[ome-devel] ome-devel Digest, Vol 63, Issue 4 - message 1 : ROI's-> give them a LABEL?

Wed Jun 10 13:40:12 BST 2009

Ghislain,

I suppose you are referring to OMERO (and not the old OME)?
Chain codes ar indeed the best way to store ROI's efficiently

My 2 cents:
For the ROI's I would suggest adding an information item: a "LABEL"
This would make it easy to make ROI from output from image analysis
packages that "call" or identify the object by its label number
All ROI's with the same LABEL, even when complex have to be described
with holes etc. would then belong to each other (to the same "outer"
object)
One could even add an Euler-like number to describe the "phase", e.g.
Outer object, A hole =  ; object in a hole, etc.

See
http://www.mathworks.com/access/helpdesk_r13/help/toolbox/images/morph20
.html

PS: would you like to share the acapella code to make the polygons/chain
codes?

Cheers, frans

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Today's Topics:

   1. ROI storage with OME (Ghislain Bonamy)

----------------------------------------------------------------------

Message: 1
Date: Tue, 9 Jun 2009 21:49:29 -0700
From: "Ghislain Bonamy" <GBonamy at gnf.org>
Subject: [ome-devel] ROI storage with OME
To: <ome-devel at lists.openmicroscopy.org.uk>
Message-ID:
	<F5A26DAD36F60843830631774C95CAE205D12A1D at EXCH2.rec.gnf.org>
Content-Type: text/plain;	charset="iso-8859-1"

Dear all,

I have programmed a tool allowing me to save objects calculated from
Acapella into a Polygonal ROI format, which works great for shapes
without holes (ex nuclei, cell borders etc).

While playing with different storage format, it became evident that
storing the polygon as a chain code (along with the coordinate of the
first point) was extremely space efficient and probably just as
computing intensive to draw back the current system to store polygons.
Using the chain code vs. set of point is about 3-4 times more efficient.

Because the volume of ROI outputted by High content imaging will become
extremely voluminous, I was thinking that perhaps adding to OME an ROI
model that stores polygon/polyline as a chain code would be very useful.

Finally for more complex shapes, perhaps a "Group of Point" model could
also be implemented. This would be useful for complex shape that can not
readily be turned into a vector (such as a donut, or other objects with
a hole in them).

Looking forward to hearing your thoughts,

Ghislain Bonamy, PhD 
_______________________________
Genomic Institute of the
Novartis Research
Foundation
Functional Genomics, G214
+1 (858) 812-1534 (W & F)
+1 (858) 354-7388 (C)
www.gnf.org <http://www.gnf.org/> 

HudsonAlpha Instiute for Biotechnology
www.hudsonalpha.org
<http://www.gnf.org/> 

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