<div dir="ltr">Thank you for answering.<div><br></div><div>I am actually refering to both case :-) I would like to be able to open an OME Tiff file, then add some ROIs with ROI Manager and then save ROIs on the OME XML stored in the OME Tiff file (if I could avoid to rewrite the entire Tiff and write only the OME XML in Tiff file it would be awesome as well !).</div>
<div><br></div><div>Best,</div></div><div class="gmail_extra"><br clear="all"><div><div dir="ltr"><br>--<br>Hadrien Mary<div><br></div><div>Ph.D student in Biology</div><div>Tournier-Gachet Team</div><div>CNRS - LBCMCP - UMR 5088<div>
<div><br></div><div><div>Université de Toulouse - Bât. 4R3B1</div><div>118, route de Narbonne - 31062 Toulouse</div></div></div></div></div></div>
<br><br><div class="gmail_quote">On Thu, Nov 14, 2013 at 6:42 PM, Roger Leigh <span dir="ltr"><<a href="mailto:r.leigh@dundee.ac.uk" target="_blank">r.leigh@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
On 13/11/2013 17:00, Hadrien Mary wrote:<br>
<br>
Dear Hadrien,<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I know ROI has been modeled in OME. I would like to know if there is a<br>
way to implement it in LOCI / Fiji ?<br>
</blockquote>
<br></div>
Are you referring to the current OME ROI model here?<br>
(<a href="http://www.openmicroscopy.org/site/support/ome-model/developers/roi.html" target="_blank">http://www.openmicroscopy.<u></u>org/site/support/ome-model/<u></u>developers/roi.html</a>)<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
I often use Analyse > Tools > ROI Manager to draw some ROIs and I save<br>
them in the .roi or .zip format to process it in a Python workflow later.<br>
<br>
Are you planning to add OME ROI support in LOCI ?<br>
</blockquote>
<br></div>
What type of support do you mean specifically?<br>
<br>
If you read an OME TIFF using the Bio-Formats importer, and select the<br>
ROI checkbox, you'll see the ROIs are loaded into the ROI manager. They<br>
also appear to be saved as well.<br>
<br>
However, if I create ROIs on a new image and export to OME TIFF, I don't<br>
see the ROIs from the manager saved with the image. Is this what you're<br>
referring to?<div class="im"><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
PS: I created a small python script to be able to parse .roi format in<br>
Python (script has been largely inspired from IJ ROI decoder java code).<br>
I post link here, just in case it can be usefull for someone:<br>
<a href="https://gist.github.com/hadim/7258178" target="_blank">https://gist.github.com/hadim/<u></u>7258178</a><br>
</blockquote>
<br></div>
Thanks, this looks very useful.<br>
<br>
<br>
Kind regards,<br>
Roger Leigh<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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</blockquote></div><br></div>