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<p>Hi Sebastien,</p>
<p>thanks for the update!<br>
</p>
<p>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? </p>
<p>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 - <a
moz-do-not-send="true"
href="https://filesender.switch.ch/filesender/?vid=20c7b50f-f673-e329-1276-00007a6287f3">the
file itself</a> is fine, at least it opens with the latest
bioformats.<br>
</p>
<p>We are still on OMERO5.3.3, could that be the reason?</p>
<p>Thanks for your help and cheers,<br>
Kai<br>
</p>
<p><br>
<blockquote type="cite">java.lang.IndexOutOfBoundsException:
Index: 0, Size: 0
<br>
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
<br>
at java.util.ArrayList.get(ArrayList.java:429)
<br>
at
loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
<br>
at loci.formats.FormatReader.setId(FormatReader.java:1397)
<br>
at loci.formats.ImageReader.setId(ImageReader.java:839)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at
loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at loci.formats.Memoizer.setId(Memoizer.java:649)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)<br>
at
ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)<br>
at
ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
<br>
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)<br>
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)<br>
at
org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)<br>
at
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)<br>
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)<br>
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)<br>
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)<br>
at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br>
at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br>
at java.lang.Thread.run(Thread.java:748)
<br>
<br>
at
org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:671)<br>
at
ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:536)<br>
at
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:471)<br>
at
ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)<br>
at
ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
<br>
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)<br>
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)<br>
at
org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)<br>
at
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)<br>
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)<br>
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)<br>
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)<br>
at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br>
at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br>
at java.lang.Thread.run(Thread.java:748)
<br>
Caused by: java.lang.IndexOutOfBoundsException: Index: 0, Size:
0
<br>
at java.util.ArrayList.rangeCheck(ArrayList.java:653)
<br>
at java.util.ArrayList.get(ArrayList.java:429)
<br>
at
loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
<br>
at loci.formats.FormatReader.setId(FormatReader.java:1397)
<br>
at loci.formats.ImageReader.setId(ImageReader.java:839)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at
loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at loci.formats.Memoizer.setId(Memoizer.java:649)
<br>
at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br>
at
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)<br>
... 16 more
</blockquote>
<br>
</p>
<p><br>
</p>
<p>[1] <a class="moz-txt-link-freetext"
href="http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742">http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742</a>
<br>
</p>
<br>
<div class="moz-cite-prefix">On 02/09/2018 09:21 AM, Sebastien
Besson (Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:628D5921-7BE8-4FEC-9B0C-6A07DFC959BA@dundee.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Kai,
<div class=""><br class="">
</div>
<div class="">thanks for getting back to us. I realise my initial
answer was incomplete to test the</div>
<div class="">full workflow. In addition to the server addition,
you will also need to add the third-party</div>
<div class="">JARs to the client you will use for the import. </div>
<div class=""><br class="">
</div>
<div class="">See [1] for adding JARs to OMERO.insight. If you are
using the CLI, you need to</div>
<div class="">add your third-party JARs under lib/client</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a
href="http://help.openmicroscopy.org/configure-client.html#jar"
class="" moz-do-not-send="true">http://help.openmicroscopy.org/configure-client.html#jar</a></div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 8 Feb 2018, at 13:56, Kai Schleicher <<a
href="mailto:kai.schleicher@unibas.ch" class=""
moz-do-not-send="true">kai.schleicher@unibas.ch</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">Hi Sebastien,</p>
<p class="">thanks for your help!</p>
<p class="">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.</p>
<p class="">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?
<br class="">
</p>
<p class="">Sorry for the vague question...</p>
<p class="">If you have some more details on that would
be greatly appreciated :)</p>
<p class="">Thanks and cheers,<br class="">
Kai<br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 02/06/2018 06:01 PM,
Sebastien Besson (Staff) wrote:<br class="">
</div>
<blockquote type="cite"
cite="mid:6F15D1CF-4BC8-4AE1-AC2D-721D729E3D16@dundee.ac.uk"
class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Hi Kai,</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">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.</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">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.</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">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.</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class=""></span><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Best,</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">Sebastien</span></div>
<br class="">
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">[1]
</span><a
href="http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/"
style="text-decoration:none;" class=""
moz-do-not-send="true"><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">http://blog.openmicroscopy.org/file-formats/community/2016/08/31/bf-partnerships/</span></a><span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">
</span></div>
<div style="line-height: 1.38; margin-top: 0pt;
margin-bottom: 0pt;" class="">
<span style="font-size: 11pt; font-family: Arial; font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; vertical-align: baseline; white-space: pre-wrap;" class="">[2]
</span><a
href="https://docs.openmicroscopy.org/omero/5.4.3/developers/Server/ExtendingOmero.html"
style="text-decoration:none;" class=""
moz-do-not-send="true"><span style="font-size: 11pt; font-family: Arial; color: rgb(17, 85, 204); font-variant-ligatures: normal; font-variant-east-asian: normal; font-variant-position: normal; text-decoration: underline; -webkit-text-decoration-skip: none; vertical-align: baseline; white-space: pre-wrap;" class="">https://docs.openmicroscopy.org/omero/5.4.3/developers/Server/ExtendingOmero.html</span></a></div>
<br class="">
<div class=""><br class="">
<blockquote type="cite" class="">
<div class="">On 5 Feb 2018, at 12:26, Kai
Schleicher <<a
href="mailto:kai.schleicher@unibas.ch"
class="" moz-do-not-send="true">kai.schleicher@unibas.ch</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div class="">Dear OME team,<br class="">
<br class="">
I'd like to import slidebook *.sld files in
OMERO.<br class="">
<br class="">
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?<br class="">
<br class="">
Thanks and cheers,<br class="">
Kai<br class="">
<br class="">
[1]: <a
href="http://sites.imagej.net/SlideBook/"
class="" moz-do-not-send="true">
http://sites.imagej.net/SlideBook/</a><br
class="">
<br class="">
-- <br class="">
<blockquote type="cite" class="">
<blockquote type="cite" class="">Please note
my NEW PHONE NUMBERS: +41 61 207 57 31
(direct) +41 61 207 22 50
(central)<<<br class="">
</blockquote>
</blockquote>
Kai Schleicher, PhD | Research Associate in
Advanced Light Microscopy | Biozentrum,
University of Basel | Klingelbergstrasse 50/70
| CH-4056 Basel |<br class="">
Phone: +41 61 207 57 31 (direct) +41 61 207 22
50 (central) | <a
href="mailto:kai.schleicher@unibas.ch"
class="" moz-do-not-send="true">
kai.schleicher@unibas.ch</a> | <a
href="http://www.biozentrum.unibas.ch/"
class="" moz-do-not-send="true">
www.biozentrum.unibas.ch</a> | <a
href="http://www.microscopynetwork.unibas.ch/"
class="" moz-do-not-send="true">
www.microscopynetwork.unibas.ch</a><br
class="">
<br class="">
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class="">
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moz-do-not-send="true">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br
class="">
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</div>
</blockquote>
</div>
<br class="">
<br class="">
<span style="font-size:10pt;" class="">The University
of Dundee is a registered Scottish Charity, No:
SC015096</span>
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</div>
_______________________________________________<br
class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk"
class="" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
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<br>
<span style="font-size:10pt;">The University of Dundee is a
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