[ome-devel] ROI Meeting

[dzmacdonald]

Hi Ghislain,

> Regarding the ROI model, another point that would be nice to take  
> into consideration for high content imaging is compactness. It would  
> be great if the ROI schema could support chain code type  
> registration of the ROI. Also, it would be great if some sort of  
> compression could be added to further reduce the space required.

We can certainly include different methods for compression:
I've not used chain code compression though it seems quite nice, I'm  
pretty certain we could move between chain code compression and   
polygon representations of the same element.  I think maybe we should  
spend some time looking at possible methods for compressing mask  
elements.

>
> Though this does not solve the "harmonization" issue, I wanted to  
> put this suggestion out there so that it might be included in the  
> standardized ROI schema.
Your comments are very helpful, I wonder if you've any other ideas for  
the model?

Regards

D.


On Jun 10, 2010, at 5:07 PM, Ghislain Bonamy wrote:

> Hi,
>
> Regarding the ROI model, another point that would be nice to take  
> into consideration for high content imaging is compactness. It would  
> be great if the ROI schema could support chain code type  
> registration of the ROI. Also, it would be great if some sort of  
> compression could be added to further reduce the space required.
>
> Though this does not solve the "harmonization" issue, I wanted to  
> put this suggestion out there so that it might be included in the  
> standardized ROI schema.
>
> Best,
>
> Ghislain Bonamy, PhD
> __________________________________________
> Research Investigator
>
> Genomic Institute of the
> Novartis Research
> Foundation
> Department of Informatics, room C117
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>
> -----Original Message-----
> From: ome-devel-bounces at lists.openmicroscopy.org.uk [mailto:ome-devel-bounces at lists.openmicroscopy.org.uk 
> ] On Behalf Of Jason Swedlow
> Sent: Tuesday, June 08, 2010 7:37 AM
> To: OME Development
> Subject: Re: [ome-devel] ROI Meeting
>
> Hi all-
>
> My own view is that harmonization of the ROI data model across these  
> projects is critical, and a major priority for all. We should do  
> whatever we need to to make this happen. The downstream pay-off for  
> all our projects is very high. The penalties for not sorting this  
> will be very high.
>
> Is there a way to standardise the specification, like we already do  
> with OME-XML, and license the implementations according to our  
> respective preferences?  If that is too hard, can we agree on some  
> code which is shared, and that is licensed so that's compatible with  
> all?  There will invariably lots of implementation-specific stuff.
>
> Cheers,
>
> Jason
>
>
>
> Wellcome Trust Centre for Gene Regulation & Expression | University  
> of Dundee | http://gre.lifesci.dundee.ac.uk/staff/jason_swedlow.html
>
> -----Original Message-----
> From: dzmacdonald <donald at lifesci.dundee.ac.uk>
> Sender: ome-devel-bounces at lists.openmicroscopy.org.uk
> Date: Tue, 8 Jun 2010 10:30:27
> To: OME-devel mailing list<ome-devel at lists.openmicroscopy.org.uk>
> Subject: [ome-devel] ROI Meeting
>
> Hi
>
> The discussion on the ROI Meeting:
>
> The ROI model is changing too often. It will have to change to cover
> 3D, NDIM and maybe we should try to add these sooner rather than
> later. Curtis mentioned that Bioformats will be working with NDIM data
> soon, maybe we should look at their solution?
> Curtis and the imageJ group are looking to develop ROI tools, possibly
> using Hotdraw/JHotdraw maybe there could be a collaboration, sharing
> of code between groups. The only problem with this might be licensing.
> When do we wish to do this?
>
> Regards
>
> D.
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