<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1252"><meta http-equiv="Content-Type" content="text/html charset=windows-1252"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Dear LOCI Team,<div>I’m working on confocal tile imaging on either Leica or Zeiss confocal microscope,</div><div>and I was wondering if it was possible to retrieve from .lif or .czi files the X,Y,Z position of the different</div><div>individual pictures present in a mosaic sequence ? Actually I looked for it in the OME metadata, but I couldn’ find it.</div><div>Am I wrong, or would it be possible ?</div><div>Thanks a lot for your help.</div><div><br></div><div>Lydia</div><div><br><div>
<div style="margin: 0px;"><b><i>Lydia Danglot, PhD</i></b></div><div style="margin: 0px;">Inserm researcher (CR1)</div><div style="margin: 0px;">National Research Group on Microscopy (GDR 2588-MIV)</div><div style="margin: 0px;">National Coordinator of the France Bio Imaging User committee</div><div style="margin: 0px;">--</div><div style="margin: 0px;">Institut Jacques Monod (CNRS UMR7592)</div><div style="margin: 0px;">Université Paris Diderot</div><div style="margin: 0px;">Inserm 950, "Membrane trafic in </div><div style="margin: 0px;">Heath & Disease"</div><div style="margin: 0px;">Bât.Buffon - 15 rue Hélène Brion</div><div style="margin: 0px;">3eme etage, porte 320B</div><div style="margin: 0px;">75205 PARIS CEDEX 13 - FRANCE</div><div style="margin: 0px;">Tel: 01 57 27 80 37</div><div style="margin: 0px;">Site web : <span class="Apple-style-span" style="color: rgb(0, 2, 255);"><span style="text-decoration: underline; color: rgb(21, 79, 174);"><a href="http://lydia.danglot.free.fr/">http://lydia.danglot.free.fr</a></span></span></div>
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<br><div><div>Le 20 févr. 2015 à 13:00, <a href="mailto:ome-users-request@lists.openmicroscopy.org.uk">ome-users-request@lists.openmicroscopy.org.uk</a> a écrit :</div><br class="Apple-interchange-newline"><blockquote type="cite">Send ome-users mailing list submissions to<br><span class="Apple-tab-span" style="white-space:pre"> </span><a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br><br>To subscribe or unsubscribe via the World Wide Web, visit<br><span class="Apple-tab-span" style="white-space:pre"> </span><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>or, via email, send a message with subject or body 'help' to<br><span class="Apple-tab-span" style="white-space:pre"> </span>ome-users-request@lists.openmicroscopy.org.uk<br><br>You can reach the person managing the list at<br><span class="Apple-tab-span" style="white-space:pre"> </span>ome-users-owner@lists.openmicroscopy.org.uk<br><br>When replying, please edit your Subject line so it is more specific<br>than "Re: Contents of ome-users digest..."<br><br><br>Today's Topics:<br><br> 1. Re: Omero server installation error: Insight login failure<br> (Kenneth Gillen (Staff))<br> 2. Re: Omero server installation error: Insight login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br> (Josh Moore)<br> 3. Re: Omero server installation error: Insight login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br> (Kieran McGourty)<br> 4. Re: Omero server installation error: Insight login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br> (Kieran McGourty)<br> 5. Re: Omero server installation error: Insight login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br> (Kieran McGourty)<br> 6. Re: Swap dimensions in OMERO (time vs. z) (Melissa Linkert)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Thu, 19 Feb 2015 14:00:31 +0000<br>From: "Kenneth Gillen (Staff)" <k.h.gillen@dundee.ac.uk><br>To: "ome-users@lists.openmicroscopy.org.uk"<br><span class="Apple-tab-span" style="white-space:pre"> </span><ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Omero server installation error: Insight<br><span class="Apple-tab-span" style="white-space:pre"> </span>login failure<br>Message-ID: <D10B9BAD.3ACEA%k.h.gillen@dundee.ac.uk><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Hi Kieran,<br><br><blockquote type="cite">I am trying to install OMERO.server on a windows 7 PC<br></blockquote><br>You?ve likely planned this well already, but I?d just like to mention it<br>just anyway: If you?re using a lab PC to host an OMERO server, take care<br>to have that PC?s OMERO database and binary repository backed up by your<br>institution?s backup system.<br><br>All the best with your deployment!<br><br>Best,<br><br>Kenny<br><br>--<br><br>Kenneth Gillen<br><br>OME System Administrator<br><br>Wellcome Trust Centre for Gene Regulation & Expression<br>College of Life Sciences<br>MSI/WTB/JBC Complex<br>University of Dundee<br>Dow Street<br>Dundee DD1 5EH<br>United Kingdom<br><br>Tel: +44 (0) 1382 386364<br>Skype: kennethgillen<br><br>http://www.twitter.com/openmicroscopy<br><br><br><br><br><br>From: Kieran McGourty <kieran.mcgourty@gmail.com><br>Reply-To: "ome-users@lists.openmicroscopy.org.uk"<br><ome-users@lists.openmicroscopy.org.uk><br>Date: Thursday, 19 February 2015 00:36<br>To: "ome-users@lists.openmicroscopy.org.uk"<br><ome-users@lists.openmicroscopy.org.uk><br>Subject: [ome-users] Omero server installation error: Insight login<br>failure<br><br><br>Hello OMERO users,<br>I'm not sure you are the correct people to speak to on this but I have<br>searched and have come up blank on what to do next so I thought I would<br>ask you.<br><br>I am trying to install OMERO.server on a windows 7 PC that we have in the<br>lab. Ideally I would take image data acquired on an ImageXpress on a HDD<br>and load them locally onto the OMERO server to store and process.<br>Potentially<br> with cell profiler and cell profiler analyst( if I can get them working).<br>I have followed the installation procedure for the OMERO server and<br>everything worked up until the point where I try to login with the insight<br>client or via the CMD prompt. It tells<br> me my username or password are incorrect.<br><br>I have attached my server diagnostics. I hope you are able to help with<br>this as I think it will be absolutely ideal for our purposes.<br><br>Also, I am running the server software on the same machine I am trying to<br>run insight on. That should not make a difference right?<br>Interestingly, I can get the webclient using the VM build of OMERO working<br>but not through insight. Finally, I can successfully connect to the demo<br>server using insight.<br><br>Thanks a lot for your time all,<br><br>All the best,<br><br>Kieran<br><br><br>The University of Dundee is a registered Scottish Charity, No: SC015096<br><br><br>------------------------------<br><br>Message: 2<br>Date: Thu, 19 Feb 2015 15:34:15 +0100<br>From: Josh Moore <josh@glencoesoftware.com><br>To: OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Omero server installation error: Insight<br><span class="Apple-tab-span" style="white-space:pre"> </span>login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><CAD3Ea=UuGqcWAYkWJz+A5CzU_V-dZvmoN_aDG_oao0wUTXLF9A@mail.gmail.com><br>Content-Type: text/plain; charset=UTF-8<br><br>Hi Kieran,<br><br>On Thu, Feb 19, 2015 at 12:48 PM, Kieran McGourty<br><kieran.mcgourty@gmail.com> wrote:<br><blockquote type="cite">OK great. Almost there. I created some users of all types in the root login<br>in insight. I was then able to successfully login from both the server<br>machine and another computer on the same network!! Thanks a lot! Success :-)<br><br>Then I went add my first sample tiff via importer. using a user login, a<br>administrator login and a root login from insight running on the server<br>machine. The import failed each time. Not sure why. I have attached the<br>insight log to this email.<br></blockquote><br>Thanks, but there doesn't seem to be anything in the log related to<br>your import. Can you submit an error report for the failed import?<br><br>Cheers,<br>~Josh.<br><br><br><blockquote type="cite">Thanks a lot again Josh.<br><br>So close now...<br><br>On 19 February 2015 at 10:08, Josh Moore <josh@glencoesoftware.com> wrote:<br><blockquote type="cite"><br>On Thu, Feb 19, 2015 at 11:03 AM, Kieran McGourty<br><kieran.mcgourty@gmail.com> wrote:<br><blockquote type="cite">Hello Josh,<br></blockquote><br>Hi,<br><br><br><blockquote type="cite">Thank you so much for the excellent support. I have taken on your<br>suggestion<br>and have had some success.<br><br>I can login bin\omero login root@localhost<br><br>I can also login to insight at under the root root account.<br></blockquote><br>Alright, that sounds very promising. As what user are you trying to<br>login as now?<br><br>After bin\omero login root@localhost, you might try:<br><br> bin\omero user list<br><br><br>Those are the other users on your system. If you were expecting more,<br>then you'll either need to add them via:<br><br> bin\omero user add -h<br><br><br>Or enable LDAP.<br><br><blockquote type="cite">...<br>Thanks a lot again for the amazing support.<br></blockquote><br>Gladly!<br>~Josh.<br><br><br><blockquote type="cite">Kieran<br><br><br>On 19 February 2015 at 07:25, Josh Moore <josh@glencoesoftware.com><br>wrote:<br><blockquote type="cite"><br>On Thu, Feb 19, 2015 at 1:36 AM, Kieran McGourty<br><kieran.mcgourty@gmail.com> wrote:<br><blockquote type="cite">Hello OMERO users,<br></blockquote><br>Hi Kieran,<br><br><br><blockquote type="cite">I'm not sure you are the correct people to speak to on this but I<br>have<br>searched and have come up blank on what to do next so I thought I<br>would<br>ask<br>you.<br></blockquote><br>This is just the spot. Hopefully we can help.<br><br><br><blockquote type="cite">I am trying to install OMERO.server on a windows 7 PC that we have in<br>the<br>lab. Ideally I would take image data acquired on an ImageXpress on a<br>HDD<br>and<br>load them locally onto the OMERO server to store and process.<br>Potentially<br>with cell profiler and cell profiler analyst( if I can get them<br>working). I<br>have followed the installation procedure for the OMERO server and<br>everything<br>worked up until the point where I try to login with the insight<br>client<br>or<br>via the CMD prompt. It tells me my username or password are<br>incorrect.<br>I have attached my server diagnostics.<br></blockquote><br><br>Your diagnosis output generally looks ok, i.e. the server is running.<br>If you could also send us the Blitz-0.log, there seem to be a number<br>errors:<br><br> Log files: Blitz-0.log 568.0 KB errors=33 warnings=90<br><br>This might just be caused by previous configuration attempts. Have you<br>tried logging in from the command-line yet?<br><br> bin\omero login root@localhost<br><br><br><br><blockquote type="cite">Also, I am running the server software on the same machine I am<br>trying<br>to<br>run insight on. That should not make a difference right?<br></blockquote><br>There shouldn't be any problem doing that, and we certainly all do it<br>for testing. Eventually, you will want to have the server safely<br>behind a firewall though.<br><br><br><blockquote type="cite">Interestingly, I can get the webclient using the VM build of OMERO<br>working<br>but not through insight. Finally, I can successfully connect to the<br>demo<br>server using insight.<br></blockquote><br>That is interesting. Hopefully a good sign, though, that most of the<br>pieces are working, and we just have to figure out what's gona awry<br>with your Windows installation.<br><br><br><blockquote type="cite">Thanks a lot for your time all,<br><br>All the best,<br>Kieran<br></blockquote><br>Cheers,<br>~Josh<br></blockquote></blockquote></blockquote></blockquote><br><br>------------------------------<br><br>Message: 3<br>Date: Thu, 19 Feb 2015 17:37:52 +0000<br>From: Kieran McGourty <kieran.mcgourty@gmail.com><br>To: OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Omero server installation error: Insight<br><span class="Apple-tab-span" style="white-space:pre"> </span>login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><CACVYweqt_ncFHjuP7G=S76E4KpVrjE-RZGuxzj7vNNxh8NsYPQ@mail.gmail.com><br>Content-Type: text/plain; charset="utf-8"<br><br>Hey Josh,<br><br>Success!<br><br>I think I figured it out... well under guidance. Import was looking for a<br>.hdt file which contains the metadata from the ImageExpress export in the<br>folder that I was uploading the images from. When I moved any one of the<br>images out of that folder they uploaded fine. Conveniently, when I only<br>selected the .hdt file it uploaded the full set of images in the folder. (I<br>guess what it was designed to do)<br><br>In summary, amazing software with fantastic support.<br><br>Thanks a lot for your help.<br><br>Kieran<br><br>p.s. now... to interface Cellprofiler and Cellanalayst. Tomorrows puzzle!!!<br><br><br><br><br><br>On 19 February 2015 at 14:34, Josh Moore <josh@glencoesoftware.com> wrote:<br><br><blockquote type="cite">Hi Kieran,<br><br>On Thu, Feb 19, 2015 at 12:48 PM, Kieran McGourty<br><kieran.mcgourty@gmail.com> wrote:<br><blockquote type="cite">OK great. Almost there. I created some users of all types in the root<br></blockquote>login<br><blockquote type="cite">in insight. I was then able to successfully login from both the server<br>machine and another computer on the same network!! Thanks a lot! Success<br></blockquote>:-)<br><blockquote type="cite"><br>Then I went add my first sample tiff via importer. using a user login, a<br>administrator login and a root login from insight running on the server<br>machine. The import failed each time. Not sure why. I have attached the<br>insight log to this email.<br></blockquote><br>Thanks, but there doesn't seem to be anything in the log related to<br>your import. Can you submit an error report for the failed import?<br><br>Cheers,<br>~Josh.<br><br><br><blockquote type="cite">Thanks a lot again Josh.<br><br>So close now...<br><br>On 19 February 2015 at 10:08, Josh Moore <josh@glencoesoftware.com><br></blockquote>wrote:<br><blockquote type="cite"><blockquote type="cite"><br>On Thu, Feb 19, 2015 at 11:03 AM, Kieran McGourty<br><kieran.mcgourty@gmail.com> wrote:<br><blockquote type="cite">Hello Josh,<br></blockquote><br>Hi,<br><br><br><blockquote type="cite">Thank you so much for the excellent support. I have taken on your<br>suggestion<br>and have had some success.<br><br>I can login bin\omero login root@localhost<br><br>I can also login to insight at under the root root account.<br></blockquote><br>Alright, that sounds very promising. As what user are you trying to<br>login as now?<br><br>After bin\omero login root@localhost, you might try:<br><br> bin\omero user list<br><br><br>Those are the other users on your system. If you were expecting more,<br>then you'll either need to add them via:<br><br> bin\omero user add -h<br><br><br>Or enable LDAP.<br><br><blockquote type="cite">...<br>Thanks a lot again for the amazing support.<br></blockquote><br>Gladly!<br>~Josh.<br><br><br><blockquote type="cite">Kieran<br><br><br>On 19 February 2015 at 07:25, Josh Moore <josh@glencoesoftware.com><br>wrote:<br><blockquote type="cite"><br>On Thu, Feb 19, 2015 at 1:36 AM, Kieran McGourty<br><kieran.mcgourty@gmail.com> wrote:<br><blockquote type="cite">Hello OMERO users,<br></blockquote><br>Hi Kieran,<br><br><br><blockquote type="cite">I'm not sure you are the correct people to speak to on this but I<br>have<br>searched and have come up blank on what to do next so I thought I<br>would<br>ask<br>you.<br></blockquote><br>This is just the spot. Hopefully we can help.<br><br><br><blockquote type="cite">I am trying to install OMERO.server on a windows 7 PC that we have<br></blockquote></blockquote></blockquote></blockquote></blockquote>in<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">the<br>lab. Ideally I would take image data acquired on an ImageXpress on<br></blockquote></blockquote></blockquote></blockquote></blockquote>a<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">HDD<br>and<br>load them locally onto the OMERO server to store and process.<br>Potentially<br>with cell profiler and cell profiler analyst( if I can get them<br>working). I<br>have followed the installation procedure for the OMERO server and<br>everything<br>worked up until the point where I try to login with the insight<br>client<br>or<br>via the CMD prompt. It tells me my username or password are<br>incorrect.<br>I have attached my server diagnostics.<br></blockquote><br><br>Your diagnosis output generally looks ok, i.e. the server is running.<br>If you could also send us the Blitz-0.log, there seem to be a number<br>errors:<br><br> Log files: Blitz-0.log 568.0 KB errors=33 warnings=90<br><br>This might just be caused by previous configuration attempts. Have<br></blockquote></blockquote></blockquote></blockquote>you<br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">tried logging in from the command-line yet?<br><br> bin\omero login root@localhost<br><br><br><br><blockquote type="cite">Also, I am running the server software on the same machine I am<br>trying<br>to<br>run insight on. That should not make a difference right?<br></blockquote><br>There shouldn't be any problem doing that, and we certainly all do it<br>for testing. Eventually, you will want to have the server safely<br>behind a firewall though.<br><br><br><blockquote type="cite">Interestingly, I can get the webclient using the VM build of OMERO<br>working<br>but not through insight. Finally, I can successfully connect to the<br>demo<br>server using insight.<br></blockquote><br>That is interesting. Hopefully a good sign, though, that most of the<br>pieces are working, and we just have to figure out what's gona awry<br>with your Windows installation.<br><br><br><blockquote type="cite">Thanks a lot for your time all,<br><br>All the best,<br>Kieran<br></blockquote><br>Cheers,<br>~Josh<br></blockquote></blockquote></blockquote></blockquote>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150219/159b9ab1/attachment-0001.html><br><br>------------------------------<br><br>Message: 4<br>Date: Thu, 19 Feb 2015 17:45:01 +0000<br>From: Kieran McGourty <kieran.mcgourty@gmail.com><br>To: OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Omero server installation error: Insight<br><span class="Apple-tab-span" style="white-space:pre"> </span>login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><CACVYweqN0xYnVSL+_98rPrPU80zpAtD+S4R3aNMV5cNGFcUdtQ@mail.gmail.com><br>Content-Type: text/plain; charset="utf-8"<br><br>Hello Kenny,<br><br>Thanks a lot for the advice. I are going to go shopping for a mini server<br>here and a QNAP NAS system for local backup. I explored setting something<br>up here in UCL with our IT team but they said that there systems were not<br>really designed for suck large amounts of data. It is cheaper to get a<br>bumbler like me to try and set one up that I manage myself.<br><br>Thanks so much for your time. It is a great community.<br><br>All the best,<br><br>Kieran<br><br>On 19 February 2015 at 14:00, Kenneth Gillen (Staff) <<br>k.h.gillen@dundee.ac.uk> wrote:<br><br><blockquote type="cite">Hi Kieran,<br><br><blockquote type="cite">I am trying to install OMERO.server on a windows 7 PC<br></blockquote><br>You?ve likely planned this well already, but I?d just like to mention it<br>just anyway: If you?re using a lab PC to host an OMERO server, take care<br>to have that PC?s OMERO database and binary repository backed up by your<br>institution?s backup system.<br><br>All the best with your deployment!<br><br>Best,<br><br>Kenny<br><br>--<br><br>Kenneth Gillen<br><br>OME System Administrator<br><br>Wellcome Trust Centre for Gene Regulation & Expression<br>College of Life Sciences<br>MSI/WTB/JBC Complex<br>University of Dundee<br>Dow Street<br>Dundee DD1 5EH<br>United Kingdom<br><br>Tel: +44 (0) 1382 386364<br>Skype: kennethgillen<br><br>http://www.twitter.com/openmicroscopy<br><br><br><br><br><br>From: Kieran McGourty <kieran.mcgourty@gmail.com><br>Reply-To: "ome-users@lists.openmicroscopy.org.uk"<br><ome-users@lists.openmicroscopy.org.uk><br>Date: Thursday, 19 February 2015 00:36<br>To: "ome-users@lists.openmicroscopy.org.uk"<br><ome-users@lists.openmicroscopy.org.uk><br>Subject: [ome-users] Omero server installation error: Insight login<br>failure<br><br><br>Hello OMERO users,<br>I'm not sure you are the correct people to speak to on this but I have<br>searched and have come up blank on what to do next so I thought I would<br>ask you.<br><br>I am trying to install OMERO.server on a windows 7 PC that we have in the<br>lab. Ideally I would take image data acquired on an ImageXpress on a HDD<br>and load them locally onto the OMERO server to store and process.<br>Potentially<br> with cell profiler and cell profiler analyst( if I can get them working).<br>I have followed the installation procedure for the OMERO server and<br>everything worked up until the point where I try to login with the insight<br>client or via the CMD prompt. It tells<br> me my username or password are incorrect.<br><br>I have attached my server diagnostics. I hope you are able to help with<br>this as I think it will be absolutely ideal for our purposes.<br><br>Also, I am running the server software on the same machine I am trying to<br>run insight on. That should not make a difference right?<br>Interestingly, I can get the webclient using the VM build of OMERO working<br>but not through insight. Finally, I can successfully connect to the demo<br>server using insight.<br><br>Thanks a lot for your time all,<br><br>All the best,<br><br>Kieran<br><br><br>The University of Dundee is a registered Scottish Charity, No: SC015096<br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150219/fc9da4b3/attachment-0001.html><br><br>------------------------------<br><br>Message: 5<br>Date: Thu, 19 Feb 2015 17:48:52 +0000<br>From: Kieran McGourty <kieran.mcgourty@gmail.com><br>To: OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Omero server installation error: Insight<br><span class="Apple-tab-span" style="white-space:pre"> </span>login<span class="Apple-tab-span" style="white-space:pre"> </span>failure<br>Message-ID:<br><span class="Apple-tab-span" style="white-space:pre"> </span><CACVYwepJAhF_Mys5s+T3H2se-iGEVEDYiVzRx0NY5i-GVCJY9A@mail.gmail.com><br>Content-Type: text/plain; charset="utf-8"<br><br>*we and *such<br><br>On 19 February 2015 at 17:45, Kieran McGourty <kieran.mcgourty@gmail.com><br>wrote:<br><br><blockquote type="cite">Hello Kenny,<br><br>Thanks a lot for the advice. I are going to go shopping for a mini server<br>here and a QNAP NAS system for local backup. I explored setting something<br>up here in UCL with our IT team but they said that there systems were not<br>really designed for suck large amounts of data. It is cheaper to get a<br>bumbler like me to try and set one up that I manage myself.<br><br>Thanks so much for your time. It is a great community.<br><br>All the best,<br><br>Kieran<br><br>On 19 February 2015 at 14:00, Kenneth Gillen (Staff) <<br>k.h.gillen@dundee.ac.uk> wrote:<br><br><blockquote type="cite">Hi Kieran,<br><br><blockquote type="cite">I am trying to install OMERO.server on a windows 7 PC<br></blockquote><br>You?ve likely planned this well already, but I?d just like to mention it<br>just anyway: If you?re using a lab PC to host an OMERO server, take care<br>to have that PC?s OMERO database and binary repository backed up by your<br>institution?s backup system.<br><br>All the best with your deployment!<br><br>Best,<br><br>Kenny<br><br>--<br><br>Kenneth Gillen<br><br>OME System Administrator<br><br>Wellcome Trust Centre for Gene Regulation & Expression<br>College of Life Sciences<br>MSI/WTB/JBC Complex<br>University of Dundee<br>Dow Street<br>Dundee DD1 5EH<br>United Kingdom<br><br>Tel: +44 (0) 1382 386364<br>Skype: kennethgillen<br><br>http://www.twitter.com/openmicroscopy<br><br><br><br><br><br>From: Kieran McGourty <kieran.mcgourty@gmail.com><br>Reply-To: "ome-users@lists.openmicroscopy.org.uk"<br><ome-users@lists.openmicroscopy.org.uk><br>Date: Thursday, 19 February 2015 00:36<br>To: "ome-users@lists.openmicroscopy.org.uk"<br><ome-users@lists.openmicroscopy.org.uk><br>Subject: [ome-users] Omero server installation error: Insight login<br>failure<br><br><br>Hello OMERO users,<br>I'm not sure you are the correct people to speak to on this but I have<br>searched and have come up blank on what to do next so I thought I would<br>ask you.<br><br>I am trying to install OMERO.server on a windows 7 PC that we have in the<br>lab. Ideally I would take image data acquired on an ImageXpress on a HDD<br>and load them locally onto the OMERO server to store and process.<br>Potentially<br> with cell profiler and cell profiler analyst( if I can get them working).<br>I have followed the installation procedure for the OMERO server and<br>everything worked up until the point where I try to login with the insight<br>client or via the CMD prompt. It tells<br> me my username or password are incorrect.<br><br>I have attached my server diagnostics. I hope you are able to help with<br>this as I think it will be absolutely ideal for our purposes.<br><br>Also, I am running the server software on the same machine I am trying to<br>run insight on. That should not make a difference right?<br>Interestingly, I can get the webclient using the VM build of OMERO working<br>but not through insight. Finally, I can successfully connect to the demo<br>server using insight.<br><br>Thanks a lot for your time all,<br><br>All the best,<br><br>Kieran<br><br><br>The University of Dundee is a registered Scottish Charity, No: SC015096<br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br><br></blockquote><br><br></blockquote>-------------- next part --------------<br>An HTML attachment was scrubbed...<br>URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150219/a84b0c3c/attachment-0001.html><br><br>------------------------------<br><br>Message: 6<br>Date: Thu, 19 Feb 2015 12:18:46 -0600<br>From: Melissa Linkert <melissa@glencoesoftware.com><br>To: Niko Ehrenfeuchter <nikolaus.ehrenfeuchter@unibas.ch><br>Cc: OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Swap dimensions in OMERO (time vs. z)<br>Message-ID: <20150219181846.GA12235@hera><br>Content-Type: text/plain; charset=us-ascii<br><br>Hi Niko,<br><br><blockquote type="cite">I just re-imported it, the log file is attached.<br></blockquote><br>According to the metadata in the original .nd file, there should be 3<br>channels and 5 Z sections. That is what I see when importing either the<br>.nd or one or the .stk files into a 5.0.8 server. If you open the .nd<br>file in a text editor, it should show that "NZSteps" is set to 5 and<br>"DoTimelapse" is set to false.<br><br>Does the acquisition software show 5 timepoints? That would definitely<br>worry me; probably the easiest thing for us to do in that case is to<br>update the reader to change dimensions based upon the recorded acquisition software.<br><br><blockquote type="cite"><blockquote type="cite"><blockquote type="cite">On top of that we have some more (non-Visitron) Metamorph TIFFs which have<br>their T interpreted as Z and their C as T. I can upload one of these,<br>although the smallest one that I have is ~850 MB. Inspecting the metadata<br>with Fiji shows the expected odd inconsistency on those, stating the images<br>should have 2 timepoints (instead of the real 165), but then giving T x C<br>"timepoints" further down.<br><br>Don't know if this is a related issue though. Let me know if I should upload<br>it!<br></blockquote><br>I'll defer to Melissa on that.<br></blockquote></blockquote><br>http://trac.openmicroscopy.org/ome/ticket/12503 is likely related if an<br>.nd file is not present. It would help to have the file if you don't<br>mind, and we'll certainly do our best - reliably determining the<br>dimensions for Metamorph TIFFs (especially distinguishing between Z and<br>T) is notoriously tricky though, so it may not be 100%.<br><br>Regards,<br>-Melissa<br><br>On Thu, Feb 19, 2015 at 12:36:53PM +0100, Niko Ehrenfeuchter wrote:<br><blockquote type="cite">Hi Josh,<br><br>On 18.02.2015 20:40, Josh Moore wrote:<br><blockquote type="cite"><blockquote type="cite">Otherwise I can also dig through the logs here, I guess you're asking for<br>the Blitz-0.log?<br></blockquote><br>Nope, I mean the log file which sits beside the fileset under<br>ManagedRepository. For example, for<br><br># jamoore@joshuas-mbp:/opt/ome6$ dist/bin/omero -q fs sets<br> # | Id | Prefix | Images | Files | Transfer<br>---+-----+---------------------------------+--------+-------+----------<br> 0 | 301 | root_0/2015-02/18/10-27-33.022/ | 1 | 1 |<br> 1 | 251 | root_0/2015-02/18/10-20-40.871/ | 1 | 1 |<br> 2 | 202 | root_0/2015-02/18/10-01-20.181/ | 1 | 1 |<br> 3 | 201 | root_0/2015-02/18/10-01-02.432/ | 1 | 1 |<br>(4 rows, starting at 0 of approx. 4)<br># jamoore@joshuas-mbp:/opt/ome6$ dist/bin/omero hql "select<br>f.templatePrefix from Image i join i.fileset as f where i.id = 251" -q<br> # | Col1<br>---+---------------------------------<br> 0 | root_0/2015-02/18/10-20-40.871/<br>(1 row)<br><br>the log file would be found under<br><br>/OMERO/ManagedRepository/root_0/2015-02/18/10-20-40.871.log<br></blockquote><br>I just re-imported it, the log file is attached.<br><br><br><blockquote type="cite"><blockquote type="cite">On top of that we have some more (non-Visitron) Metamorph TIFFs which have<br>their T interpreted as Z and their C as T. I can upload one of these,<br>although the smallest one that I have is ~850 MB. Inspecting the metadata<br>with Fiji shows the expected odd inconsistency on those, stating the images<br>should have 2 timepoints (instead of the real 165), but then giving T x C<br>"timepoints" further down.<br><br>Don't know if this is a related issue though. Let me know if I should upload<br>it!<br></blockquote><br>I'll defer to Melissa on that.<br></blockquote><br>Alright, I'll happily wait then :-)<br><br>Cheers,<br>~Niko<br></blockquote><br><br><blockquote type="cite">_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br></blockquote><br><br><br>------------------------------<br><br>Subject: Digest Footer<br><br>_______________________________________________<br>ome-users mailing list<br>ome-users@lists.openmicroscopy.org.uk<br>http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users<br><br><br>------------------------------<br><br>End of ome-users Digest, Vol 119, Issue 23<br>******************************************<br></blockquote></div><br></div></body></html>