<div dir="ltr">Hi Laurent,<div><br></div><div>The CellProfiler is using standard OMERO jars which you can download from OME's website and replace in prokaryote.jar. Probably better way of doing it is simply building the prokaryote module from source. OmeroReader.class which CellProfiler is using to access the images is located in blitz.jar so you should replace the OMERO version in this block: <a href="https://github.com/CellProfiler/prokaryote/blob/1.0.11/pom.xml#L10">https://github.com/CellProfiler/prokaryote/blob/1.0.11/pom.xml#L10</a> with the one that matches your server version and then build and install the module.</div><div><br></div><div>Please mind that as of OMERO 5.3 OmeroReader is deprecated (<a href="https://github.com/openmicroscopy/openmicroscopy/blob/dev_5_3/components/blitz/src/loci/ome/io/OmeroReader.java#L90">https://github.com/openmicroscopy/openmicroscopy/blob/dev_5_3/components/blitz/src/loci/ome/io/OmeroReader.java#L90</a>) and might be removed in the future versions.</div><div><br></div><div>Cheers,</div><div>Emil</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Fri, Sep 15, 2017 at 9:16 AM, Laurent Guerard <span dir="ltr"><<a href="mailto:laurent.guerard@unibas.ch" target="_blank">laurent.guerard@unibas.ch</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p><font face="Ubuntu">Hi Emil,</font></p>
<p><font face="Ubuntu">I think that, in the long run, the python
readers would indeed be the most useful way, but right now we'll
probably go for the jar method since it would probably be the easiest
to set up and deploy on all machines.</font></p>
<p><font face="Ubuntu">Do you know where I can find the CellProfiler's
OMERO jar ? <br>
</font></p>
<p><font face="Ubuntu">Thanks again for your help !</font></p>
<p><font face="Ubuntu">Best,<br>
</font></p>
<div class="m_-8434175930559358014moz-signature">--------------- <br>
Laurent Guerard <br>
<br>
<br>
</div><div><div class="h5">
<div class="m_-8434175930559358014moz-cite-prefix">On 13/09/2017 20:19, Emil Rozbicki
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div>Hi Laurent,</div>
<div><br>
</div>
<div>Repackaging the prokaryote.jar with appropriate jars would
be probably the most efficient route in your case. Sorry, I
wasn't aware you're using the GUI mode - should have asked. We
have not attempted yet to package the CellProflier itself with
the python readers as we're mainly using it in the headless
mode. I happy to document the set up process for python
readers if you're interested.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Emil</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Wed, Sep 13, 2017 at 3:26 PM,
Laurent Guerard <span dir="ltr"><<a href="mailto:laurent.guerard@unibas.ch" target="_blank">laurent.guerard@unibas.ch</a>></span>
wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div text="#000000" bgcolor="#FFFFFF">
<p><font face="Ubuntu">Hi Emil,</font></p>
<p><font face="Ubuntu">If I understood everything, all the
jars are part of the prokaryote.jar which I would need
to extract and rearchive right ?</font></p>
<p>Using python readers would be the best solution indeed,
and we would be interested in that. However, since we
would need to fix this on multiple computers, is it
easily deployable ? And would you have some
documentation on how to set it up ? :)</p>
<p>Thanks again !</p>
<p>Best,<br>
</p>
<div class="m_-8434175930559358014m_-4976640546338776689moz-signature">---------------
<br>
Laurent Guerard <br>
<br>
<br>
</div>
<div>
<div class="m_-8434175930559358014h5">
<div class="m_-8434175930559358014m_-4976640546338776689moz-cite-prefix">On
13/09/2017 10:42, Emil Rozbicki wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">Hi Kai,
<div><br>
</div>
<div>Have you also updated CellProfiler's OMERO
jars? It's possible that your CellProfiler
installation is still using OMERO 5.2 jars hence
the connection issue.</div>
<div><br>
</div>
<div>If that's the case the simplest solution is
to replace the jars to match your server
version. Alternative solution is to use python
readers instead of java readers - details here: <a href="https://github.com/CellProfiler/CellProfiler/issues/1772" target="_blank">https://github.com/CellP<wbr>rofiler/CellProfiler/issues/<wbr>1772</a>.
It needs some work to set it up put pays back on
performance and the issue free upgrades.</div>
<div><br>
</div>
<div>Cheers,</div>
<div>Emil</div>
</div>
<div class="gmail_extra"><br>
<div class="gmail_quote">On Tue, Sep 12, 2017 at
5:19 PM, Kai Schleicher <span dir="ltr"><<a 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>
We were using CellProfilers "LoadData" module
successfully with OMERO 5.2.4 to fetch images
directly from OMERO.<br>
<br>
We recently upgraded to the really awesome
OMERO 5.3.3 (yay :)), but coincidentally we
seem to now have issues using CPs LoadData
module to fetch the images.<br>
<br>
Can you confirm if this connection is still
possible with OMERO 5.3.3 or if there is maybe
an issue?<br>
<br>
Thanks for your help and cheers,<br>
Kai<span class="m_-8434175930559358014m_-4976640546338776689HOEnZb"><font color="#888888"><br>
<br>
-- <br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"> Please note
my NEW PHONE NUMBERS: <a href="tel:%2B41%2061%20207%2057%2031" value="+41612075731" target="_blank">+41 61 207 57
31</a> (direct) <a href="tel:%2B41%2061%20207%2022%2050" value="+41612072250" target="_blank">+41 61 207 22
50</a> (central)<<<br>
</blockquote>
</blockquote>
Kai Schleicher, PhD | Research Associate
in Advanced Light Microscopy | Biozentrum,
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