<html>
<head>
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
</head>
<body text="#000000" bgcolor="#FFFFFF">
<p>Hi Sebastian,</p>
<p>thanks for clarifying! I am happy that the bug is already fixed
:)</p>
<p>Have a nice weekend and cheers,<br>
Kai<br>
</p>
<br>
<div class="moz-cite-prefix">On 06/16/2017 02:11 PM, Sebastien
Besson (Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CBCF1CB4-F540-495C-B2FE-0B4200A1F7F0@dundee.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Kai,
<div class=""><br class="">
</div>
<div class="">thanks for the update. I could also confirm the
error while reimporting your image into the</div>
<div class="">OMERO server.</div>
<div class=""><br class="">
</div>
<div class="">The issue is actually a bug associated with the
reading of the CZI file. Luckily this bug has</div>
<div class="">been fixed and released in the most recent
Bio-Formats version as you could confirm by</div>
<div class="">opening the file using Fiji.</div>
<div class=""><br class="">
</div>
<div class="">This version is not yet included in the latest
release of OMERO but the import of the file into</div>
<div class="">one of our development server went through without
errors. So I expect your problem to be</div>
<div class="">fixed with the imminent release of OMERO 5.3.3.</div>
<div class=""><br class="">
</div>
<div class="">Answering one of your initial questions, if
Bio-Formats reads pyramidal subresolutions available</div>
<div class="">within the file, OMERO should not recalculate
pyramids. In this case, the client message was slightly</div>
<div class="">misleading as the issue is rather at the file import
level.</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 16 Jun 2017, at 13:02, Kai Schleicher <<a
href="mailto:kai.schleicher@unibas.ch" class=""
moz-do-not-send="true">kai.schleicher@unibas.ch</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">Hi,</p>
<p class="">I have an update to this: while there was no
error during upload, I received an error during
processing "failed to read pixels" for one of the
images (<a
href="https://demo.openmicroscopy.org/webclient/?show=image-576"
class="" moz-do-not-send="true">example image ID 576</a>
, see attached error log)<br class="">
</p>
thanks for your help and cheers,<br class="">
Kai<br class="">
<br class="">
<br class="">
<br class="">
<div class="moz-cite-prefix">On 06/16/2017 11:45 AM, Kai
Schleicher wrote:<br class="">
</div>
<blockquote type="cite"
cite="mid:7b066162-389a-75b8-d633-d077dfa174f8@unibas.ch"
class="">
<p class="">Hi,</p>
<p class="">first, even though its already a bit in
the past: Thanks for the great OME meeting! I was
happy to meet everyone and see all the new and
amazing things to come :)<br class="">
</p>
<p class="">second, thanks for the freshly installed
5.3.2 OMERO demo server! For testing I have uploaded
some jpegXR compressed multi-sceen BF and FL images
of our AxioScan slidescanner (*czi), which uploaded
with no issue (<a moz-do-not-send="true"
href="https://demo.openmicroscopy.org/webclient/?show=dataset-17"
class="">dataset ID 17</a>, <a
moz-do-not-send="true"
href="https://demo.openmicroscopy.org/webclient/?show=image-576"
class="">
example image ID 576</a> ).</p>
<p class="">I noticed however that the OMERO sever
spends some time calculating a pyramid for my
images.
<br class="">
</p>
<p class="">Since these images already contained
pyramids that where calculated by Zen after
acquisition, do you think it would be possible to
skip pyramid creation on the OMERO server side and
use the ones provided in the czi instead?
<br class="">
</p>
<p class="">While I could confirm that
FIJI/Bio-formats recognises the pyramids in those
images, I don't really know if they are on the same
zoom-level that OMERO expects/ likes to use.</p>
<p class="">Let me know if you wish to have the
example images uploaded somewhere else other than
your demo server :)</p>
<p class="">Thanks and cheers,<br class="">
Kai<br class="">
</p>
<pre class="moz-signature" cols="72">--
>>Please note my NEW PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22 50 (central)<<
Kai Schleicher, PhD | Research Associate in Advanced Light Microscopy | Biozentrum, University of Basel | Klingelbergstrasse 50/70 | CH-4056 Basel |
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50 (central) | <a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch" moz-do-not-send="true">kai.schleicher@unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.biozentrum.unibas.ch/" moz-do-not-send="true">www.biozentrum.unibas.ch</a> | <a class="moz-txt-link-abbreviated" href="http://www.microscopynetwork.unibas.ch/" moz-do-not-send="true">www.microscopynetwork.unibas.ch</a></pre>
<br class="">
<fieldset class="mimeAttachmentHeader"></fieldset>
<br class="">
<pre class="" wrap="">_______________________________________________
ome-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a>
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" moz-do-not-send="true">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a>
</pre>
</blockquote>
<br class="">
</div>
<span
id="cid:ED099BD0-2E38-4445-8CFF-C347654B8347@lifesci.dundee.ac.uk"><Axioscan-pixel-processing-errorlog.txt></span>_______________________________________________<br
class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk"
class="" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><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>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
ome-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a>
</pre>
</blockquote>
<br>
</body>
</html>