<html><head><meta http-equiv="Content-Type" content="text/html charset=windows-1253"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Further to this reported problem with Bio-Formats importer failing to populate the ImagePlus object with a slice name based on the BioFormats channel name (see <a href="https://trac.openmicroscopy.org/ome/ticket/13306" class="">https://trac.openmicroscopy.org/ome/ticket/13306</a>) I put forward the following:<div class=""><br class=""></div><div class="">The code for setting the line label is to be found in the function constructSliceLabel() in the file:</div><div class=""><br class=""></div><div class=""><a href="https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/in/ImagePlusReader.java" class="">https://github.com/openmicroscopy/bioformats/blob/develop/components/bio-formats-plugins/src/loci/plugins/in/ImagePlusReader.java</a></div><div class=""><br class=""></div><div class=""><div class="">In particular, I put forward that line 625</div><div class=""><br class=""></div><br class=""> String imageName = meta.getImageName(series);<br class=""><br class=""><div class="">Should be changed to </div><div class=""><br class=""></div><div class=""> String imageName = meta.getChannelName(ndx, cCount);</div><div class=""><br class=""></div><div class="">That is to say, the BioFormats channel name (where present), will be happened to the constructed slice name, rather than appending the BioFormats image name.</div><div class=""><br class=""></div><div class="">I have tried to build my own copy of the BioFormats ImageJ plugins but have so far failed.</div><div class=""><br class=""></div><div class="">Is there any way this one line fix could incorporated?</div><div class=""><br class=""></div><div class="">I really think this is probably what was intended in the first place as it would seem to be of little value to repeat the image name for every slice when the image name is already present in the ImagePlus as the image title.</div><div class=""><br class=""></div><div class="">— Michael Ellis</div><div class=""><br class=""></div><div class=""><div class=""><br class=""><div><blockquote type="cite" class=""><div class="">On 19 Oct 2016, at 10:52, Balaji Ramalingam (Staff) <<a href="mailto:b.ramalingam@dundee.ac.uk" class="">b.ramalingam@dundee.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
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<div class="">Hi,</div>
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<div class="">Thank you for the update again.</div>
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<div class="">We have been reviewing the body of work on the Bio-Formats import/export front, which includes populating the ImagePlus object appropriately.</div>
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<div class="">I have updated the ticket again, with your latest comments. </div>
<div class="">This will get looked into at the earliest.</div>
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<div class="">Thanks again,</div>
<div class="">Best,</div>
<div class="">Balaji</div>
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<div style="color: rgb(40, 40, 40);" class=""><span style="background-color: rgb(255, 255, 255);" class="">__________________</span></div>
<div style="color: rgb(40, 40, 40);" class=""><div style="margin-top: 0px; margin-bottom: 0px;" class="">Mr Balaji Ramalingam</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">Software Developer<br class="">
</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">OME Team</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">School of Life Sciences</div><div style="margin-top: 0px; margin-bottom: 0px;" class="">University of Dundee</div>
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<span style="font-weight:bold" class="">From: </span>ome-devel <<a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" class="">ome-devel-bounces@lists.openmicroscopy.org.uk</a>> on behalf of Michael Ellis <<a href="mailto:michael.ellis@dsuk.biz" class="">michael.ellis@dsuk.biz</a>><br class="">
<span style="font-weight:bold" class="">Reply-To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a>><br class="">
<span style="font-weight:bold" class="">Date: </span>Tuesday, 18 October 2016 at 15:50<br class="">
<span style="font-weight:bold" class="">To: </span>OME External Developer List <<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a>><br class="">
<span style="font-weight:bold" class="">Cc: </span>ImageJ Interest Group <<a href="mailto:IMAGEJ@LIST.NIH.GOV" class="">IMAGEJ@LIST.NIH.GOV</a>><br class="">
<span style="font-weight:bold" class="">Subject: </span>Re: [ome-devel] BioFormats Export/Import of Composite Images<br class="">
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Dear Balaji,
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<div class="">Thank you for the update. It seems the the ImageJ BioFormats Importer also fails to set the ImageJ pixel size in accordance with the metadata physicalSizeX/YZ parameters.</div>
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<div class=""> Unit<Length> unit = UNITS.MICROMETER;</div>
<div class=""> Length physicalSizeX = new Length(1.0, unit);</div>
<div class=""> Length physicalSizeY = new Length(1.5, unit);</div>
<div class=""> Length physicalSizeZ = new Length(2, unit);</div>
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<div class="">— Michael Ellis</div>
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<blockquote type="cite" class="">
<div class="">On 18 Oct 2016, at 15:25, Balaji Ramalingam (Staff) <<a href="mailto:b.ramalingam@dundee.ac.uk" class="">b.ramalingam@dundee.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hi,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Thank
you for sharing your issue and the code as well.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">We
were able to reproduce the issue and I have added a reference to an</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">existing
ticket (to handle the slice labels appropriately in the</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Bio-Formats
Exporter as well),</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="https://trac.openmicroscopy.org/ome/ticket/13306" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">https://trac.openmicroscopy.org/ome/ticket/13306</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">This
will get looked into at the earliest, and since you are already part</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">of
the cc list, you will get notified when there is a status change on the</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ticket.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hope
that helps.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Best,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Balaji</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">__________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Mr
Balaji Ramalingam</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Software
Developer</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">OME
Team</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">School
of Life Sciences</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">University
of Dundee</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">On
13/10/2016, 15:43, "ome-devel on behalf of Michael Ellis"</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""><</span><a href="mailto:ome-devel-bounces@lists.openmicroscopy.org.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-devel-bounces@lists.openmicroscopy.org.uk</a><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""><span class="Apple-converted-space"> </span>on
behalf of</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:michael.ellis@dsuk.biz" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">michael.ellis@dsuk.biz</a><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">>
wrote:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
Is it possible to use the BioFormat Exporter to save a multi-slice<br class="">
composite images, and then have the BioFormats Importer import that image<br class="">
restoring the ImageJ slice names and slice LUTS?<br class="">
<br class="">
This ImageJ script creates a 4 channel composite image, with channel<br class="">
names and luts specified.<br class="">
<br class="">
newImage("MyStack", "8-bit random", 256, 256, 4);<br class="">
run("Make Composite", "display=Composite");<br class="">
setSlice(1);<br class="">
run("Set Label...", "label=Dapi");<br class="">
run("Blue");<br class="">
setSlice(2);<br class="">
run("Set Label...", "label=Fitc");<br class="">
run("Green");<br class="">
setSlice(3);<br class="">
run("Set Label...", "label=TxRed");<br class="">
run("Red");<br class="">
setSlice(4);<br class="">
run("Set Label...", "label=Aqua");<br class="">
run("Cyan");<br class="">
<br class="">
If I use BioFormats Exporter/Importer on this image, the slice labels and<br class="">
slice LUTS are not restored.<br class="">
<br class="">
The created file certainly has the slice name information as can be seen<br class="">
from the .ome.tif header<br class="">
<br class="">
<OME UUID="urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f327"<br class="">
xmlns="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a>"<br class="">
xmlns:xsi="<a href="http://www.w3.org/2001/XMLSchema-instance" class="">http://www.w3.org/2001/XMLSchema-instance</a>"<br class="">
xsi:schemaLocation="<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01</a><br class="">
<a href="http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd" class="">http://www.openmicroscopy.org/Schemas/OME/2015-01/ome.xsd</a>"><br class="">
<Image ID="Image:0"><br class="">
<Pixels BigEndian="false" DimensionOrder="XYCZT" ID="Pixels:0"<br class="">
Interleaved="false" PhysicalSizeX="1.0" PhysicalSizeXUnit="ìm"<br class="">
PhysicalSizeY="1.0" PhysicalSizeYUnit="ìm" PhysicalSizeZ="1.0"<br class="">
PhysicalSizeZUnit="ìm" SignificantBits="8" SizeC="4" SizeT="1"<br class="">
SizeX="256" SizeY="256" SizeZ="1" TimeIncrement="0.0"<br class="">
TimeIncrementUnit="s" Type="uint8"><br class="">
<Channel Color="-16776961" ID="Channel:0:0" Name="Dapi"<br class="">
SamplesPerPixel="1"><br class="">
<LightPath/><br class="">
<Channel Color="-16711936" ID="Channel:0:1" Name="Fitc"<br class="">
SamplesPerPixel="1"><br class="">
<LightPath/><br class="">
<Channel Color="-65536" ID="Channel:0:2" Name="TxRed" SamplesPerPixel="1"><br class="">
<LightPath/><br class="">
<Channel Color="-16711681" ID="Channel:0:3" Name="Aqua"<br class="">
SamplesPerPixel="1"><br class="">
<LightPath/><br class="">
<TiffData FirstC="0" FirstT="0" FirstZ="0" IFD="0" PlaneCount="1"><br class="">
<UUID<br class="">
FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32<br class="">
7</UUID><br class="">
<TiffData FirstC="1" FirstT="0" FirstZ="0" IFD="1" PlaneCount="1"><br class="">
<UUID<br class="">
FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32<br class="">
7</UUID><br class="">
<TiffData FirstC="2" FirstT="0" FirstZ="0" IFD="2" PlaneCount="1"><br class="">
<UUID<br class="">
FileName="FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32<br class="">
7</UUID><br class="">
<TiffData FirstC="3" FirstT="0" FirstZ="0" IFD="3" PlaneCount="1"><br class="">
<UUID<br class="">
FileName=³FromImageJ.ome.tif">urn:uuid:9ac10dd4-2ed8-4a6e-a5ec-8a7a8309f32<br class="">
7</UUID><br class="">
<br class="">
<br class="">
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
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</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">The
University of Dundee is a registered Scottish Charity, No: SC015096</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-devel@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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</blockquote>
</div>
<br class="">
<div class="">
<div style="text-align: right;" class="">Michael Ellis (Managing Director)</div>
<div style="text-align: right;" class="">Digital Scientific UK Ltd.</div>
<div style="text-align: right;" class=""><a href="http://www.dsuk.biz/" class="">http://www.dsuk.biz</a></div>
<div style="text-align: right;" class=""><a href="mailto:michael.ellis@dsuk.biz" class="">michael.ellis@dsuk.biz</a></div>
<div style="text-align: right;" class="">tel: +44(0)1223 911215</div>
<div style="text-align: right;" class=""><br class="">
</div>
<div style="text-align: right;" class="">The Commercial Centre</div>
<div style="text-align: right;" class="">6 Green End</div>
<div style="text-align: right;" class="">Cambridge</div>
<div style="text-align: right;" class="">CB23 7DY</div>
</div>
<br class="">
</div>
</div>
</div>
</div>
</span><br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
_______________________________________________<br class="">ome-devel mailing list<br class=""><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel<br class=""></div></blockquote></div><br class=""><div class="">
<div style="text-align: right;" class="">Michael Ellis (Managing Director)</div><div style="text-align: right;" class="">Digital Scientific UK Ltd.</div><div style="text-align: right;" class=""><a href="http://www.dsuk.biz" class="">http://www.dsuk.biz</a></div><div style="text-align: right;" class=""><a href="mailto:michael.ellis@dsuk.biz" class="">michael.ellis@dsuk.biz</a></div><div style="text-align: right;" class="">tel: +44(0)1223 911215</div><div style="text-align: right;" class=""><br class=""></div><div style="text-align: right;" class="">The Commercial Centre</div><div style="text-align: right;" class="">6 Green End</div><div style="text-align: right;" class="">Cambridge</div><div style="text-align: right;" class="">CB23 7DY</div>
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