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<div>Hi Eric,</div>
<div><br>
</div>
<div>Testing this in better detail, shows that the error seems to be upstream of Bio-Formats.</div>
<div><br>
</div>
<div>This whole workflow depends on the intelligence of the concatenation algorithm (within ImageJ/Fiji), and the error propagates if algorithm fails to set the "image properties” correctly for the resulting image.Bio-Formats just exports whatever is stored
as "Image Properties" in ImageJ/Fiji.</div>
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<div><br>
</div>
<div>One can Manually edit these properties in ImageJ/Fiji by clicking on,</div>
</div>
<div>Image —> Properties (Please do this post concatenation)</div>
<div><br>
</div>
<div>Any updates over here gets read by Bio-formats and will eventually be available in OMERO as well, if you follow the workflow I had suggested earlier.</div>
<div>(Export with Bio-Formats Exporter and import the resulting ome-tiff into OMERO).</div>
<div><br>
</div>
<div>Hope that helps.</div>
<div><br>
</div>
<div>Best,</div>
<div>Balaji</div>
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<div><br>
</div>
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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);">
<p style="margin-top: 0px; margin-bottom: 0px;">Mr Balaji Ramalingam</p>
<p style="margin-top: 0px; margin-bottom: 0px;">Software Developer<br>
</p>
<p style="margin-top: 0px; margin-bottom: 0px;">OME Team</p>
<p style="margin-top: 0px; margin-bottom: 0px;">College of Life Sciences</p>
<p style="margin-top: 0px; margin-bottom: 0px;">University of Dundee</p>
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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">Date: </span>Tuesday, 12 May 2015 22:15<br>
<span style="font-weight:bold">To: </span>Balaji Ramalingam <<a href="mailto:b.ramalingam@dundee.ac.uk">b.ramalingam@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>
</div>
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</div>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
Hi Balaji,
<div><br>
</div>
<div>I have tried this and it doesn't totally work. </div>
<div><br>
</div>
<div>I open the images from the Fiji-OMERO plugin. </div>
<div><br>
</div>
<div>When I concatenate the images, however, the size reverts back to microns=pixels, suggesting I've lost the metadata. </div>
<div><br>
</div>
<div>I've used the Bioformats Exporter to save the concatenated image as a ome.tiff, and when I open it back up, I still don't see the proper image size. I'm trying to reimport the image into Omero to see if this would fix the metadata issue with regards to
time and size. I'll let you know what I find.</div>
<div><br>
</div>
<div>Best regards,</div>
<div><br>
</div>
<div>Eric</div>
<div><br>
</div>
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Centre for Gene Regulation and Expression</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>
<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>> wrote:</div>
<br class="Apple-interchange-newline">
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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>
<div style="font-family: Helvetica; font-size: 13px;">
<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>
</div>
</div>
<div>
<div><br>
</div>
<div>
<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>
</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>
</div>
<div><br>
</div>
<div>
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space; ">
<div><br>
</div>
Hi Eric,
<div><br>
</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>
</div>
<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>
<br class="Apple-interchange-newline">
<blockquote type="cite">
<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>
<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>
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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>
<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>
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</blockquote>
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<br>
<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span></div>
</div>
</span></div>
</blockquote>
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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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