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<p>Hi Sebastian,</p>
<p>
<blockquote type="cite">
<div>Did you rename the file as xxx.jar before putting them
under your Java</div>
<div>folder?</div>
</blockquote>
yes I did, I renamed it to "SlideBook6Reader.jar". Sorry, I should
have written that in my previous mail.</p>
<p>cheers,<br>
Kai<br>
</p>
<br>
<div class="moz-cite-prefix">On 02/09/2018 04:21 PM, Sebastien
Besson (Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:93174DCA-D8F0-40C0-9A95-FE66679AC076@dundee.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Kai,
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 9 Feb 2018, at 13:43, 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 the update!<br class="">
</p>
<p class="">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>
</div>
</div>
</blockquote>
No the 3i Slidebook JAR should be the only requirement.<br
class="">
<blockquote type="cite" class="">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">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"
class="">
the file itself</a> is fine, at least it opens with
the latest bioformats.</p>
</div>
</div>
</blockquote>
<div>The file format not valid error indicates an error
client-side i.e. during the</div>
<div>detection of the file as a format support by Bio-Formats.</div>
I can see you downloaded the file straight away from the 3i
Fiji update site.</div>
<div>Did you rename the file as xxx.jar before putting them
under your Java</div>
<div>folder?</div>
<div><br class="">
</div>
<div>Sebastien<br class="">
<blockquote type="cite" class="">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">We are still on OMERO5.3.3, could that be
the reason?</p>
<p class="">Thanks for your help and cheers,<br class="">
Kai<br class="">
</p>
<p class=""><br class="">
</p>
<blockquote type="cite" class="">java.lang.IndexOutOfBoundsException:
Index: 0, Size: 0
<br class="">
at
java.util.ArrayList.rangeCheck(ArrayList.java:653) <br
class="">
at java.util.ArrayList.get(ArrayList.java:429) <br
class="">
at
loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
<br class="">
at
loci.formats.FormatReader.setId(FormatReader.java:1397)
<br class="">
at
loci.formats.ImageReader.setId(ImageReader.java:839) <br
class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at
loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
<br class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at
loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
<br class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at loci.formats.Memoizer.setId(Memoizer.java:649)
<br class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)<br
class="">
at
ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)<br
class="">
at
ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
<br class="">
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)<br
class="">
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)<br
class="">
at
org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)<br
class="">
at
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br
class="">
at java.lang.Thread.run(Thread.java:748) <br
class="">
<br class="">
at
org.openmicroscopy.shoola.env.data.util.StatusLabel.update(StatusLabel.java:671)<br
class="">
at
ome.formats.importer.ImportCandidates.safeUpdate(ImportCandidates.java:536)<br
class="">
at
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:471)<br
class="">
at
ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)<br
class="">
at
ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
<br class="">
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)<br
class="">
at
ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)<br
class="">
at
org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5945)<br
class="">
at
org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1068)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br
class="">
at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br
class="">
at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br
class="">
at java.lang.Thread.run(Thread.java:748) <br
class="">
Caused by: java.lang.IndexOutOfBoundsException: Index:
0, Size: 0 <br class="">
at
java.util.ArrayList.rangeCheck(ArrayList.java:653) <br
class="">
at java.util.ArrayList.get(ArrayList.java:429) <br
class="">
at
loci.formats.in.SlidebookReader.initFile(SlidebookReader.java:654)
<br class="">
at
loci.formats.FormatReader.setId(FormatReader.java:1397)
<br class="">
at
loci.formats.ImageReader.setId(ImageReader.java:839) <br
class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at
loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
<br class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at
loci.formats.ChannelSeparator.setId(ChannelSeparator.java:291)
<br class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at loci.formats.Memoizer.setId(Memoizer.java:649)
<br class="">
at
loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
<br class="">
at
ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)<br
class="">
... 16 more </blockquote>
<br class="">
<div class=""><br class="webkit-block-placeholder">
</div>
<p class=""><br class="">
</p>
<p class="">[1] <a class="moz-txt-link-freetext"
href="http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742"
moz-do-not-send="true">
http://sites.imagej.net/SlideBook/jars/bio-formats/SlideBook6Reader.jar-20161214162742</a>
<br class="">
</p>
<br class="">
<div class="moz-cite-prefix">On 02/09/2018 09:21 AM,
Sebastien Besson (Staff) wrote:<br class="">
</div>
<blockquote type="cite"
cite="mid:628D5921-7BE8-4FEC-9B0C-6A07DFC959BA@dundee.ac.uk"
class="">
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 class="">
<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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</blockquote>
</div>
<br class="">
<br class="">
<span style="font-size:10pt;" class="">The
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<span style="font-size:10pt;">The University of Dundee is a
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