<html><head><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"><meta http-equiv="Content-Type" content="text/html charset=iso-8859-1"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">Dear Roger,<div>I uploaded my lif file on the provides link.</div><div>The name was the following:</div><div><span style="color: rgb(85, 85, 85); font-family: Arial, Verdana, Lucida, Helvetica, sans-serif; font-size: 14px; font-weight: bold; white-space: nowrap; background-color: rgb(235, 255, 235);">Manipdu01-12-2014.lif</span></div><div><font color="#555555" face="Arial, Verdana, Lucida, Helvetica, sans-serif"><span style="font-size: 14px; white-space: nowrap; background-color: rgb(235, 255, 235);"><b><br></b></span></font></div><div>I also added a text file with the description of the problem, which are the following:</div><div><font color="#555555" face="Arial, Verdana, Lucida, Helvetica, sans-serif"><span style="font-size: 14px; white-space: nowrap; background-color: rgb(235, 255, 235);"><b><br></b></span></font></div><div><font color="#555555" face="Arial, Verdana, Lucida, Helvetica, sans-serif"><span style="background-color: rgb(235, 255, 235);"><b><div><span style="font-size: 14px; white-space: nowrap;">The metadata that I could load on fiji are the following:</span></div><div><br></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 1 (stain) #1<span class="Apple-tab-span" style="white-space:pre"> </span>Leica/DAPI</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 2 (left) #1<span class="Apple-tab-span" style="white-space:pre"> </span>495.324675324675</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 2 (right) #1<span class="Apple-tab-span" style="white-space:pre"> </span>553.116883116883</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 2 (stain) #1<span class="Apple-tab-span" style="white-space:pre"> </span>Leica/ALEXA 488</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 3 (left) #1<span class="Apple-tab-span" style="white-space:pre"> </span>570</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 3 (right) #1<span class="Apple-tab-span" style="white-space:pre"> </span>627.012987012987</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 3 (stain) #1<span class="Apple-tab-span" style="white-space:pre"> </span>Leica/Cy3</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 4 (left) #1<span class="Apple-tab-span" style="white-space:pre"> </span>650</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 4 (right) #1<span class="Apple-tab-span" style="white-space:pre"> </span>750</span></div><div><span style="font-size: 14px; white-space: nowrap;">Rat-6div-TIV-488-AP3-CY3-MAP2 HardwareSetting|FilterSettingRecord|SP Mirror Channel 4 (stain) #1<span class="Apple-tab-span" style="white-space:pre"> </span>Leica/Cy5</span></div><div><span style="font-size: 14px; white-space: nowrap;"><br></span></div><div><span style="font-size: 14px; white-space: nowrap;">However the picture are loaded in this order in FIJI:</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel1: Leica/Cy5</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel2: Leica/CY3</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel3: Leica/ALEXA 488</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel4: Leica/DAPI</span></div><div><span style="font-size: 14px; white-space: nowrap;"><br></span></div><div><span style="font-size: 14px; white-space: nowrap;">The picture are loaded in the same order in ICY:</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel1: Leica/Cy5</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel2: Leica/CY3</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel3: Leica/ALEXA 488</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel4: Leica/DAPI</span></div><div><span style="font-size: 14px; white-space: nowrap;"><br></span></div><div><span style="font-size: 14px; white-space: nowrap;">And ICY displays that names:</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel 1 : Leica/DAPI</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel 2: Leica/ALEXA 488</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel3: Leica/Cy3</span></div><div><span style="font-size: 14px; white-space: nowrap;">Channel4: Leica/Cy5</span></div><div><span style="font-size: 14px; white-space: nowrap;"><br></span></div><div><span style="font-size: 14px; white-space: nowrap;">So it seems that the channel name are conserved but not the channel order.</span></div><div><span style="font-size: 14px; white-space: nowrap;">Could you find a solution ?</span></div><div><span style="font-size: 14px; white-space: nowrap;">Thanks a lot.</span></div><div><span style="font-size: 14px; white-space: nowrap;">Lydia.</span></div><div><span style="font-size: 14px; white-space: nowrap;"><br></span></div></b></span></font><div><div>Le 4 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: Lif channel name in bioformat (Roger Leigh)<br> 2. Re: Unable to move project from one group to an other<br> (Mark Carroll (Staff))<br> 3. Re: Unable to move project from one group to an other<br> (Philippe Mailly)<br><br><br>----------------------------------------------------------------------<br><br>Message: 1<br>Date: Wed, 4 Feb 2015 09:44:49 +0000<br>From: Roger Leigh <rleigh@dundee.ac.uk><br>To: <ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Lif channel name in bioformat<br>Message-ID: <54D1EA11.9070606@dundee.ac.uk><br>Content-Type: text/plain; charset="windows-1252"; format=flowed<br><br>On 03/02/15 20:22, ImageJLyd wrote:<br><br><blockquote type="cite">I'm currently working with lif files generated on a Leica SP5 confocal<br>microscope.<br>I would like to warn you about the fact that the channel names are wrong<br>when opening .lif file with Icy software.<br>Channel names :<br>channel 1 is wrongly indicating the name of the channel 4<br>Channel 2 is wrongly indicating the name of the channel 3<br>Channel 3 is wrongly indicating the name of the channel 2<br>Channel 4 is wrongly indicating the name of the channel 1<br><br>When I read the metadata of the lif file in Fiji, it appears,that<br>actually even if LUT are respected in fiji (and not in icy), the channel<br>names are inverted in comparison with leica software. Could it come from<br>the bioformat ?<br></blockquote><br>If you could possibly upload an example file which is showing the<br>problem using:<br><br> http://qa.openmicroscopy.org.uk/qa/upload/<br><br>then we can take a look at it and provide an answer to your question,<br>and if there's a problem we can look into what might need fixing.<br><br><br>Kind regards,<br>Roger<br><br>--<br>Dr Roger Leigh -- Open Microscopy Environment<br>Wellcome Trust Centre for Gene Regulation and Expression,<br>College of Life Sciences, University of Dundee, Dow Street,<br>Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br><br>The University of Dundee is a registered Scottish Charity, No: SC015096<br><br><br>------------------------------<br><br>Message: 2<br>Date: Wed, 4 Feb 2015 10:56:38 +0000<br>From: "Mark Carroll (Staff)" <m.t.b.carroll@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] Unable to move project from one group to an<br><span class="Apple-tab-span" style="white-space:pre"> </span>other<br>Message-ID: <1423047397214.36726@dundee.ac.uk><br>Content-Type: text/plain; charset="iso-8859-1"<br><br>Dear Philippe,<br><br><blockquote type="cite">However, this image (10000) is only in this dataset, I get only one row ??<br></blockquote><br>Yes, it does seem so. I don't suppose it is possible that the dataset could be in multiple projects?<br><br>bin/omero hql "select parent from ProjectDatasetLink where child = 736"<br><br>Cheers,<br><br>Mark<br><br>The University of Dundee is a registered Scottish Charity, No: SC015096<br><br><br>------------------------------<br><br>Message: 3<br>Date: Wed, 04 Feb 2015 12:42:43 +0100<br>From: Philippe Mailly <philippe.mailly@college-de-france.fr><br>To: OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>Subject: Re: [ome-users] Unable to move project from one group to an<br><span class="Apple-tab-span" style="white-space:pre"> </span>other<br>Message-ID: <54D205B3.5040800@college-de-france.fr><br>Content-Type: text/plain; charset="windows-1252"; Format="flowed"<br><br>Hi Mark,<br><br>Finally, I remove the dataset and transfer the data to the good location.<br><br><br>Philippe<br><br>Le 04/02/2015 11:56, Mark Carroll (Staff) a ?crit :<br><blockquote type="cite">Dear Philippe,<br><br><blockquote type="cite">However, this image (10000) is only in this dataset, I get only one row ??<br></blockquote>Yes, it does seem so. I don't suppose it is possible that the dataset could be in multiple projects?<br><br>bin/omero hql "select parent from ProjectDatasetLink where child = 736"<br><br>Cheers,<br><br>Mark<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>-------------- next part --------------<br>A non-text attachment was scrubbed...<br>Name: philippe_mailly.vcf<br>Type: text/x-vcard<br>Size: 349 bytes<br>Desc: not available<br>URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-users/attachments/20150204/a99a803a/attachment-0001.vcf><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 5<br>*****************************************<br></blockquote></div><br></div></body></html>