<div dir="ltr">Thank you guys for a thorough check on my question! I'll start using Color attribute and also write LUTs. So in most cases things should work fine. Thank you so much!<div><br></div><div>-dmitry</div></div><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 29, 2015 at 9:35 AM, Curtis Rueden <span dir="ltr"><<a href="mailto:ctrueden@wisc.edu" target="_blank">ctrueden@wisc.edu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr">Hi again Dmitry and everyone,<div><br></div><div>I spoke with Melissa about the channel coloring issue in ImageJ, and she pointed out that this feature should already be working [1].</div><div><br></div><div>That is: if you have a Channel Color set in the OME metadata, the Bio-Formats Importer in ImageJ should show the associated LUT as expected. Please let us know if you experience otherwise.</div><div><br></div><div>Regards,</div><div>Curtis</div><div><br></div><div>[1] <font color="#1155cc"><u><a href="https://github.com/openmicroscopy/bioformats/blob/v5.1.1/components/bio-formats-plugins/src/loci/plugins/in/Colorizer.java#L317-L379" target="_blank">https://github.com/openmicroscopy/bioformats/blob/v5.1.1/components/bio-formats-plugins/src/loci/plugins/in/Colorizer.java#L317-L379</a></u></font></div><div><div class="h5"><div class="gmail_extra"><br><div class="gmail_quote">On Wed, Apr 29, 2015 at 8:09 AM, Stéphane Dallongeville <span dir="ltr"><<a href="mailto:stephane.dallongeville@pasteur.fr" target="_blank">stephane.dallongeville@pasteur.fr</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
<div bgcolor="#FFFFFF" text="#000000">
Hi Curtis,<br>
<br>
With Icy we were initially relying on the 8/16 bit color table
information of Bio-Formats but definitely almost time it's empty or
not filled according to the Channel Color field so now we check both
informations to provide default image channel color.<br>
<br>
Best,<span><font color="#888888"><br>
<br>
<pre cols="72">--
Stephane Dallongeville
Unité d'Analyse d'Images Biologiques
CNRS UMR 3691
Institut Pasteur
25 rue du Dr. Roux
75724 Paris cedex 15 (FRANCE)
Tel: <a href="tel:%2B33%20%280%291%2045%2068%2087%2001" value="+33145688701" target="_blank">+33 (0)1 45 68 87 01</a>
Fax: <a href="tel:%2B33%20%280%291%2040%2061%2033%2030" value="+33140613330" target="_blank">+33 (0)1 40 61 33 30</a>
<a href="http://www.bioimageanalysis.org/" target="_blank">http://www.bioimageanalysis.org/</a></pre></font></span><div><div>
<br>
<br>
<div>Le 29/04/2015 15:01, Curtis Rueden a
écrit :<br>
</div>
<blockquote type="cite">
<p dir="ltr">Hi Roger,</p>
<p dir="ltr">The ImageJ plugin does apply color tables from the
reader to the images; see ImageProcessorReader.</p>
<p dir="ltr">I think the question is more: does that Channel Color
property in the OME-XML get transformed into an 8-bit color
table in the relevant Bio-Formats readers? When I checked the
code last night I could not find any such logic, but may have
missed it.</p>
<p dir="ltr">Regards,<br>
Curtis</p>
<div class="gmail_quote">On Apr 29, 2015 4:12 AM, "Roger Leigh"
<<a href="mailto:rleigh@dundee.ac.uk" target="_blank">rleigh@dundee.ac.uk</a>>
wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">On 29/04/15
05:18, Dmitry Fedorov wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left-width:1px;border-left-color:rgb(204,204,204);border-left-style:solid;padding-left:1ex">
Hi Roger,<br>
<br>
Thank you, the Color property is exactly what I needed!
Somehow I missed<br>
that and I would never have guessed the encoding:) This was
super<br>
helpful! Do you know if bioformats, in ImageJ for example,
would pickup<br>
the stored lookup table and use it for visualization?<br>
</blockquote>
<br>
Looking at the code in<br>
components/bio-formats-plugins/src/loci/plugins/in/ImportProcess.java<br>
it does get an 8-bit LUT, but then doesn't do anything with
it, so it<br>
looks like support on import into ImageJ is unfortunately
incomplete at<br>
present, limited to channel colour only.<br>
<br>
We do have a ticket for improving this here<br>
<a href="https://trac.openmicroscopy.org/ome/ticket/12168" target="_blank">https://trac.openmicroscopy.org/ome/ticket/12168</a><br>
as part of the model and code changes needed to improve
support for<br>
rendering.<br>
<br>
<br>
Regards,<br>
Roger<br>
<br>
--<br>
Dr Roger Leigh -- Open Microscopy Environment<br>
Wellcome Trust Centre for Gene Regulation and Expression,<br>
College of Life Sciences, University of Dundee, Dow Street,<br>
Dundee DD1 5EH Scotland UK Tel: (01382) 386364<br>
<br>
The University of Dundee is a registered Scottish Charity, No:
SC015096<br>
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<br></blockquote></div><br><br clear="all"><div><br></div>-- <br><div class="gmail_signature">__________________________________<br><br>Dmitry Fedorov Levit <<a href="mailto:dima@dimin.net" target="_blank">dima@dimin.net</a>><br>Web: <a href="http://www.dimin.net/" target="_blank">http://www.dimin.net/</a><br>__________________________________<br><br>Center for Bio-Image Informatics:<br> <<a href="http://www.bioimage.ucsb.edu/" target="_blank">http://www.bioimage.ucsb.edu/</a>><br><br>Vision Research Lab, Electrical and Computer Engineering:<br> <<a href="http://vision.ece.ucsb.edu/" target="_blank">http://vision.ece.ucsb.edu/</a>><br><br>University of California, Santa Barbara<br>_________________________________</div>
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