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Thank you very much for the quick and comprehensive answer.
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<div>-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).<br>
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Interesting use case.<br>
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May I advocate for that option to be included if/when you touch the
ROI GUI? Having a show all/hide all button could be handy too. And I
did not found how to delete one roi, only either one shape or all
rois. (and also: is it possible to measure stuff (ie mean
fluorescence, etc...) at the level of roi, not shapes?)<br>
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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?<br>
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<div>Following various discussions, we made a proposal to add
support for ROI 3D. </div>
<div><a moz-do-not-send="true"
href="http://www.ome-xml.org/wiki/ROI/ProposalSeptember2010">http://www.ome-xml.org/wiki/ROI/ProposalSeptember2010</a></div>
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<div>If you can have a look at it and let us know what you
think.</div>
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<div>The ROI model-DB/clients alignment will happen later in
the year.</div>
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Interesting. A few semi-random comments I can share:<br>
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Wouldn't a few well chosen 3D primitive be useful as well? Like,
sphere/ellipsoid, tube (=line with a 3D width)... And I am guessing
input/output of VertexArray into standard format for viewing or
processing (CGAL for computational geometry comes to mind, openGL
stuff as well I guess) would be useful too, although that may be
more for scripts/outside clients...<br>
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What about shapes intrinsically in 4D or even 5D? It might be a pain
to deal with but one can think of cases where it may come in handy
(tracking of stuff merging/splitting for example, or maybe sometime
having one track=one shape could be useful; for channel: FRET pairs
and photo-switchable protein, maybe?).<br>
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The other point is hierarchical roi: would it be possible to have
nested roi (rois having some kind of RoiRoisSeq field for example)?
it would allow for intra-cellular localisation in particular, but
most likely other uses. <br>
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Is there a time-scale for the changes in the model?<br>
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Many Thanks...<br>
<pre class="moz-signature" cols="72">--
Anatole Chessel
Research associate
The Gurdon Institute
University of Cambridge
Tennis Court Road, Cambridge CB2 1QN
tel: +44 (0)1223 767197
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