<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
Hi Laurent</div>
<div dir="auto" style="word-wrap: break-word; -webkit-nbsp-mode: space; line-break: after-white-space;" class="">
<div>
<div><br class="">
</div>
<div>A quick search suggests the CellProfiler wiki [1] is probably the placeholder for the building</div>
<div>instructions although I cannot see any details on the dependency management.</div>
<div><br class="">
</div>
<div>For any more specific answers, the CellProfiler forum [2] is probably the reference place</div>
<div>to post your question. I suspect you are not the only person interesting in doing this</div>
<div>and the answer would be of general interest for the CellProfile community.</div>
<div><br class="">
</div>
<div><br class="">
</div>
<div>Best,</div>
<div>Sebastien </div>
<div><br class="">
</div>
[1] <a href="https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-(Linux)" class="">https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-(Linux)</a></div>
<div class="">[2] <a href="http://forum.cellprofiler.org/" class="">http://forum.cellprofiler.org/</a> </div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On 23 Apr 2018, at 08:22, Laurent Guerard <<a href="mailto:laurent.guerard@unibas.ch" class="">laurent.guerard@unibas.ch</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class=""><font face="Ubuntu" class="">Hello Chris,<br class="">
<br class="">
Once again thanks for your help.<br class="">
<br class="">
<blockquote type="cite" class="">may have to build CellProfiler, and some of its dependencies, from source as a result</blockquote>
<br class="">
Is there any documentation about how to do that and what to modify for each version ? We're in the process of upgrading OMERO to 5.4.x and the link with CellProfiler was one of the things we wanted to test before completely upgrading.</font></div>
</div>
</blockquote>
</div>
<div>
<blockquote type="cite" class="">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class=""><font face="Ubuntu" class=""><br class="">
<blockquote type="cite" class="">The way CellProfiler interacts with OMERO is actually via Bio-Formats and the OmeroReader so the number of potential locations to investigate such a problem is actually quite high.
<br class="">
</blockquote>
<br class="">
Hmm I see, not that simple then. I guess closing CellProfiler and reopening it again once the connection is closed is the best solution so far.<br class="">
<br class="">
Thanks again.<br class="">
<br class="">
</font>
<div class="moz-signature"><font face="Ubuntu" class="">Best,</font><br class="">
<font face="Ubuntu" class="">Laurent Guerard</font><br class="">
<pre class="moz-signature" cols="72"></pre>
</div>
<div class="moz-cite-prefix">On 20/04/2018 16:14, Chris Allan wrote:<br class="">
</div>
<blockquote type="cite" cite="mid:44031c1c-a596-2412-7172-d3eb10191cde@glencoesoftware.com" class="">
Hello, Laurent: <br class="">
<br class="">
Comments inline. <br class="">
<br class="">
On 4/19/2018 12:56, Laurent Guerard wrote: <br class="">
<blockquote type="cite" class="">Hi all, <br class="">
<br class="">
It is possible to connect between CellProfiler and OMERO using the LoadData module and a CSV generated from OMERO.
<br class="">
</blockquote>
<br class="">
That's correct. However, CellProfiler 3.0.0, released back in October 2017, currently has broken OMERO support. It also targets OMERO 5.3.x. If you want to use CellProfiler with OMERO you will have to be quite specific about which versions you would like
to work with and may have to build CellProfiler, and some of its dependencies, from source as a result.
<br class="">
<br class="">
<blockquote type="cite" class=""><br class="">
However, it seems that after a while the connection between OMERO and CellProfiler is closed and it doesn't prompt again for it. Is there a command using Python that I could use to improve that module and check if the connection is still open ?
<br class="">
</blockquote>
<br class="">
Not that I am aware of. The way CellProfiler interacts with OMERO is actually via Bio-Formats and the OmeroReader so the number of potential locations to investigate such a problem is actually quite high.
<br class="">
<br class="">
<blockquote type="cite" class=""><br class="">
Thanks. <br class="">
<br class="">
-- <br class="">
Best, <br class="">
Laurent Guerard <br class="">
</blockquote>
<br class="">
Hope that helps. <br class="">
<br class="">
-Chris <br class="">
</blockquote>
<br class="">
</div>
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</body>
</html>