupportedCompressionException: Sorry, CCITT Group 3
> 1-Dimensional Modified Huffman compression mode is not supported
>     at
> loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:276)
>     at loci.formats.tiff.TiffParser.getTile(TiffParser.java:745)
>     at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:990)
>     at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:785)
>     at loci.formats.in
> .MinimalTiffReader.openBytes(MinimalTiffReader.java:299)
>     at loci.formats.DelegateReader.openBytes(DelegateReader.java:227)
>     at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
>     at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:225)
>     at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
>     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>     at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
>     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>     at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>     at
> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
>     at loci.plugins.in
> .ImagePlusReader.readProcessors(ImagePlusReader.java:416)
>     at loci.plugins.in
> .ImagePlusReader.readPlanes(ImagePlusReader.java:380)
>     at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
>     at loci.plugins.in
> .ImagePlusReader.readImages(ImagePlusReader.java:238)
>     at loci.plugins.in
> .ImagePlusReader.readImages(ImagePlusReader.java:216)
>     at loci.plugins.in
> .ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
>     at loci.plugins.in.Importer.readPixels(Importer.java:146)
>     at loci.plugins.in.Importer.run(Importer.java:85)
>     at loci.plugins.LociImporter.run(LociImporter.java:78)
>     at ij.IJ.runUserPlugIn(IJ.java:212)
>     at ij.IJ.runPlugIn(IJ.java:176)
>     at ij.Executer.runCommand(Executer.java:132)
>     at ij.Executer.run(Executer.java:65)
>     at java.lang.Thread.run(Thread.java:619)
>
> --
>
> Eric Denarier
> Grenoble Institut des Neurosciences
> Inserm U836
> Chemin Fortuné Ferrini
> 38700 La Tronche
> France
>
>
> Tél :[phone]
> Fax :[phone]
>
> http://neurosciences.ujf-grenoble.fr/
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[ERIC]

Thank you Curtis,

I have been recommanded by a list member to use the JIMI plugin .
http://rsb.info.nih.gov/ij/plugins/jimi.html
It worked great even in a macro.

Regards

Eric



Tél :[phone]
Fax :[phone]

http://neurosciences.ujf-grenoble.fr/

Le 04/12/2015 21:30, Curtis Rueden a écrit :

> Hi Eric,
>
> Apologies for the very long delay in reply.
>
>> I try to open matlab(2015) tif file and even with a new version of
>> Bio-Format it does not open (error message below).
> ...
>> loci.formats.UnsupportedCompressionException: Sorry, CCITT Group 3
>> 1-Dimensional Modified Huffman compression mode is not supported
> The error says it all: Bio-Formats does not support the compression scheme
> that MATLAB used.
>
> There is a (very old!) issue for it in the Bio-Formats issue tracker:
>      http://trac.openmicroscopy.org/ome/ticket/4117
>
> You could contact the Bio-Formats development team [1] to renew the request
> for support, if you like. Or if you have development chops available
> locally, I'm sure a patch would be very welcome [2].
>
> On the flip side: it is almost certainly possible to tell MATLAB to write
> the TIFF file with a different (or no) compression scheme, to avoid this
> limitation altogether.
>
> Regards,
> Curtis
>
> [1] https://www.openmicroscopy.org/site/community
> [2] https://github.com/openmicroscopy/bioformats/blob/v5.1.6/CONTRIBUTING.md
>
> On Fri, Sep 18, 2015 at 10:55 AM, Eric Denarier <
> [hidden email]> wrote:
>
>> Hi All,
>> I try to open matlab(2015) tif file and even with a new version of
>> Bio-Format it does not open (error message below).
>> However the file can be opened by Windows "Paint" and Photoshop.
>> Any advices ?
>>
>> Moreover when I join the image my message is rejected by ImageJ list !!! :
>>
>> Your  posting to  the IMAGEJ  list  has been  rejected because  it
>> contains  an
>> attachment of type 'APPLICATION/APPLEFILE'.
>>
>>
>> Thank you
>>
>>
>>
>>
>> loci.formats.UnsupportedCompressionException: Sorry, CCITT Group 3
>> 1-Dimensional Modified Huffman compression mode is not supported
>>      at
>> loci.formats.tiff.TiffCompression.decompress(TiffCompression.java:276)
>>      at loci.formats.tiff.TiffParser.getTile(TiffParser.java:745)
>>      at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:990)
>>      at loci.formats.tiff.TiffParser.getSamples(TiffParser.java:785)
>>      at loci.formats.in
>> .MinimalTiffReader.openBytes(MinimalTiffReader.java:299)
>>      at loci.formats.DelegateReader.openBytes(DelegateReader.java:227)
>>      at loci.formats.ChannelFiller.openBytes(ChannelFiller.java:156)
>>      at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:225)
>>      at loci.formats.ChannelSeparator.openBytes(ChannelSeparator.java:157)
>>      at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>>      at loci.formats.DimensionSwapper.openBytes(DimensionSwapper.java:233)
>>      at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>>      at loci.formats.ReaderWrapper.openBytes(ReaderWrapper.java:335)
>>      at
>> loci.plugins.util.ImageProcessorReader.openProcessors(ImageProcessorReader.java:186)
>>      at loci.plugins.in
>> .ImagePlusReader.readProcessors(ImagePlusReader.java:416)
>>      at loci.plugins.in
>> .ImagePlusReader.readPlanes(ImagePlusReader.java:380)
>>      at loci.plugins.in.ImagePlusReader.readImage(ImagePlusReader.java:277)
>>      at loci.plugins.in
>> .ImagePlusReader.readImages(ImagePlusReader.java:238)
>>      at loci.plugins.in
>> .ImagePlusReader.readImages(ImagePlusReader.java:216)
>>      at loci.plugins.in
>> .ImagePlusReader.openImagePlus(ImagePlusReader.java:111)
>>      at loci.plugins.in.Importer.readPixels(Importer.java:146)
>>      at loci.plugins.in.Importer.run(Importer.java:85)
>>      at loci.plugins.LociImporter.run(LociImporter.java:78)
>>      at ij.IJ.runUserPlugIn(IJ.java:212)
>>      at ij.IJ.runPlugIn(IJ.java:176)
>>      at ij.Executer.runCommand(Executer.java:132)
>>      at ij.Executer.run(Executer.java:65)
>>      at java.lang.Thread.run(Thread.java:619)
>>
>> --
>>
>> Eric Denarier
>> Grenoble Institut des Neurosciences
>> Inserm U836
>> Chemin Fortuné Ferrini
>> 38700 La Tronche
>> France
>>
>>
>> Tél :[phone]
>> Fax :[phone]
>>
>> http://neurosciences.ujf-grenoble.fr/
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html