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

Tue Jan 15 19:56:13 GMT 2008

Hi Mario, Linda, and everyone,

I isolated the most serious problem to a change we made on December
11th (r3465). I have fixed several problems including that one, and
placed a working loci_tools.jar you can try here:

http://skyking.microscopy.wisc.edu/curtis/jar/loci_tools.jar

Just overwrite the one in /OME/java with that one, and hopefully
things will work better.

We will try to make another official release of the library soon, to
minimize the number of new OME installations that are affected by this
problem.

Please note what Ilya and I said earlier about rearranging the order
of importers, though -- if you don't, Bio-Formats will not be used for
certain formats including Deltavision, BMP, Molecular Dynamics GEL,
Metamorph STK, DICOM, TIFF & OME-TIFF, Bio-Rad PIC, and Zeiss LSM.

Also please note that there are undoubtably still some (hopefully more
minor) bugs -- in particular, the file stitching is not working
properly. This means you cannot yet import a single Image distributed
across multiple numbered files (e.g., data1.tiff, data2.tiff,
data3.tiff, etc.). This functionality used to work, so is probably
just a matter of me fixing more bugs in the Bio-Formats file stitching
code somewhere.

Linda, to revisit your earlier question about metadata: this updated
version of Bio-Formats should properly include all the original
key/value metadata pairs in the OME import. To see these values, after
importing the Image, click the Image thumbnail to bring up the Image
details screen. Among other things, you'll see a "Module executions"
box on the top right. The first link in that box should say "Image
import" -- click it, and you'll receive a detailed list of
information, including the key/value pairs in their original format
beneath a section labeled "OriginalMetadata." Please let me know if it
doesn't work for you.

Lastly, in the process of debugging, I regenerated several old
versions of loci_tools.jar. I placed them online, in case anyone else
wants them to do their own testing:

http://skyking.microscopy.wisc.edu/curtis/archive/

Please let me know if you continue to have trouble, or have any
additional questions.

-Curtis

On Jan 11, 2008 12:22 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
> 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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