[ome-users] install Slidebook file format extension for OMERO
Kai Schleicher
kai.schleicher at unibas.ch
Fri Feb 9 16:21:44 GMT 2018
Hi Sebastian,
> Did you rename the file as xxx.jar before putting them under your Java
> folder?
yes I did, I renamed it to "SlideBook6Reader.jar". Sorry, I should have
written that in my previous mail.
cheers,
Kai
On 02/09/2018 04:21 PM, Sebastien Besson (Staff) wrote:
> Hi Kai,
>
>
>> On 9 Feb 2018, at 13:43, Kai Schleicher <kai.schleicher at unibas.ch
>> <mailto:kai.schleicher at unibas.ch>> wrote:
>>
>> Hi Sebastien,
>>
>> thanks for the update!
>>
>> We have added the JAR [1] to the insight client as described. Do you
>> think that this one file was is all thats needed or should there be
>> some more JARs?
>>
> No the 3i Slidebook JAR should be the only requirement.
>>
>> Upload unfortunately still fails with "file format not valid", but
>> this time we also receive an exception which might contain some
>> further hints (see below). It seems like it actually tried to read my
>> file but found some issues with it - the file itself
>> <https://filesender.switch.ch/filesender/?vid=20c7b50f-f673-e329-1276-00007a6287f3>
>> is fine, at least it opens with the latest bioformats.
>>
> The file format not valid error indicates an error client-side i.e.
> during the
> detection of the file as a format support by Bio-Formats.
> I can see you downloaded the file straight away from the 3i Fiji
> update site.
> Did you rename the file as xxx.jar before putting them under your Java
> folder?
>
> Sebastien
>>
>> We are still on OMERO5.3.3, could that be the reason?
>>
>> Thanks for your help and cheers,
>> Kai
>>
>>
>>> java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
>>> at java.util.ArrayList.rangeCheck(ArrayList.java:653)
>>> at java.util.ArrayList.get(ArrayList.java:429)
>>> at
>>> loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
>>> at loci.formats.FormatReader.setId(FormatReader.java:1397)
>>> at loci.formats.ImageReader.setId(ImageReader.java:839)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at loci.formats.Memoizer.setId(Memoizer.java:649)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at
>>> ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
>>> at
>>> ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
>>> at
>>> ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
>>>
>>> at
>>> ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
>>> at
>>> ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
>>> at
>>> org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)
>>> at
>>> org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
>>> at java.lang.Thread.run(Thread.java:748)
>>>
>>> at
>>> org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:671)
>>> at
>>> ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:536)
>>> at
>>> ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:471)
>>> at
>>> ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
>>> at
>>> ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
>>>
>>> at
>>> ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
>>> at
>>> ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
>>> at
>>> org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)
>>> at
>>> org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
>>> at
>>> org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
>>> at
>>> org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
>>> at java.lang.Thread.run(Thread.java:748)
>>> Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
>>> at java.util.ArrayList.rangeCheck(ArrayList.java:653)
>>> at java.util.ArrayList.get(ArrayList.java:429)
>>> at
>>> loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
>>> at loci.formats.FormatReader.setId(FormatReader.java:1397)
>>> at loci.formats.ImageReader.setId(ImageReader.java:839)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at loci.formats.Memoizer.setId(Memoizer.java:649)
>>> at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
>>> at
>>> ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
>>> ... 16 more
>>
>>
>>
>> [1]
>> http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742
>>
>>
>>
>> On 02/09/2018 09:21 AM, Sebastien Besson (Staff) wrote:
>>> Hi Kai,
>>>
>>> thanks for getting back to us. I realise my initial answer was
>>> incomplete to test the
>>> full workflow. In addition to the server addition, you will also
>>> need to add the third-party
>>> JARs to the client you will use for the import.
>>>
>>> See [1] for adding JARs to OMERO.insight. If you are using the CLI,
>>> you need to
>>> add your third-party JARs under lib/client
>>>
>>> Best,
>>> Sebastien
>>>
>>> [1] http://help.openmicroscopy.org/configure-client.html#jar
>>>
>>>
>>>
>>>> On 8 Feb 2018, at 13:56, Kai Schleicher <kai.schleicher at unibas.ch
>>>> <mailto:kai.schleicher at unibas.ch>> wrote:
>>>>
>>>> Hi Sebastien,
>>>>
>>>> thanks for your help!
>>>>
>>>> We have tried and put the jar file under lib/server and restarted
>>>> the server. However, that seems to not have been enough - upload of
>>>> *.sld files still fails.
>>>>
>>>> Probably we missed additional steps, but unfortunately it is not
>>>> too clear to us right now what else needs to happen. Are there
>>>> additional files that need to be placed at other locations?
>>>>
>>>> Sorry for the vague question...
>>>>
>>>> If you have some more details on that would be greatly appreciated :)
>>>>
>>>> Thanks and cheers,
>>>> Kai
>>>>
>>>>
>>>> On 02/06/2018 06:01 PM, Sebastien Besson (Staff) wrote:
>>>>> Hi Kai,
>>>>>
>>>>> Since Bio-Formats 5.2.0, the native support for 3i Slidebook files
>>>>> is indeed provided via a external third-party JAR developed and
>>>>> maintained by Intelligent Imaging [1]. In Fiji, the installation
>>>>> of this JAR is managed via the Slidebook update site maintained by 3i.
>>>>>
>>>>> Adding support for this reader in OMERO should work the same way
>>>>> as other server extensions [2]. The critical part is to have the
>>>>> Slidebook classes available to the server, typically by putting
>>>>> the appropriate JAR under lib/server and restarting the latter.
>>>>>
>>>>> It would be really interesting to hear from the 3i developer or
>>>>> support team whether they have tested this workflow or if they
>>>>> have plans to support it in the future.
>>>>> Best,
>>>>> Sebastien
>>>>>
>>>>> [1]
>>>>> http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/
>>>>> [2]
>>>>> https://docs.openmicroscopy.org/omero/5.4.3/developers/Server/ExtendingOmero.html
>>>>>
>>>>>
>>>>>> On 5 Feb 2018, at 12:26, Kai Schleicher <kai.schleicher at unibas.ch
>>>>>> <mailto:kai.schleicher at unibas.ch>> wrote:
>>>>>>
>>>>>> Dear OME team,
>>>>>>
>>>>>> I'd like to import slidebook *.sld files in OMERO.
>>>>>>
>>>>>> Since Bio-Formats relies on a plugin from an external update site
>>>>>> [1] to enable import of SlideBook SLD files, I was wondering if
>>>>>> there is a way to integrate this plugin into our OMERO as well?
>>>>>>
>>>>>> Thanks and cheers,
>>>>>> Kai
>>>>>>
>>>>>> [1]: http://sites.imagej.net/SlideBook/
>>>>>>
>>>>>> --
>>>>>>>> Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41
>>>>>>>> 61 207 22 50 (central)<<
>>>>>> Kai Schleicher, PhD | Research Associate in Advanced Light
>>>>>> Microscopy | Biozentrum, University of Basel | Klingelbergstrasse
>>>>>> 50/70 | CH-4056 Basel |
>>>>>> Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) |
>>>>>> kai.schleicher at unibas.ch <mailto:kai.schleicher at unibas.ch> |
>>>>>> www.biozentrum.unibas.ch <http://www.biozentrum.unibas.ch/> |
>>>>>> www.microscopynetwork.unibas.ch
>>>>>> <http://www.microscopynetwork.unibas.ch/>
>>>>>>
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>>>>>
>>>>>
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>
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