<html>
<head>
<meta http-equiv="Content-Type" content="text/html; charset=us-ascii">
</head>
<body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
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="">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="">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 wrap="" class="">_______________________________________________
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 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="">ome-users@lists.openmicroscopy.org.uk</a><br class="">
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<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>