[ome-users] OME-XML image re-imported has wrong colors

[Curtis Rueden]

Hi Mario,

The "premature end of file" error was a bug in Bio-Formats, which is fixed
in today's release. I did some tests, and I'm guessing the color inversion
is a bug in the OME Perl OME-XML importer module
(OME::ImportEngine::XMLreader). I tried importing your file with the
XMLreader module set before Bio-Formats, and saw the color inversion. Then I
tried reimporting with the XMLreader module removed, so that it would use
Bio-Formats instead, and the colors look correct.

So one workaround to the problem is to use Bio-Formats instead of
OME::ImportEngine::XMLreader for OME-XML files. However, please note that
this method is less thoroughly tested. I noticed some differences between
the imports, such as loss of group and ownership information with the BF
import, that we will need to address in a future release.

-Curtis

On Jan 31, 2008 4:19 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:

> Hi Mario,
>
> The exported .ome file is not inverted when read with Bio-Formats
> (showinf). However, there is a strange "premature end of file" error. This
> message is probably coming from the library responsible for zlib
> decompression and/or base64 decoding. It may be a bug in Bio-Formats, or it
> may be that the exported content really is truncated. Either way, there is a
> bug somewhere. We'll analyze your exported file further and I'll reply again
> when I know more.
>
> -Curtis
>
>
> On Jan 31, 2008 10:39 AM, Mario Valle <mvalle at cscs.ch> wrote:
>
> > I have exported an image from our Linux installation of OME 2.6.1 as
> > OME-XML then imported
> > it on the Mac installation.
> > The import was ok, but the loaded image is the negative of the original
> > image.
> > The original image and the exported one are on ftp.cscs.ch/out/mvalle
> > and are called:
> > -rw-r--r--  1 mvalle csvis  8755901 2008-01-31 17:32 Hoechst_ND -
> > n000000.ome
> > -rw-r--r--  1 mvalle csvis 11026676 2008-01-31 17:31 Hoechst_ND -
> > n000000.tif
> > What happens?
> > Thanks for the help!
> >                        mario
> >
> > --
> > Ing. Mario Valle
> > Visualization Group                              |
> > http://www.cscs.ch/~mvalle <http://www.cscs.ch/%7Emvalle>
> > Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)
> > 610.82.60
> > v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)
> > 610.82.82
> > _______________________________________________
> > ome-users mailing list
> > ome-users at lists.openmicroscopy.org.uk
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> >
>
>
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