[ome-devel] OME ROI ?

[Hadrien Mary]

Thank you for answering.

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 !).

Best,


--
Hadrien Mary

Ph.D student in Biology
Tournier-Gachet Team
CNRS - LBCMCP - UMR 5088

Université de Toulouse - Bât. 4R3B1
118, route de Narbonne - 31062 Toulouse


On Thu, Nov 14, 2013 at 6:42 PM, Roger Leigh <r.leigh at dundee.ac.uk> wrote:

> On 13/11/2013 17:00, Hadrien Mary wrote:
>
> Dear Hadrien,
>
>
>  I know ROI has been modeled in OME. I would like to know if there is a
>> way to implement it in LOCI / Fiji ?
>>
>
> Are you referring to the current OME ROI model here?
> (http://www.openmicroscopy.org/site/support/ome-model/developers/roi.html)
>
>
>  I often use Analyse > Tools > ROI Manager to draw some ROIs and I save
>> them in the .roi or .zip format to process it in a Python workflow later.
>>
>> Are you planning to add OME ROI support in LOCI ?
>>
>
> What type of support do you mean specifically?
>
> If you read an OME TIFF using the Bio-Formats importer, and select the
> ROI checkbox, you'll see the ROIs are loaded into the ROI manager.  They
> also appear to be saved as well.
>
> However, if I create ROIs on a new image and export to OME TIFF, I don't
> see the ROIs from the manager saved with the image.  Is this what you're
> referring to?
>
>
>  PS: I created a small python script to be able to parse .roi format in
>> Python (script has been largely inspired from IJ ROI decoder java code).
>> I post link here, just in case it can be usefull for someone:
>> https://gist.github.com/hadim/7258178
>>
>
> Thanks, this looks very useful.
>
>
> Kind regards,
> Roger Leigh
>
> --
> Dr Roger Leigh -- Open Microscopy Environment
> Wellcome Trust Centre for Gene Regulation and Expression,
> College of Life Sciences, University of Dundee, Dow Street,
> Dundee DD1 5EH Scotland UK   Tel: (01382) 386364
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
> _______________________________________________
> ome-devel mailing list
> ome-devel at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20131114/9a9974c8/attachment.html>