[ome-devel] About ROIs...

[jburel]

Dear Anatole

Some points you have highlighted in your e-mail, have already been  
discussed within the team, see http://trac.openmicroscopy.org.uk/ome/ticket/4317
>
>
> I begun working with ROIs, specifically trying to do back and forth  
> of segmentations between omero and matlab. Their implementation is  
> quite powerful once you get your head around it (as for most  
> omero :)...). I have a few questions I could not really find  
> documentation on, though:
> -What is the format for polygon? It seems like it is expecting a  
> string with 'points[...] points1[...] points2[...] mask[...]'. What  
> is what? I put the same coordinate lists in all three 'points' and  
> zeros in mask and it seems to work, but...
Such structure is requested when drawing bezier curves by the drawing  
library we used (jhotdraw) . This was a convenient way to store the  
points but not in synch with the model.
ROIs save using OMERO.insight started to save Polyline and Polygon  
that way
You might have also noticed that we use translate, rotate, instead of  
matrix for Transform. This is not compatible with the model.

> -What about the various miscellaneous fields (colors, styles, etc),  
> are they all implemented (the examples seems to indicates some might  
> not be)? And what are the possible values (for colors in particular)?

This is "SVG legacy"  and several fields are not part the model.  
FillColor and stroke are both used and filled by OMERO.insight. The  
value is the RGB value representing the color in the default sRGB  
ColorModel.

To see what can be filled, have a look at
http://www.ome-xml.org/wiki/ROI/2010-04

> -The field 'theC' seems not to be set in roi created under insight,  
> and roi naturally seems to exists across channel (for measurements,  
> ect). Is that field actually used?

Actually theC, theT and theZ are optional so you can have "ROI template"
insight does not set theC values. Some adjustments will be required to  
turn on/off when ROIs are linked to a channel (see http://trac.openmicroscopy.org.uk/ome/ticket/4858)

> -Rois are not shown on the projections. Obviously showing shapes  
> from various z on a single plane is not straightforward, but it  
> might be very handy in some cases (a 2D segmentation propagated to  
> the whole stack for example).

Interesting use case.
>
> More generally, if I understand correctly, rois are defined as a  
> collection of 2D x-y shapes each of them having a depth z, a time t  
> and possibly a channel c. One can imagine cases when this modeling  
> would not make things easy (3D segmentation, single tracks in time,  
> tubular objects in 3D...). A related note is hierarchical ROI,  
> holding for example a segmented cell and intracellular compartment/ 
> objects. But this would be trying to see roi as an intrinsic way to  
> hold arbitrary geometrical data, which they I guess were not  
> designed to be. Any thought on this/plan to extend the current model?

Following various discussions, we made a proposal to add support for  
ROI 3D.
http://www.ome-xml.org/wiki/ROI/ProposalSeptember2010

If you can have a look at it and let us know what you think.

The ROI model-DB/clients alignment will happen later in the year.
Thanks

Jmarie
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