<html>
<head>
<meta content="text/html; charset=windows-1252"
http-equiv="Content-Type">
</head>
<body 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,<br>
<br>
<pre class="moz-signature" 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: +33 (0)1 45 68 87 01
Fax: +33 (0)1 40 61 33 30
<a class="moz-txt-link-freetext" href="http://www.bioimageanalysis.org/">http://www.bioimageanalysis.org/</a></pre>
<br>
<br>
<div class="moz-cite-prefix">Le 29/04/2015 15:01, Curtis Rueden a
écrit :<br>
</div>
<blockquote
cite="mid:CADN69y=1sFVzDHAABgL4kspG-S_bYM3AxK0jpYUYO=dJ+oQMEA@mail.gmail.com"
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 moz-do-not-send="true" href="mailto:rleigh@dundee.ac.uk">rleigh@dundee.ac.uk</a>>
wrote:<br type="attribution">
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc solid;padding-left:1ex">On 29/04/15
05:18, Dmitry Fedorov wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0
.8ex;border-left:1px #ccc 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 moz-do-not-send="true"
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>
_______________________________________________<br>
ome-users mailing list<br>
<a moz-do-not-send="true"
href="mailto:ome-users@lists.openmicroscopy.org.uk"
target="_blank">ome-users@lists.openmicroscopy.org.uk</a><br>
<a moz-do-not-send="true"
href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users"
target="_blank">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</a><br>
</blockquote>
</div>
<br>
<fieldset class="mimeAttachmentHeader"></fieldset>
<br>
<pre wrap="">_______________________________________________
ome-users mailing list
<a class="moz-txt-link-abbreviated" href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.openmicroscopy.org.uk</a>
<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>
</pre>
</blockquote>
<br>
</body>
</html>