[ome-devel] About ROIs...

[Anatole Chessel]

Dear all...


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...
-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)?
-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?
-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).

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?

Many thanks...

A.

-- 
Anatole Chessel
Research associate
The Gurdon Institute
University of Cambridge
Tennis Court Road, Cambridge CB2 1QN
tel: +44 (0)1223 767197