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Hi Curtis,<br>
<br>
Thank you also for clarifying the bio-formats update site and
including OMERO 5.2 update site!
<br>
<br>
I have tested 5.2 and I can login, view and browse my tree without
problem.<br>
<br>
Once I want to open an image I receive following error: Data
Retrieval Failure (see log below).<br>
<br>
That might be because of the version (we have OMERO 5.2.5). When I
uncheck all OMERO update sites, download the latest FIJI-OMERO
connector manually and place it in FIJIs plugin folder it works just
fine.<br>
<br>
Thanks for your help and cheers,<br>
Kai<br>
<br>
java.lang.Exception: java.lang.NoSuchMethodError:
omero.gateway.facility.ROIFacility.getROICount(Lomero/gateway/SecurityContext;J)I<br>
at
org.openmicroscopy.shoola.env.data.views.calls.ROICountLoader$1.doCall(ROICountLoader.java:50)<br>
at
org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)<br>
at
org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)<br>
at
org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)<br>
at java.lang.Thread.run(Thread.java:745)<br>
<br>
at
org.openmicroscopy.shoola.env.ui.UserNotifierImpl.showErrorDialog(UserNotifierImpl.java:189)<br>
at
org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:289)<br>
at
org.openmicroscopy.shoola.env.ui.UserNotifierImpl.notifyError(UserNotifierImpl.java:257)<br>
at
org.openmicroscopy.shoola.agents.metadata.ROICountLoader.handleException(ROICountLoader.java:110)<br>
at
org.openmicroscopy.shoola.env.data.events.DSCallAdapter.eventFired(DSCallAdapter.java:84)<br>
at
org.openmicroscopy.shoola.env.data.views.BatchCallMonitor$1.run(BatchCallMonitor.java:124)<br>
at
java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:311)<br>
at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:756)<br>
at java.awt.EventQueue.access$500(EventQueue.java:97)<br>
at java.awt.EventQueue$3.run(EventQueue.java:709)<br>
at java.awt.EventQueue$3.run(EventQueue.java:703)<br>
at java.security.AccessController.doPrivileged(Native Method)<br>
at
java.security.ProtectionDomain$JavaSecurityAccessImpl.doIntersectionPrivilege(ProtectionDomain.java:76)<br>
at java.awt.EventQueue.dispatchEvent(EventQueue.java:726)<br>
at
java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:201)<br>
at
java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:116)<br>
at
java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:105)<br>
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:101)<br>
at
java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:93)<br>
at java.awt.EventDispatchThread.run(EventDispatchThread.java:82)<br>
<br>
<br>
<div class="moz-cite-prefix">On 09/15/2016 06:47 AM, Curtis Rueden
wrote:<br>
</div>
<blockquote
cite="mid:%3CCADN69ynYX7rHDM69EsSmNgPGk+aFNVmMvoku=eEY2Pmzn-3CEQ@mail.gmail.com%3E"
type="cite">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
<div dir="ltr">Hi again Kai,
<div><br>
</div>
<div>> I will try to find time to update that to OMERO 5.2.x.</div>
<div><br>
</div>
<div>I cut a new release of ImageJ-OMERO (0.4.0) built on OMERO
5.2, and uploaded it to a newly created OMERO-5.2 update site.</div>
<div><br>
</div>
<div>Note that this initial 5.2-compatible version is only very
lightly tested. Please give it a try and let us know how it
goes!</div>
<div><br>
</div>
<div>Regards,</div>
<div>Curtis</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><span style="font-size:12.8px">--</span></div>
<div><span style="font-size:12.8px">Curtis Rueden</span><br>
</div>
<div><span style="font-size:12.8px">LOCI software
architect - <a moz-do-not-send="true"
href="http://loci.wisc.edu/software"
target="_blank">http://loci.wisc.edu/software</a></span></div>
<div>ImageJ2 lead, Fiji maintainer - <span
style="font-size:12.8px"><a
moz-do-not-send="true"
href="http://imagej.net/User:Rueden"
target="_blank">http://imagej.net/User:Rueden</a></span></div>
<div>Did you know ImageJ has a forum? <a
moz-do-not-send="true"
href="http://forum.imagej.net/"
target="_blank">http://forum.imagej.net/</a></div>
<div><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<br>
<div class="gmail_quote">On Wed, Sep 14, 2016 at 2:49 PM, Curtis
Rueden <span dir="ltr"><<a moz-do-not-send="true"
href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">Hi Kai,<span class="">
<div><br>
</div>
<div>
<div>> I realised that updating to the latest
version is only possible when</div>
<div>> Java 8 is check in the update manager while
at the same time</div>
<div>> bio-formats IS NOT checked. If only
bio-formats or both are checked,</div>
<div>> then version 5.1.10 is installed.</div>
</div>
<div><br>
</div>
</span>
<div>The Bio-Formats update site is intended for
previewing _unreleased and hence unstable_ versions of
Bio-Formats.</div>
<div><br>
</div>
<div>Unfortunately, it was still configured to build the
5.1.x development branch, and hence had fallen out of
date compared to the Bio-Formats 5.2.x releases which
have already taken place.</div>
<div><br>
</div>
<div>I have now updated it to build the develop branch
(currently 5.2.x). So if you update your Fiji with the
Bio-Formats update site enabled, you should see (as of
this writing) Revision 011d303e, with release listed
as"5.2.2-DEV" (note that unlike Maven SNAPSHOTs, this
refers to a state _after_ the 5.2.2 release).</div>
<span class="">
<div><br>
</div>
<div>
<div>> Since we are also running OMERO, I am a big
fan of the omero-fiji</div>
<div>> connector, which works great for me! As we
are currently running OMERO</div>
<div>> 5.2.5, I was wondering whether this
connector could also be included</div>
<div>> in an update site for fiji. Currently we
find only 5.0 and 5.1.</div>
</div>
<div><br>
</div>
</span>
<div>Are you talking about the OMERO-5.0 and OMERO-5.1
update sites, which ship the ImageJ-OMERO project [1]?</div>
<div><br>
</div>
<div>If so, I will try to find time to update that to
OMERO 5.2.x.</div>
<div><br>
</div>
<div>Regards,</div>
<div>Curtis</div>
<div><br>
</div>
<div>[1] <a moz-do-not-send="true"
href="https://github.com/imagej/imagej-omero"
target="_blank">https://github.com/imagej/imag<wbr>ej-omero</a></div>
<div class="gmail_extra"><br clear="all">
<div>
<div data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<div>
<div dir="ltr">
<div><span style="font-size:12.8px">--</span></div>
<div><span style="font-size:12.8px">Curtis
Rueden</span><br>
</div>
<div><span style="font-size:12.8px">LOCI
software architect - <a
moz-do-not-send="true"
href="http://loci.wisc.edu/software"
target="_blank">http://loci.wisc.edu/software</a></span></div>
<div>ImageJ2 lead, Fiji maintainer - <span
style="font-size:12.8px"><a
moz-do-not-send="true"
href="http://imagej.net/User:Rueden"
target="_blank">http://imagej.net/User:Ruede<wbr>n</a></span></div>
<div>Did you know ImageJ has a forum? <a
moz-do-not-send="true"
href="http://forum.imagej.net/"
target="_blank">http://forum.imagej.net/</a></div>
<div><br>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div class="h5">
<br>
<div class="gmail_quote">On Wed, Sep 14, 2016 at
6:12 AM, Kai Schleicher <span dir="ltr"><<a
moz-do-not-send="true"
href="mailto:kai.schleicher@unibas.ch"
target="_blank">kai.schleicher@unibas.ch</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0
0 .8ex;border-left:1px #ccc
solid;padding-left:1ex">Hi,<br>
<br>
I encountered a bug when using the bio-formats
exporter to save individual *.tifs (per channel
as well as per timepoint) from a two channel
timelaps hyperstack recorded on a Deltavision
microscope with softworx (*.dv). I have uploaded
said image as ID 17340 here:<br>
<a moz-do-not-send="true"
href="https://www.openmicroscopy.org/qa2/qa/feedback/17340/?token=817ba470200e9765b861241874bd8077"
rel="noreferrer" target="_blank">https://www.openmicroscopy.org<wbr>/qa2/qa/feedback/17340/?token=<wbr>817ba470200e9765b861241874bd80<wbr>77</a><br>
<br>
In detail I believe that channels and timepoints
get mixed up as the image for Channel 0
timepoint 1 is actually channel 1 timepoint 0
and so on.<br>
<br>
I am using the latest bio-formats version 5.2.2.<br>
<br>
Concerning this I realised that updating to the
latest version is only possible when Java 8 is
check in the update manager while at the same
time bio-formats IS NOT checked.<br>
If only bio-formats or both are checked, then
version 5.1.10 is installed.<br>
<br>
This seems a bit counter-intuitive to me, if
possible I think it'd be easiest from a user
perspective to keep updating the bio-formats
from the respective update site.<br>
Just as a comment, I was also wondering if it'd
be possible to show the bio-formats version
number in the splash screen of the importer?
This way it'd easier for our facility users to
find out which version they have installed.<br>
<br>
Since we are also running OMERO, I am a big fan
of the omero-fiji connector, which works great
for me! As we are currently running OMERO 5.2.5,
I was wondering whether this connector could
also be included in an update site for fiji.
Currently we find only 5.0 and 5.1.<br>
<br>
Thanks for your help and cheers,<br>
Kai<span><font color="#888888"><br>
<br>
-- <br>
<br>
Kai Schleicher, PhD | Research Associate in
Advanced Light Microscopy | Biozentrum,
University of Basel | Klingelbergstrasse
50/70 | CH-4056 Basel |<br>
Phone: <a moz-do-not-send="true"
href="tel:%2B41%2061%20267%2022%2050"
value="+41612672250" target="_blank">+41
61 267 22 50</a> | <a
moz-do-not-send="true"
href="mailto:kai.schleicher@unibas.ch"
target="_blank">kai.schleicher@unibas.ch</a>
| <a moz-do-not-send="true"
href="http://www.biozentrum.unibas.ch"
rel="noreferrer" target="_blank">www.biozentrum.unibas.ch</a>
| <a moz-do-not-send="true"
href="http://www.microscopynetwork.unibas.ch"
rel="noreferrer" target="_blank">www.microscopynetwork.unibas.c<wbr>h</a><br>
<br>
______________________________<wbr>_________________<br>
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</font></span></blockquote>
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