[ome-users] Bioformats works only outside OME (more data)

[Curtis Rueden]

Hi Mario & Ilya,

As I said yesterday, there is a critical problem with the latest
Bio-Formats and OME server. I was afraid of this, as I have honestly
been too neglectful of testing with OME server recently. I am looking
into the problem today, and hope to have a solution as soon as
possible. In the meantime, Ilya, if you have a working version of
loci_tools.jar that you could post online somewhere temporarily for
people to use, that would be really helpful. Otherwise I can try
building a few of the old versions until I find one that works well.

My sincerest apologies to Mario, Linda and any others who have been
struggling with the Bio-Formats/OME connectivity.

-Curtis

On Jan 11, 2008 9:08 AM, Ilya Goldberg <igg at nih.gov> wrote:
> It seems more and more people are struggling with OME server's over-
> riding the new and better bioformats with its old and deprecated
> importers.
> See Curits's earlier post about re-arranging the importer priority to
> either eliminate OME's importers altogether, or move bioformats up in
> the priority list.
> We will make these changes permanent in future releases so that BF
> takes priority over everything else.
>
> There may be other problems with the connection, but in the default
> configuration, OME's importers will over-ride TIFF, LSM, and STK.
> They should still import them, but apparently there are potentially
> other issues with these files, and BF does a better job.  LIFF and
> LIF should have been delegated to BF, because there are no "native"
> importers for these.  Which makes me think there may be an unrelated
> problem with the BF setup.
>
> -Ilya
>
>
> On Jan 11, 2008, at 6:31 AM, Mario Valle wrote:
>
> > Continuing investigation I have found:
> >
> > - From the OME web interface I can import only TIFF files. No
> > error, nothing, only
> > "unrecognized format"
> >
> > - From the command line: ome import -d "dataset" image
> >   I can import TIFF, STK, ie. everything except formats supported
> > by the bioformats
> >   library.
> >
> > So seems there are two problems:
> >   1) the bioformats library not found
> >   2) the web server accessing only a minimal subset of the import
> > functionality.
> >
> > Help!
> >       mario
> >
> >
> > Mario Valle wrote:
> >> I'm still stuck at the image importing step...
> >>
> >> 1) Moved to OME 2.6.1 on Mac (here I'm administrator, so I can
> >> experiment)
> >> 2) installed latest loci_tools.jar under /OME/java
> >> 3) downloaded bftools, unpacked and added the same loci_tools.jar
> >> ar OME in the resulting
> >> directory
> >> 3) tried bfview with TIFF, LIF, LSM, STK, LIFF files. Everything
> >> works. Only TIFF with
> >> character encoding Mac cannot be visualized, but this is another
> >> problem.
> >> 3) tried to import the same files in OME, only the tiff files are
> >> imported.
> >> Seems like OME is using some old import method, but no other copy
> >> of loci_tools.jar is
> >> anywhere on the machine.
> >> Help!
> >>      mario
> >>
> >>
> >
> > --
> > Ing. Mario Valle
> > Visualization Group                              | http://
> > www.cscs.ch/~mvalle
> > Swiss National Supercomputing Centre (CSCS)      | Tel:  +41 (91)
> > 610.82.60
> > v. Cantonale Galleria 2, 6928 Manno, Switzerland | Fax:  +41 (91)
> > 610.82.82
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> >
>
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