[ome-users] install Slidebook file format extension for OMERO

Fri Feb 9 13:43:49 GMT 2018

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?

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.

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/ 
>>>> <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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