[ome-devel] OME ROI ?

[Hadrien Mary]

Thank you Roger for the bug report !


--
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 6:56 PM, Hadrien Mary <hadrien.mary at gmail.com>wrote:

> 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
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>>
>
>
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