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<pre><span lang="EN-US">Hi,<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">I have a similar question to the one below which I found on the ome-users list.<o:p></o:p></span></pre>
<pre><span lang="EN-US">My data is ome-tif, and I have different images with several channels. I would like to merge one or more of each to a resulting ome-tif, also copying the according metadata. Is there a plugin out there that does this? <o:p></o:p></span></pre>
<pre><span lang="EN-US">The route I found was to use LOCI channel splitter, convert to a hyperstack, and then merge in there. That does not keep the metadata, though, I fear.<o:p></o:p></span></pre>
<pre><span lang="EN-US">For writing a plugin myself, my questions would be<o:p></o:p></span></pre>
<pre style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman""> </span></span></span><![endif]><span lang="EN-US">Can IMetadata give me the complete “channel” metadata? Or should I cut it out of the xml string?<o:p></o:p></span></pre>
<pre style="margin-left:36.0pt;text-indent:-18.0pt;mso-list:l0 level1 lfo2"><![if !supportLists]><span lang="EN-US"><span style="mso-list:Ignore">-<span style="font:7.0pt "Times New Roman""> </span></span></span><![endif]><span lang="EN-US">Is there a more intelligent way of copying a whole channel than to go through all frames and z-positions and do it pixelwise via stack.setVoxel? (I did find the ImageProcessor.getPixels() but did not understand how to use its return value)<o:p></o:p></span></pre>
<pre style="margin-left:36.0pt"><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">And more generally, I sometimes feel that I fail to know basic methods and utils within the loci / bio-formats framework. Are there collections of ome-tiff plugins around (more than those in ImageJ->plugins->Loci and components/loci-plugins/utils)? Also, is there a guide/introduction on how to do things? I often write things that work but at the same time guessing there might be a useful class I don’t know of that would make it more elegant…<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">Best<o:p></o:p></span></pre>
<pre><span lang="EN-US"> Heinrich<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<p class="MsoNormal"><b><span lang="EN-US">Melissa Linkert</span></b><span lang="EN-US">
</span><a href="mailto:ome-users%40lists.openmicroscopy.org.uk?Subject=Re%3A%20%5Bome-users%5D%20Combine%20two%20tif%20to%20a%20multilayer%20tif&In-Reply-To=%3C20120514180726.GC31887%40medusa%3E" title="[ome-users] Combine two tif to a multilayer tif">melissa
at glencoesoftware.com </a><br>
<i>Mon May 14 19:07:26 BST 2012</i> <o:p></o:p></p>
<ul type="disc">
<li class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto;mso-list:l1 level1 lfo1">
<span lang="EN-US">Previous message: </span><a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-May/003057.html"><span lang="EN-US">[ome-users] Combine two tif to a multilayer tif
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<span lang="EN-US">Next message: </span><a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-May/003059.html"><span lang="EN-US">[ome-users] Importing .dv File via BioFormats
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<b><span lang="EN-US">Messages sorted by:</span></b><span lang="EN-US"> </span><a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2012-May/date.html#3058"><span lang="EN-US">[ date ]</span></a>
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<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">Hi Jürgen,<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">><i> I have some image data in MetaMorph format. The Image format is not<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> supported by Omero and I have to create an OME-XML header prior to<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> importing the data.<o:p></o:p></i></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">MetaMorph data is definitely supposed to be supported. Could you please<o:p></o:p></span></pre>
<pre><span lang="EN-US">tell us what goes wrong when you try to import it into OMERO (as the<o:p></o:p></span></pre>
<pre><span lang="EN-US">simplest solution is almost always to just import the original data)?<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">><i> Each channel (I have two, DAPI and GFP) is saved in a single separate image.<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> For further processing I would like to combine the two channel<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> images into a multi-layer tif file with a single header.<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> I can do using convert from the imagemagick pckage:<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> convert file1.tif file2.tif output.tif<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> But that literally just concatenates the two files, resulting in a<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> multi-layer file but also in two headers, so I have<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> Exif.Image.Description<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> as well as:<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> Exif.Image2.Description<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> Does anyone know of a tool to properly combine the two tiff files<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> resulting in a new multi-layer tif file with a single header?<o:p></o:p></i></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">I believe this:<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><a href="http://www.imagemagick.org/Usage/color_basics/#combine"><span lang="EN-US">http://www.imagemagick.org/Usage/color_basics/#combine</span></a><span lang="EN-US"><o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">and this:<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><a href="http://www.imagemagick.org/discourse-server/viewtopic.php?f=1&t=13534"><span lang="EN-US">http://www.imagemagick.org/discourse-server/viewtopic.php?f=1&t=13534</span></a><span lang="EN-US"><o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">explain how to do what you want in ImageMagick.<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">Regards,<o:p></o:p></span></pre>
<pre><span lang="EN-US">-Melissa<o:p></o:p></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">On Mon, May 14, 2012 at 06:15:24PM +0200, Dr. Juergen helmers wrote:<o:p></o:p></span></pre>
<pre><span lang="EN-US">><i> Hi!<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> I have some image data in MetaMorph format. The Image format is not<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> supported by Omero and I have to create an OME-XML header prior to<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> importing the data.<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> Each channel (I have two, DAPI and GFP) is saved in a single separate image.<o:p></o:p></i></span></pre>
<pre>><i> <o:p></o:p></i></pre>
<pre><span lang="EN-US">><i> For further processing I would like to combine the two channel<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> images into a multi-layer tif file with a single header.<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> I can do using convert from the imagemagick pckage:<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> convert file1.tif file2.tif output.tif<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> But that literally just concatenates the two files, resulting in a<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> multi-layer file but also in two headers, so I have<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> Exif.Image.Description<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> as well as:<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> Exif.Image2.Description<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> <o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> Does anyone know of a tool to properly combine the two tiff files<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> resulting in a new multi-layer tif file with a single header?<o:p></o:p></i></span></pre>
<pre>><i> <o:p></o:p></i></pre>
<pre>><i> Thanks Juergen<o:p></o:p></i></pre>
<pre>><i> <o:p></o:p></i></pre>
<pre>><i> -- <o:p></o:p></i></pre>
<pre>><i> *Dr. Jürgen Helmers*<o:p></o:p></i></pre>
<pre><span lang="EN-US">><i> /Chief Developer/ | webnow | </i></span><i><a href="http://www.web-now.de"><span lang="EN-US">http://www.web-now.de</span></a></i><i><span lang="EN-US"><o:p></o:p></span></i></pre>
<pre><span lang="EN-US">><i> *email:*</i></span><i><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"><span lang="EN-US">juergen.helmers at gmail.com</span></a></i><i><span lang="EN-US"> | *tel:*+49 30 37301306 | *skype:*<o:p></o:p></span></i></pre>
<pre><span lang="EN-US">><i> helmerj<o:p></o:p></i></span></pre>
<pre><span lang="EN-US"><o:p> </o:p></span></pre>
<pre><span lang="EN-US">><i> _______________________________________________<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> ome-users mailing list<o:p></o:p></i></span></pre>
<pre><span lang="EN-US">><i> </i></span><i><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"><span lang="EN-US">ome-users at lists.openmicroscopy.org.uk</span></a></i><i><span lang="EN-US"><o:p></o:p></span></i></pre>
<pre><span lang="EN-US">><i> </i></span><i><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"><span lang="EN-US">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</span></a></i><i><span lang="EN-US"><o:p></o:p></span></i></pre>
<p class="MsoNormal"><span lang="EN-US"><o:p> </o:p></span></p>
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