[ome-devel] OME ROI ?

[Roger Leigh]

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