[ome-devel] Some trouble with RGB image export and import

[Alexander Görtz]

Hi,

I new to the list and developing with the Bioformats library but on my way I 
came across some problems that for now I was able to solve on my one or with 
the help of the very friendly #ome irc channel at freenode. But this one seems 
to be a bit harder to solve ;)

My motivation for the following scenario was that I'm currently concerned with 
the task of analyzing microscopy images with the OpenCV library for 
integration into a bigger C++ based software. In my current use case I only 
have non RGB channels which made the conversion from the bioformats PixelBuffer 
to a OpenCV Mat quiet easy, but I wanted to test how RGB data is handled in 
the C++ library. So I tried to create a RGB OME TIFF image from a simple RGB 
jpg I downloaded from the net (http://nyloc.de/public/test.jpg).
For that I used ImageJ and the command line bfconvert function to create a 
.ome.tif image (http://nyloc.de/public/test.ome.tif).
With the c++ library I can read the metadata and the results look ok (http://
paste.pound-python.org/show/KjrtdMefBfzgqAr3ZH5M/) and don't differ from the 
results given by showinf (http://paste.pound-python.org/show/
LmzoDQ7j4vryhmtTs5VM/)
But ImageJ shows different meta data if I import the RGB OME TIFF image 
(https://dpaste.de/ROip)
The image opened by ImageJ shows 3 channels but each channel seems to contain 
the entire RGB image not only a single color as the isRGB false would suggest.

And if I try to open the image data with the OMETIFFReader::openBytes function 
it crashes with
terminate called after throwing an instance of 
'ome::bioformats::tiff::Exception'
  what():  TIFFReadEncodedStrip: 2720: Strip out of range, max 2160

This was checked with bioformats 5.14 and 5.13 and mtbc from the IRC also 
mentioned that the "Bio-Formats remote importer [...] complain that there are 
18768 bits per sample".

If you need any more information to clear this up I would be happy to provide 
them.

Sincerely
Alex (nyloc)
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