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<p>Hi David,</p>
<p>thank you for reproducing the problem.</p>
<p>I have tested the issue a bit further and found that the
bio-formats exporter does actually save the LUT in some way.<br>
</p>
<p>It seems to rather be the importer that does not import it
afterwards. Opening the image with ImageJ open instead works, see
below macro code.</p>
<blockquote type="cite">run("M51 Galaxy (177K, 16-bits)");<br>
run("cool", "display=m51.tif
view=net.imagej.display.DefaultDatasetView@7a6b36cd");<br>
run("Bio-Formats Exporter",
"save=/home/kai/Desktop/m51_cool.tif");<br>
// does not work with bio-formats importer<br>
run("Bio-Formats Importer", "open=/home/kai/Desktop/m51_cool.tif
autoscale color_mode=Default rois_import=[ROI manager]
view=Hyperstack stack_order=XYCZT");<br>
// but works with Imagej open<br>
open("/home/kai/Desktop/m51_cool.tif");$</blockquote>
<p>I have also tested several different formats of the Bio-formats
exporter (ICS-1, ome.tif, tif, ch5), but importing an image with
custom LUT also shows as grayscale.<br>
</p>
<p>Thanks for investigating and cheers,<br>
Kai<br>
</p>
<p><br>
</p>
<div class="moz-cite-prefix">On 11/5/18 5:01 PM, David Gault (Staff)
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CC34C25A-36FF-4D10-B5F1-E24AF5082F77@dundee.ac.uk">
<meta http-equiv="Content-Type" content="text/html;
charset=windows-1252">
Hi Kai,
<div class=""><br class="">
</div>
<div class="">Thank you for raising this issue, using the process
you followed should be expected to work and does appear to be
fine when exporting to other formats such as TIFF. </div>
<div class="">Unfortunately it looks like this is a bug in the
ICSWriter which is not saving the custom LUT values during the
export. I have opened a Bio-Formats Trello card for this bug at <a
href="https://trello.com/c/LzWW3y7F/291-icswriter-not-preserving-luts"
class="" moz-do-not-send="true">https://trello.com/c/LzWW3y7F/291-icswriter-not-preserving-luts</a> </div>
<div class=""><br class="">
</div>
<div class="">With Thanks,</div>
<div class="">David Gault</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 2 Nov 2018, at 17:47, Kai Schleicher <<a
href="mailto:kai.schleicher@unibas.ch" class=""
moz-do-not-send="true">kai.schleicher@unibas.ch</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear OME team,<br class="">
<br class="">
I wish to apply a custom LUT in ImageJ and then save the
image as ICS-1 using Bio-formats.<br class="">
<br class="">
When I import the image again with Bio-formats, it does
not show the LUT (see imageJ macro in below quote to
reproduce the steps).<br class="">
<br class="">
Did I miss an option during import, or is there maybe a
different way the LUT should be applied to the image for
the exporter to save it?<br class="">
<br class="">
Thanks and cheers from Basel,<br class="">
Kai<br class="">
<br class="">
<blockquote type="cite" class="">run("M51 Galaxy (177K,
16-bits)");<br class="">
run("cool", "display=m51.tif
view=net.imagej.display.DefaultDatasetView@7a6b36cd");<br
class="">
run("Bio-Formats Exporter",
"save=/home/kai/Desktop/m51_cool.ids");<br class="">
run("Bio-Formats Importer",
"open=/home/kai/Desktop/m51_cool.ids autoscale
color_mode=Default rois_import=[ROI manager]
view=Hyperstack stack_order=XYCZT");<br class="">
</blockquote>
<br class="">
-- <br class="">
<blockquote type="cite" class="">
<blockquote type="cite" class="">Please note my NEW
PHONE NUMBERS: +41 61 207 57 31 (direct) +41 61 207 22
50 (central)<<<br class="">
</blockquote>
</blockquote>
Kai Schleicher, PhD | Research Associate in Advanced Light
Microscopy | Biozentrum, University of Basel |
Klingelbergstrasse 50/70 | CH-4056 Basel |<br class="">
Phone: +41 61 207 57 31 (direct) +41 61 207 22 50
(central) | <a href="mailto:kai.schleicher@unibas.ch"
class="" moz-do-not-send="true">
kai.schleicher@unibas.ch</a> | <a
href="http://www.biozentrum.unibas.ch" class=""
moz-do-not-send="true">
www.biozentrum.unibas.ch</a> | <a
href="http://www.microscopynetwork.unibas.ch" class=""
moz-do-not-send="true">
www.microscopynetwork.unibas.ch</a><br class="">
<br class="">
_______________________________________________<br
class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk"
class="" moz-do-not-send="true">ome-users@lists.openmicroscopy.org.uk</a><br
class="">
<a class="moz-txt-link-freetext" href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br
class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br>
<span style="font-size:10pt;">The University of Dundee is a
registered Scottish Charity, No: SC015096</span>
<br>
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