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<font face="Ubuntu">Hi Sebastien,<br>
<br>
Thanks for the answer.<br>
<br>
The problem with the CellProfiler forum is that it's really not
active. I actually <a moz-do-not-send="true"
href="http://forum.cellprofiler.org/t/connection-to-omero-reset/5961">posted
there</a> and waited a couple of days without answer before
asking here. It's now 21 days and still nothing..<br>
<br>
As for the wiki, last time I asked about something there, Chris
was actually the one answering which led me here this time as
well... :).<br>
<br>
</font>
<div class="moz-signature"><font face="Ubuntu">Best,</font><br>
<font face="Ubuntu">Laurent Guerard</font><br>
<pre class="moz-signature" cols="72">
</pre>
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<div class="moz-cite-prefix">On 30/04/2018 12:36, Sebastien Besson
(Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:324C87BD-D75F-422E-9CB9-8F8DD6936B06@dundee.ac.uk">
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<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-%28Linux%29"
class="" moz-do-not-send="true">https://github.com/CellProfiler/CellProfiler/wiki/Source-installation-(Linux)</a></div>
<div class="">[2] <a href="http://forum.cellprofiler.org/"
class="" moz-do-not-send="true">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=""
moz-do-not-send="true">laurent.guerard@unibas.ch</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class=""><font
class="" face="Ubuntu">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
class="" face="Ubuntu"><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 class="" face="Ubuntu">Best,</font><br
class="">
<font class="" face="Ubuntu">Laurent Guerard</font><br
class="">
</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>
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