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

[David Gault (Staff)]

Hi Alexander ,

I just wanted to provide you with an update on the issue you reported.
We have been able to confirm the issue is related to C++ version of bio formats and are currently investigating a fix.
We will provide a further update for you next week.

With Thanks,
David Gault

OME Software Developer

________________________________________
From: ome-devel <ome-devel-bounces at lists.openmicroscopy.org.uk> on behalf of Alexander Görtz <ome at nyloc.de>
Sent: 16 September 2015 12:00
To: ome-devel at lists.openmicroscopy.org.uk
Subject: [ome-devel] Some trouble with RGB image export and import

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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