<div dir="ltr">Thanks Will,<div><br></div><div>If you need more logs or those .svs files I can upload them for you.</div><div><br></div><div><div dir="ltr"><span style="font-family:arial, sans-serif;font-size:13px;border-collapse:collapse;color:rgb(80, 0, 80)"><div>
Have a great day,</div><div>Leon Kolchinsky</div></span></div><br>
<br><br><div class="gmail_quote">On Thu, Nov 24, 2011 at 18:31, Will Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk">will@lifesci.dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex;">
<div style="word-wrap:break-word">Hi Leon,<div><br></div><div> I've created a ticket to look at this. </div><div><a href="http://trac.openmicroscopy.org.uk/ome/ticket/7298" target="_blank">http://trac.openmicroscopy.org.uk/ome/ticket/7298</a></div>
<div><br></div><div>Not sure what is going on just yet, but at least it seems like the difference between import on my laptop and your system is that on my laptop, the "too big" image is processed last (pyramid generation hangs). This means that the other images are processed reasonably quickly first, whereas on your system this blocker is encountered before any other images are processed??</div>
<div><br></div><div> Hopefully we can fix this for you soon,</div><div><br></div><div> Will. </div><div><br></div><div><br></div><div><br><div><div><div class="h5"><div>On 21 Nov 2011, at 05:23, Leon Kolchinsky wrote:</div>
<br></div></div><blockquote type="cite"><div><div class="h5"><div dir="ltr">Hello Will,<br><br>Sorry for a late reply (I've been on the training last week and off I go for another week from tomorrow ;).<br><br>Anyway, I've tested again with:<br>
237M - 3066.svs<br><br>I've tested this file on another OMERO server with Insight client.<br>
Import went fine but I can't see the images (see the snapshots).<br>It's definetely not 8 min ;(<br><br>Logs are here - <a href="https://cloudstor.aarnet.edu.au/filesender/?vid=09D4E374-EF48-AF26-D9E6-C49263129BD7" target="_blank">https://cloudstor.aarnet.edu.au/filesender/?vid=09D4E374-EF48-AF26-D9E6-C49263129BD7</a><br>
<br>May be it takes a reeeeally long time.<br><br>Thanks,<br><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(80,0,80)"><div>Leon Kolchinsky</div></span></div>
<br>
<br><br><div class="gmail_quote">On Wed, Nov 16, 2011 at 09:41, Will Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk" target="_blank">will@lifesci.dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word">Hi Kim (& Leon),<div><br></div><div> I'm not sure what the "Version 5.0" logging statement means. </div><div>Could you show us that part of the log? Our roadmap for when and what OMERO 5.0 is has evolved over time. We probably need to clear that up.</div>
<div><br></div><div>Could you give us some more details on how slow you're finding the import?</div><div>I just tried it again with your sample file, running the server on my laptop (Recent Macbook Pro) and it took about 8 minutes to generate image pyramids for all the images apart from the largest (which fails). </div>
<div>Is it taking you longer than this? </div><div><br></div><div>I have also noticed incidentally that my laptop seems to be working hard at the failing image (fan going etc) until I delete it using Insight. </div><div>
Haven't investigated this fully yet. My logs are attached.</div>
<div><br></div><div></div></div><br><div style="word-wrap:break-word"><div></div><div><br></div><div> Cheers,</div><div><br></div><div> Will. </div><div><br></div><div><br></div><div><br><div><div>On 14 Nov 2011, at 03:30, Kim Linton wrote:</div>
<br><blockquote type="cite">Hi Will,<br><br>Thanks for looking into this issue for us. So all the functionality is there i.e. it will load all the images but it is very slow. It says in the log that it will be fixed in Version 5.0. Is there an approximate timeframe for this?<br>
<br>Thanks for your help,<br><br>Kim Linton<br><br><div class="gmail_quote">On 11 November 2011 21:13, Will Moore <span dir="ltr"><<a href="mailto:will@lifesci.dundee.ac.uk" target="_blank">will@lifesci.dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0pt 0pt 0pt 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div style="word-wrap:break-word">Hi Leon,<div><br></div><div> The file seems to import OK, except for the largest of the 7 images. 95k x 45k (see screen-shots). </div><div><br></div><div>The largest image doesn't import - This is a known issue: <a href="http://trac.openmicroscopy.org.uk/ome/ticket/6500" target="_blank">http://trac.openmicroscopy.org.uk/ome/ticket/6500</a> </div>
<div>"SizeX * SizeY exceeds Integer.MAX_VALUE."</div><div><br></div><div>When we give you the warning "Please try again later", this is when the image pyramids are being built on the server. Just takes time. </div>
<div><br></div><div><br></div><div> Will. </div><div><br></div><div><br></div><div><img height="735" width="1255"><img height="720" width="981"></div><div><br><div><div><div>On 11 Nov 2011, at 00:54, Leon Kolchinsky wrote:</div>
<br></div><blockquote type="cite"><div dir="ltr"><div>Hello,<div><br></div><div>We're trying to use .svs files with OMERO (latest 4.3.3 version) and experiencing some issues with that.</div><div><br></div></div>
<div>When .svs file uploaded via "Insight" it appears in the client as following - (checkout the screenshot <span style="font-family:arial,sans-serif;font-size:13px;background-color:rgb(245,245,245)"></span>)</div>
<div>
<div>It should look like this - (checkout screenshot <a href="https://mail.google.com/mail/?ui=2&ik=c2449854ef&view=att&th=133901bdcecab120&attid=0.1&disp=safe&realattid=f_guugh9y10&zw" style="font-size:13px;color:rgb(34,34,34);font-family:arial,sans-serif;background-color:rgb(245,245,245)" target="_blank">svs thumbnail.tiff</a>).</div>
<div><br></div><div>Can you please test it and tell us how to fix the problem?</div><div><br></div><div>Sample .svs file provided here - <a href="https://cloudstor.aarnet.edu.au/filesender/?vid=99FF5385-A079-29C7-3B5D-90178BFC6ED7" target="_blank">https://cloudstor.aarnet.edu.au/filesender/?vid=99FF5385-A079-29C7-3B5D-90178BFC6ED7</a></div>
<div><br></div><div><div dir="ltr"><span style="font-family:arial,sans-serif;font-size:13px;border-collapse:collapse;color:rgb(80,0,80)"><div>Thanks,</div><div>Leon Kolchinsky</div></span></div><br>
<br><br><div class="gmail_quote">---------- Forwarded message ----------<br>From: <b class="gmail_sendername">Kim Linton</b> <span dir="ltr"><<a href="mailto:kim.linton@monash.edu" target="_blank">kim.linton@monash.edu</a>></span><br>
Date: Fri, Nov 11, 2011 at 11:44<br>Subject: OMERO - SVS file format functionality<br>To: Leon Kolchinsky <<a href="mailto:leon.kolchinsky@monash.edu" target="_blank">leon.kolchinsky@monash.edu</a>><br><br><br><div>
he Rendering Engine. Image not ready. Please try again later.' I also get an error message when trying to view the image in Image J via the OMERO plugin. I have tried loading the file including archive and without.<br>
<br>Attached is a the thumbnail of the image.</div></div><br></div></div></div>
<span><svs thumbnail.tiff></span><span><2011-11-11_115031.jpg></span>_______________________________________________<br>ome-users mailing list<br><a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
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<div><div><div><div><div style="font-size:13px;margin:5px 15px;padding-bottom:20px"><div style="color:rgb(0,0,0)"><div><font color="#888888">Kim Linton<br>Senior Research Systems Facilitator<br>
Monash e-Research Centre<br>Building 75<br>Monash University<br>Clayton Victoria 3800, Australia<br>Ph: <a value="+61399058681" style="color:rgb(0,0,204)">+61 3 99020712</a><br>Fax: <a value="+61399020193" style="color:rgb(0,0,204)">+61 3 9902-0193</a><br>
Email: <a href="mailto:kim.linton@monash.edu" style="color:rgb(0,0,204)" target="_blank">kim.linton@monash.edu</a><br>Web: <a href="http://www.monash.edu.au/eresearch" style="color:rgb(0,0,204)" target="_blank">http://www.monash.edu.au/eresearch</a></font></div>
</div><div><font color="#999999">Part time: Mon, Tues, Thurs & Fri</font></div></div></div></div></div></div></div></div></div></div></div></div></div></td></tr></tbody></table></span><div><font color="#888888" face="arial, sans-serif"><span style="border-collapse:collapse"><br>
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