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<div>Hi Eric,</div>
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<div>Thanks for the heads up.</div>
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<div>We’ve had a dig into the server logs and it looks you have hit a small bug with the particular images you were working with, one which we seem to be able to replicate.</div>
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<div>As always, we’ll be improving OMERO and Bio-Formats with the fix, so thanks for the heads up. </div>
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<div>All the best,</div>
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<div>Kenny</div>
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<div style="font-family: Calibri; font-size: medium; "><span style="font-size: 12px; font-style: italic; font-weight: bold; font-family: Arial; ">Kenneth Gillen</span></div>
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<span style="font-weight:bold">From: </span>"Eric Griffis (Staff)" <<a href="mailto:e.griffis@dundee.ac.uk">e.griffis@dundee.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Tuesday, 12 May 2015 23:04<br>
<span style="font-weight:bold">Cc: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] OMERO Question<br>
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Hi All,
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</div>
<div>I've been having a lot of issues with nightshade tonight. Everything is taking a very long time.</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Eric</div>
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Centre for Gene Regulation and Expression</div>
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College of Life Sciences</div>
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University of Dundee</div>
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MSI/WTB/JBC Complex</div>
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Dow Street</div>
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Dundee DD1 5EH</div>
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United KIngdom</div>
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+44 (0)1382 385118</div>
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<a href="mailto:e.griffis@dundee.ac.uk">e.griffis@dundee.ac.uk</a></div>
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<a href="http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html">http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html</a></div>
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<div>On 11 May 2015, at 12:57, "Balaji Ramalingam (Staff)" <<a href="mailto:b.ramalingam@dundee.ac.uk">b.ramalingam@dundee.ac.uk</a>></div>
<div> wrote:</div>
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<div><span style="font-family: Helvetica; font-size: 13px;">Hi Eric,</span>
<div style="font-family: Helvetica; font-size: 13px;"><br>
</div>
<div style="font-family: Helvetica; font-size: 13px;">Here are some workflows that might help your case,</div>
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<ol>
<li>Open both the stacks on ImageJ.
<ol>
<li>Images on disk : (Plugins —> Bio-Formats —> Bio-Formats Importer) or</li><li>Images on Omero Server : (Plugins —> OMERO —> login to OMERO) : Then open the image of interest.</li></ol>
</li><li>Image —> Stacks —> Tools —> Concatenate. (This concatenates the two stacks).</li><li>Plugins —> Bioformats —> Bioformats Exporter (Export the concatenated file locally) : This should preserve the metadata, while writing out the stack as an ome.tiff.</li><li>Now import the ome.tiff into OMERO. This should hopefully preserve the image and the associated metadata, for later use (in OMERO.Figure).</li></ol>
<div><br>
</div>
</div>
<div style="font-family: Helvetica; font-size: 13px;">**You can also do the following post concatenating the images, (But this workflow has a bug, which will get looked into at the earliest)</div>
<div style="font-family: Helvetica; font-size: 13px;">Plugins—> OMERO —> Upload and save to OMERO : should save the stack to OMERO directly from ImageJ.</div>
<div style="font-family: Helvetica; font-size: 13px;"><br>
</div>
<div style="font-family: Helvetica; font-size: 13px;">Requirements for the above workflows:</div>
<div style="font-family: Helvetica; font-size: 13px;">
<ol>
<li>Bioformats_package.jar in your ImageJ/Plugins folder. (Can be downloaded from : <a href="http://downloads.openmicroscopy.org/bio-formats/5.1.1/">http://downloads.openmicroscopy.org/bio-formats/5.1.1/</a>)</li><li>Omero-ImageJ/Fiji plugin in your ImageJ/plugins folder. (Can be downloaded from : <a href="http://downloads.openmicroscopy.org/omero/5.1.1/">http://downloads.openmicroscopy.org/omero/5.1.1/</a>)</li></ol>
<div><br>
</div>
<div>For more information on the above workflows please visit our help page,</div>
<div><a href="http://help.openmicroscopy.org/imagej.html">http://help.openmicroscopy.org/imagej.html</a></div>
<div><br>
</div>
<div>Hope that helps,</div>
<div><br>
</div>
<div>Best,</div>
<div>Balaji</div>
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<div><br>
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<div style="color: rgb(40, 40, 40);"><span style="background-color: rgb(255, 255, 255);">__________________</span></div>
<div style="color: rgb(40, 40, 40);">
<div style="margin-top: 0px; margin-bottom: 0px; ">Mr Balaji Ramalingam</div>
<div style="margin-top: 0px; margin-bottom: 0px; ">Software Developer<br>
</div>
<div style="margin-top: 0px; margin-bottom: 0px; ">OME Team</div>
<div style="margin-top: 0px; margin-bottom: 0px; ">College of Life Sciences</div>
<div style="margin-top: 0px; margin-bottom: 0px; ">University of Dundee</div>
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<span style="font-weight:bold">From: </span>"William Moore (Staff)" <<a href="mailto:W.Moore@dundee.ac.uk">W.Moore@dundee.ac.uk</a>><br>
<span style="font-weight:bold">Reply-To: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Date: </span>Sunday, 10 May 2015 22:33<br>
<span style="font-weight:bold">To: </span>"Eric Griffis (Staff)" <<a href="mailto:e.griffis@dundee.ac.uk">e.griffis@dundee.ac.uk</a>><br>
<span style="font-weight:bold">Cc: </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>><br>
<span style="font-weight:bold">Subject: </span>Re: [ome-users] OMERO Question<br>
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Hi Eric,
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</div>
<div> I can't tell you myself how to do this, but I know that someone on the team will, so I'm forwarding to the e-mail list, and we'll go from there…</div>
<div><br>
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<div> Cheers,</div>
<div><br>
</div>
<div> Will.</div>
<div><br>
</div>
<div><br>
<div>
<div>On 8 May 2015, at 13:44, Eric Griffis (Staff) <<a href="mailto:e.griffis@dundee.ac.uk">e.griffis@dundee.ac.uk</a>> wrote:</div>
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<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Hi Will,
<div><br>
</div>
<div>I have an issue with a dataset. I have a cell that was imaged until the end of a timelapse, and then I started a new timelapse. I would like to be able to concatenate these two images and have all of the metadata merge together. I can do the concatenation
by exporting and then separately opening the images in FIJI. However, the saved image loses all of the metadata and is therefore more difficult to work with in Figure than I would like. Is there a better way?</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Eric</div>
<div><br>
</div>
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<br class="Apple-interchange-newline">
Centre for Gene Regulation and Expression</div>
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College of Life Sciences</div>
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University of Dundee</div>
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MSI/WTB/JBC Complex</div>
<div style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
Dow Street</div>
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Dundee DD1 5EH</div>
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United KIngdom</div>
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+44 (0)1382 385118</div>
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<a href="mailto:e.griffis@dundee.ac.uk">e.griffis@dundee.ac.uk</a></div>
<div style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
<a href="http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html">http://www.lifesci.dundee.ac.uk/groups/eric_griffis/GriffisLab/index.html</a></div>
<div style="font-family: Helvetica; font-size: medium; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: 2; text-align: -webkit-auto; text-indent: 0px; text-transform: none; white-space: normal; widows: 2; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px; ">
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</blockquote>
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
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</span></div>
</blockquote>
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<br>
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
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</span><br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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