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<p>Hi</p>
<p>So I uploaded an image file (fond clair zeiss 40x 17 ms) via the link provided, <a href="https://www.openmicroscopy.org/qa2/qa/upload/">https://www.openmicroscopy.org/qa2/qa/upload/</a></p>
<p>Hope it worked, I could not log in OMERO though I thought I was registered</p>
<p>Thanks </p>
<p>Pierre</p>
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<pre><span style="font-size: x-small;">-- <br />Pierre Godement
Institut de Genomique Fonctionnelle de Lyon
UMR 5242 du CNRS
Ecole Normale Superieure de Lyon
46, Allee d'Italie
69364 Lyon Cedex 07
France
Tel: 33 (0)4 26 73 13 21
Fax: 33 (0)4 26 73 13 75
E-mail: <a href="mailto:Pierre.Godement@ens-lyon.fr">Pierre.Godement@ens-lyon.fr</a>
------------------------------------------------------
Mailing address:
46 Allee d'Italie
69364 Lyon cedex 07
The IGFL is now located at:
32-34 Avenue Tony Garnier, Lyon 69007
For deliveries:
29 rue Alexander Fleming, Lyon 69007</span></pre>
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<p><br /></p>
<p>Le 30/05/2017 13:00, ome-users-request@lists.openmicroscopy.org.uk a écrit :</p>
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<div class="pre" style="margin: 0; padding: 0; font-family: monospace">Send ome-users mailing list submissions to<br /> <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 /> <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 /> <a href="mailto:ome-users-request@lists.openmicroscopy.org.uk">ome-users-request@lists.openmicroscopy.org.uk</a><br /> <br /> You can reach the person managing the list at<br /> <a href="mailto:ome-users-owner@lists.openmicroscopy.org.uk">ome-users-owner@lists.openmicroscopy.org.uk</a><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: Jenkins downtime due to secvuln (Sebastien Besson (Staff))<br /> 2. open Carl Zeiss 2011 .czi files of transmitted light images<br /> correctly (Godement Pierre)<br /> 3. Re: open Carl Zeiss 2011 .czi files of transmitted light<br /> images correctly (David Gault (Staff))<br /> <br /> <br /> ----------------------------------------------------------------------<br /> <br /> Message: 1<br /> Date: Mon, 29 May 2017 12:40:33 +0000<br /> From: "Sebastien Besson (Staff)" <<a href="mailto:s.besson@dundee.ac.uk">s.besson@dundee.ac.uk</a>><br /> To: users OME <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br /> Subject: Re: [ome-users] Jenkins downtime due to secvuln<br /> Message-ID: <<a href="mailto:9467DB7F-5841-47C0-8072-9EFE92FDCA79@dundee.ac.uk">9467DB7F-5841-47C0-8072-9EFE92FDCA79@dundee.ac.uk</a>><br /> Content-Type: text/plain; charset="utf-8"<br /> <br /> Dear all,<br /> <br /> following our email from last month, we wanted to notify you that our Continuous Integration<br /> server has been successfully upgraded to the latest LTS version and is now available<br /> online again.<br /> <br /> We thank you for your patience. Please let us know of any issue,<br /> The OME Team<br /> <br />
<blockquote type="cite" style="padding: 0 0.4em; border-left: #1010ff 2px solid; margin: 0">On 28 Apr 2017, at 18:14, Kenneth Gillen (Staff) <<a href="mailto:k.h.gillen@dundee.ac.uk">k.h.gillen@dundee.ac.uk</a>> wrote:<br /> <br /> All,<br /> <br /> A sizable number of security vulnerabilities have recently been released<br /> for Jenkins [<a href="https://jenkins.io/security/advisory/2017-04-26/">1</a>]. This is the software that runs<br /> <a href="https://ci.openmicroscopy.org">https://ci.openmicroscopy.org</a>, our public continuous integration server.<br /> Until the system can be upgraded and re-tested, we have taken it offline.<br /> If you have any concerns or difficulty before it comes back online, don?t<br /> hesitate to get in touch with us via the forum or mailing lists<br /> <br /> Otherwise, we apologize for the hassle and thank you for your<br /> understanding.<br /> The OME Team.<br /> <br /> [1] <a href="https://jenkins.io/security/advisory/2017-04-26/">https://jenkins.io/security/advisory/2017-04-26/</a><br /> <br /> <br /> The University of Dundee is a registered Scottish Charity, No: SC015096<br /> _______________________________________________<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></blockquote>
<br /> <br /> The University of Dundee is a registered Scottish Charity, No: SC015096<br /> <br /> ------------------------------<br /> <br /> Message: 2<br /> Date: Mon, 29 May 2017 18:33:40 +0200<br /> From: Godement Pierre <<a href="mailto:pierre.godement@ens-lyon.fr">pierre.godement@ens-lyon.fr</a>><br /> To: <a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a><br /> Subject: [ome-users] open Carl Zeiss 2011 .czi files of transmitted<br /> light images correctly<br /> Message-ID: <<a href="mailto:a7baa63ddbb1b2ea6b3d05813a1ef8c1@ens-lyon.fr">a7baa63ddbb1b2ea6b3d05813a1ef8c1@ens-lyon.fr</a>><br /> Content-Type: text/plain; charset="us-ascii"<br /> <br /> Hello <br /> <br /> seems that the latest version of FIJI and/or the Bioformats package<br /> cannot open Carl Zeiss 2011 .czi files of transmitted light images<br /> correctly unless these are made with the latest ZEN version: with<br /> Hyperstack one gets in composite mode 3 images in black and white LUT<br /> from which the path to a single RGB image is arduous to the very least<br /> (e.g. I did not find it). <br /> <br /> Or, using a custom mode one then needs to apply an RGB LUT, then<br /> transform in Composite, and finally in RGB to get things OK. <br /> <br /> Does anyone have a solution - it would help a lot ! <br /> <br /> Thanks ! <br /> <br /> Have a good day ! <br /> <br /> Pierre<br /> <br /> -- <br /> Pierre Godement<br /> Institut de Genomique Fonctionnelle de Lyon<br /> UMR 5242 du CNRS<br /> Ecole Normale Superieure de Lyon<br /> 46, Allee d'Italie<br /> 69364 Lyon Cedex 07<br /> France<br /> Tel: 33 (0)4 26 73 13 21<br /> Fax: 33 (0)4 26 73 13 75<br /> E-mail: <a href="mailto:Pierre.Godement@ens-lyon.fr">Pierre.Godement@ens-lyon.fr</a><br /> <br /> ------------------------------------------------------<br /> <br /> Mailing address:<br /> <br /> 46 Allee d'Italie<br /> 69364 Lyon cedex 07<br /> <br /> The IGFL is now located at:<br /> 32-34 Avenue Tony Garnier, Lyon 69007<br /> <br /> For deliveries:<br /> 29 rue Alexander Fleming, Lyon 69007<br /> -------------- next part --------------<br /> An HTML attachment was scrubbed...<br /> URL: <<a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170529/eada3d08/attachment-0001.html">http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20170529/eada3d08/attachment-0001.html</a>><br /> <br /> ------------------------------<br /> <br /> Message: 3<br /> Date: Tue, 30 May 2017 10:14:55 +0000<br /> From: "David Gault (Staff)" <<a href="mailto:d.gault@dundee.ac.uk">d.gault@dundee.ac.uk</a>><br /> To: OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br /> Subject: Re: [ome-users] open Carl Zeiss 2011 .czi files of<br /> transmitted light images correctly<br /> Message-ID: <<a href="mailto:EAC75C8E-D741-4D35-B23B-5D441128F62D@dundee.ac.uk">EAC75C8E-D741-4D35-B23B-5D441128F62D@dundee.ac.uk</a>><br /> Content-Type: text/plain; charset="us-ascii"<br /> <br /> Hi Pierre,<br /> <br /> Thanks for reporting this issue, there have been a number of bug fixes to the CZIReader in recent releases which may have resulted in this.<br /> In order for us to debug this problem would you be able to upload a sample file that shows this problem to the link below:<br /> <a href="https://www.openmicroscopy.org/qa2/qa/upload/">https://www.openmicroscopy.org/qa2/qa/upload/</a><br /> <br /> With Thanks,<br /> David Gault<br /> <br />
<blockquote type="cite" style="padding: 0 0.4em; border-left: #1010ff 2px solid; margin: 0">On 29 May 2017, at 17:33, Godement Pierre <<a href="mailto:pierre.godement@ens-lyon.fr">pierre.godement@ens-lyon.fr</a>> wrote:<br /> <br /> Hello<br /> <br /> seems that the latest version of FIJI and/or the Bioformats package cannot open Carl Zeiss 2011 .czi files of transmitted light images correctly unless these are made with the latest ZEN version: with Hyperstack one gets in composite mode 3 images in black and white LUT from which the path to a single RGB image is arduous to the very least (e.g. I did not find it).<br /> <br /> Or, using a custom mode one then needs to apply an RGB LUT, then transform in Composite, and finally in RGB to get things OK.<br /> <br /> Does anyone have a solution - it would help a lot !<br /> <br /> Thanks !<br /> <br /> Have a good day !<br /> <br /> Pierre<br /> <br /> --<br /> Pierre Godement<br /> Institut de Genomique Fonctionnelle de Lyon<br /> UMR 5242 du CNRS<br /> Ecole Normale Superieure de Lyon<br /> 46, Allee d'Italie<br /> 69364 Lyon Cedex 07<br /> France<br /> Tel: 33 (0)4 26 73 13 21<br /> Fax: 33 (0)4 26 73 13 75<br /> E-mail:<br /> <a href="mailto:Pierre.Godement@ens-lyon.fr">Pierre.Godement@ens-lyon.fr</a><br /> <br /> <br /> ------------------------------------------------------<br /> <br /> Mailing address:<br /> <br /> 46 Allee d'Italie<br /> 69364 Lyon cedex 07<br /> <br /> The IGFL is now located at:<br /> 32-34 Avenue Tony Garnier, Lyon 69007<br /> <br /> For deliveries:<br /> 29 rue Alexander Fleming, Lyon 69007<br /> <br /> _______________________________________________<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></blockquote>
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