<html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:w="urn:schemas-microsoft-com:office:word" xmlns:m="http://schemas.microsoft.com/office/2004/12/omml" xmlns="http://www.w3.org/TR/REC-html40">
<head>
<meta http-equiv="Content-Type" content="text/html; charset=iso-8859-1">
<meta name="Generator" content="Microsoft Word 15 (filtered medium)">
<style><!--
/* Font Definitions */
@font-face
{font-family:"Cambria Math";
panose-1:2 4 5 3 5 4 6 3 2 4;}
@font-face
{font-family:Calibri;
panose-1:2 15 5 2 2 2 4 3 2 4;}
@font-face
{font-family:Consolas;
panose-1:2 11 6 9 2 2 4 3 2 4;}
/* Style Definitions */
p.MsoNormal, li.MsoNormal, div.MsoNormal
{margin:0cm;
margin-bottom:.0001pt;
font-size:11.0pt;
font-family:"Calibri",sans-serif;
color:black;}
a:link, span.MsoHyperlink
{mso-style-priority:99;
color:#0563C1;
text-decoration:underline;}
a:visited, span.MsoHyperlinkFollowed
{mso-style-priority:99;
color:#954F72;
text-decoration:underline;}
pre
{mso-style-priority:99;
mso-style-link:"HTML Preformatted Char";
margin:0cm;
margin-bottom:.0001pt;
font-size:10.0pt;
font-family:"Courier New";
color:black;}
span.EmailStyle17
{mso-style-type:personal;
font-family:"Calibri",sans-serif;
color:windowtext;}
span.HTMLPreformattedChar
{mso-style-name:"HTML Preformatted Char";
mso-style-priority:99;
mso-style-link:"HTML Preformatted";
font-family:"Consolas",serif;
color:black;}
span.EmailStyle20
{mso-style-type:personal-reply;
font-family:"Calibri",sans-serif;
color:windowtext;}
.MsoChpDefault
{mso-style-type:export-only;
font-size:10.0pt;}
@page WordSection1
{size:612.0pt 792.0pt;
margin:70.85pt 70.85pt 2.0cm 70.85pt;}
div.WordSection1
{page:WordSection1;}
--></style><!--[if gte mso 9]><xml>
<o:shapedefaults v:ext="edit" spidmax="1026" />
</xml><![endif]--><!--[if gte mso 9]><xml>
<o:shapelayout v:ext="edit">
<o:idmap v:ext="edit" data="1" />
</o:shapelayout></xml><![endif]-->
</head>
<body bgcolor="white" lang="EN-US" link="#0563C1" vlink="#954F72">
<div class="WordSection1">
<p class="MsoNormal"><span style="color:windowtext">Hi Damir and Sebastien,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Thanks for your replys! I tested the files again with OMERO 5.2.2 and can confirm that it works. Concerning the script I am sure it would be great to have. In case Niko or I will have one we’ll of course let
you know.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Thanks and cheers,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:windowtext">Kai<o:p></o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="color:windowtext"><o:p> </o:p></span></a></p>
<div>
<div style="border:none;border-top:solid #E1E1E1 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal"><b><span style="color:windowtext">From:</span></b><span style="color:windowtext"> Damir Sudar [mailto:dsudar@lbl.gov]
<br>
<b>Sent:</b> Dienstag, 8. März 2016 18:35<br>
<b>To:</b> OME User Support List<br>
<b>Subject:</b> Re: [ome-users] Problem displaying OME.Tiff exports from zeiss Zen blue<o:p></o:p></span></p>
</div>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-bottom:12.0pt">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<span style="font-size:12.0pt"><o:p></o:p></span></p>
<div>
<p class="MsoNormal">On 3/8/2016 3:00 AM, Sebastien Besson (Staff) wrote:<o:p></o:p></p>
</div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<p class="MsoNormal">Hi Kai, <o:p></o:p></p>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">thanks for reporting this issue. Looking at the images, they were imported back into February<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">using OMERO 5.2.1 / Bio-Formats 5.1.6. The pyramid generation was broken with exactly the<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">same stack trace than the one reported by Damir in a forum thread [1] and fixed in Bio-Formats<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">5.1.8.<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">There are a different answers to your email:<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">- re-importing the same image into an OMERO 5.2.2 instance e.g. the demo server should work<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> out-of-the-box and the pyramid should be properly generated<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">- in a production environment, deleting the stale pyramid files using the command suggested<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> in the thread linked above should also work without forcing a new import<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">- from our side, we have created a card to improve the behavior illustrated by this use case both<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"> server-side during pyramid generation and client-side e.g. via scripts [2]<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">Best,<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">Sebastien<o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<p class="MsoNormal">[1] <a href="https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7907">https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=7907</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal">[2] <a href="https://trello.com/c/TM1Si3UN/38-pyramids">https://trello.com/c/TM1Si3UN/38-pyramids</a><o:p></o:p></p>
</div>
<div>
<p class="MsoNormal"><o:p> </o:p></p>
</div>
<div>
<div>
<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
<div>
<p class="MsoNormal">On 7 Mar 2016, at 14:01, Kai Schleicher <<a href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a>> wrote:<o:p></o:p></p>
</div>
<p class="MsoNormal"><o:p> </o:p></p>
<div>
<div>
<p class="MsoNormal">Hi,<o:p></o:p></p>
<p class="MsoNormal"> <o:p></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></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">These OME-Tiffs open correctly in FIJI using the latest Bioformats.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">However, they fail to open after being imported into OMERO.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></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></o:p></p>
<p class="MsoNormal"> <o:p></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></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">The images in question have the ID 203547 and 203548.<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">Thanks for your help and cheers,<o:p></o:p></p>
<p class="MsoNormal">Kai<o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
<p class="MsoNormal">--<o:p></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></o:p></p>
<p class="MsoNormal">Phone: +41 61 267 22 50 | <span style="color:#0563C1"><a href="mailto:kai.schleicher@unibas.ch">kai.schleicher@unibas.ch</a></span> |
<a href="http://www.biozentrum.unibas.ch/">www.biozentrum.unibas.ch</a> | <a href="http://www.microscopynetwork.unibas.ch/">
www.microscopynetwork.unibas.ch</a><o:p></o:p></p>
<p class="MsoNormal"> <o:p></o:p></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif">_______________________________________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></span></p>
</div>
</blockquote>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><o:p> </o:p></span></p>
</div>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><br>
</span><span style="font-size:10.0pt;font-family:"Times New Roman",serif">The University of Dundee is a registered Scottish Charity, No: SC015096</span><span style="font-size:12.0pt;font-family:"Times New Roman",serif">
<br>
<br>
<br>
<o:p></o:p></span></p>
<pre>_______________________________________________<o:p></o:p></pre>
<pre>ome-users mailing list<o:p></o:p></pre>
<pre><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><o:p></o:p></pre>
<pre><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><o:p></o:p></pre>
</blockquote>
<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Times New Roman",serif"><br>
<br>
<o:p></o:p></span></p>
<pre>-- <o:p></o:p></pre>
<pre>Damir Sudar - Staff Scientist<o:p></o:p></pre>
<pre>Lawrence Berkeley Natl Laboratory / MBIB<o:p></o:p></pre>
<pre>One Cyclotron Road, MS 977, Berkeley, CA 94720, USA<o:p></o:p></pre>
<pre>T: 510/486-5346 - F: 510/486-5586 - E: <a href="mailto:DSudar@lbl.gov">DSudar@lbl.gov</a><o:p></o:p></pre>
<pre><o:p> </o:p></pre>
<pre>Visiting Scientist, Oregon Health & Science University<o:p></o:p></pre>
</div>
</body>
</html>