<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,
                              University of Basel | Klingelbergstrasse
                              50/70 | CH-4056 Basel |<br>
                              Phone: <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) | <a href="mailto:kai.schleicher@unibas.ch" target="_blank">kai.schleicher@unibas.ch</a>
                              | <a href="http://www.biozentrum.unibas.ch" rel="noreferrer" target="_blank">www.biozentrum.unibas.ch</a>
                              | <a href="http://www.microscopynetwork.unibas.ch" rel="noreferrer" target="_blank">www.microscopynetwork.unibas.c<wbr>h</a><br>
                              <br>
                              ______________________________<wbr>_________________<br>
                              ome-devel mailing list<br>
                              <a href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy<wbr>.org.uk</a><br>
                              <a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" rel="noreferrer" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-deve<wbr>l</a><br>
                            </font></span></blockquote>
                      </div>
                      <br>
                    </div>
                    <br>
                    <fieldset class="m_-8434175930559358014m_-4976640546338776689mimeAttachmentHeader"></fieldset>
                    <br>
                    <pre>______________________________<wbr>_________________
ome-devel mailing list
<a class="m_-8434175930559358014m_-4976640546338776689moz-txt-link-abbreviated" href="mailto:ome-devel@lists.openmicroscopy.org.uk" target="_blank">ome-devel@lists.openmicroscopy<wbr>.org.uk</a>
<a class="m_-8434175930559358014m_-4976640546338776689moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-deve<wbr>l</a>
</pre>
                  </blockquote>
                  <br>
                </div>
              </div>
            </div>
          </blockquote>
        </div>
        <br>
      </div>
    </blockquote>
    <br>
  </div></div></div>

</blockquote></div><br></div>