[ome-users] Bioformats works only outside OME (answering my own mail)
Mario Valle
mvalle at cscs.ch
Thu Jan 31 13:49:52 GMT 2008
Seems that OME was not able to import the two images in a single import session.
Now I loaded 2007-11-13_DMEM_GFPcells.lif by itself without problems.
Now the good news: with the new loci_tools.jar we are able to import all the formats we need:
Zeiss .lsm
OpenLab .liff
Leice .lif
Metamorph .stk
TIFF .tiff
Thanks again!
mario
Mario Valle wrote:
> Ciao Curtis!
> The new loci_tools.jar seems better, but there are apparent good Leica files (.lif) that
> are not imported.
> As per your suggestion, I have changed the order of readers in the database to put
> Bioformats in the first position.
> You can find the two files under ftp.cscs.ch/out/mvalle/
>
> 2007-11-12_L15_AF001.lif (21MB)
> this file has been correctly imported as a set of distinct images
>
> 2007-11-13_DMEM_GFPcells.lif (11MB)
> this instead has been rejected as 'unknown format'
>
> Could you check those images? BTW, the both open correctly in bfview, even if the show
> only a single contained image instead of 14. Any idea?
>
> Also I had to set permissions on the images to rwxrwxrwx; with r--r--r-- no import takes
> places in OME 2.6.1 on Mac.
>
> Thanks for your help!
> mario
>
>
> Curtis Rueden wrote:
>> Hi again,
>>
>> It looks like I spoke too soon about the new loci_tools.jar not being
>> able to stitch files. Upon further investigation, it seems to be
>> working fine. I think my problem before was that OME's Perl Bio-Rad
>> PIC reader was overriding Bio-Formats on my system at the time, so it
>> read my test dataset as 12 separate Images, rather than a single
>> Image.
>>
>> Once again, you can find the updated loci_tools.jar here:
>> http://skyking.microscopy.wisc.edu/curtis/jar/loci_tools.jar
>>
>> Please let me know if it doesn't work for you.
>>
>> -Curtis
>>
>> On Jan 15, 2008 1:56 PM, Curtis Rueden <ctrueden at wisc.edu> wrote:
>>> 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
>>>>>> _______________________________________________
>>>>>> ome-users mailing list
>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>
>>>>> _______________________________________________
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>>>>>
>
--
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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