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Hi Kai,<br>
<br>
As Sebastien mentions, I have the exact same problem. Sebastien
provided guidance how to write a script to delete the broken pyramid
files that block new ones from being generated and as soon as my
current grant is out the door, I'll look at writing such a script.
But in case you do it sooner than me, please let us all know. No
doubt there are others with the same issue.<br>
<br>
Note that pyramid generation for those very large
Axioscan/ZEN-generated OME-TIFFs takes a fairly long time, even on a
powerful server. But I can attest that it does work on 5.2.2.<br>
<br>
Cheers,<br>
- Damir<br>
<br>
<div class="moz-cite-prefix">On 3/8/2016 3:00 AM, Sebastien Besson
(Staff) wrote:<br>
</div>
<blockquote
cite="mid:6EEB05B9-78F9-4083-89DE-DCDB5691B6F8@dundee.ac.uk"
type="cite">
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Hi Kai,
<div class=""><br class="">
</div>
<div class="">thanks for reporting this issue. Looking at the
images, they were imported back into February</div>
<div class="">using OMERO 5.2.1 / Bio-Formats 5.1.6. The pyramid
generation was broken with exactly the</div>
<div class="">same stack trace than the one reported by Damir in a
forum thread [1] and fixed in Bio-Formats</div>
<div class="">5.1.8.</div>
<div class=""><br class="">
</div>
<div class="">There are a different answers to your email:</div>
<div class=""><br class="">
</div>
<div class="">- re-importing the same image into an OMERO 5.2.2
instance e.g. the demo server should work</div>
<div class=""> out-of-the-box and the pyramid should be properly
generated</div>
<div class="">- in a production environment, deleting the stale
pyramid files using the command suggested</div>
<div class=""> in the thread linked above should also work
without forcing a new import</div>
<div class="">- from our side, we have created a card to improve
the behavior illustrated by this use case both</div>
<div class=""> server-side during pyramid generation and
client-side e.g. via scripts [2]</div>
<div class=""><br class="">
</div>
<div class="">Best,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
</div>
<div class="">[1] <a moz-do-not-send="true"
href="https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7907"
class="">https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7907</a></div>
<div class="">[2] <a moz-do-not-send="true"
href="https://trello.com/c/TM1Si3UN/38-pyramids" class="">https://trello.com/c/TM1Si3UN/38-pyramids</a></div>
<div class=""><br class="">
</div>
<div class="">
<div>
<blockquote type="cite" class="">
<div class="">On 7 Mar 2016, at 14:01, Kai Schleicher <<a
moz-do-not-send="true"
href="mailto:kai.schleicher@unibas.ch" class=""><a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a></a>>
wrote:</div>
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<p class="MsoNormal">Hi,<o:p class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">I recorded images in the czi
format on the Zeiss Axioscan Slidescanner and
exported them via Zen Blue to OME-TIFFs.<o:p
class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">These OME-Tiffs open correctly in
FIJI using the latest Bioformats.<o:p class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">However, they fail to open after
being imported into OMERO.<o:p class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">Import to is handled without
error but the images cannot be displayed in the
viewer. The also do not have a preview, instead the
“watch”-icon is shown.<o:p class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">I am using the latest version of
OMERO (your demo server) and this client:
OMERO.insight-5.2.2-ice35-b17-win.<o:p class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">The images in question have the
ID 203547 and 203548.<o:p class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">Thanks for your help and cheers,<o:p
class=""></o:p></p>
<p class="MsoNormal">Kai<o:p class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
<p class="MsoNormal">--<o:p class=""></o:p></p>
<p class="MsoNormal">Kai Schleicher, PhD | Research
Associate in Advanced Light Microscopy | Biozentrum,
University of Basel | Klingelbergstrasse 50/70 |
CH-4056 Basel<o:p class=""></o:p></p>
<p class="MsoNormal">Phone: +41 61 267 22 50 | <a
moz-do-not-send="true"
href="mailto:kai.schleicher@unibas.ch" class="">
<span style="color:#0563C1" class=""><a class="moz-txt-link-abbreviated" href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a></span></a>
| <a moz-do-not-send="true"
href="http://www.biozentrum.unibas.ch/" class="">
<span style="color:#0563C1" class="">www.biozentrum.unibas.ch</span></a>
| <a moz-do-not-send="true"
href="http://www.microscopynetwork.unibas.ch/"
class="">
<span style="color:#0563C1" class="">www.microscopynetwork.unibas.ch</span></a><o:p
class=""></o:p></p>
<p class="MsoNormal"><o:p class=""> </o:p></p>
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<pre class="moz-signature" cols="72">--
Damir Sudar - Staff Scientist
Lawrence Berkeley Natl Laboratory / MBIB
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: <a class="moz-txt-link-abbreviated" href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a>
Visiting Scientist, Oregon Health & Science University</pre>
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