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

Wed Jun 10 19:44:53 BST 2009

Dear Frans,

Thanks for the insightful information!

Actually I was referring to the OME storage standard for ROI. I have
been in touch with Curtis Rueden who suggested I discuss this with the
OME-developers. More precisely, the XML schema used for current ROI
storage (cf. attached XML file from Curtis) would need to be amended to
provide a way to store storage ROI as chain code. 

I see your point about using labels for complex objects. In fact, I
already had considered to map objects to their parents (ie, nucleus to
cell body) via the cell features. I suppose I can extend this model to
ROI, where you have complex forms.

I think you lost me at the Euler number part though. Do you mean that
for each objects we would add an extra index, corresponding to the
different objects parts? I think this is also a good idea, but would
also require to edit the ROI object model. Another thing which should be
added to the OME ROI model, would be an object group (ie, an image
usually has several different nuclei/cells...) an in addition to this,
you may want to save the object organization (ie. a cell, may have
several nuclei...), so adding a parentType and a parentID would be
useful (the parent type of every objects is obviously "Image")

I have attached an example of single cells features and associated ROI.
As you can see in the feature list (.feat), each objects is linked to a
parent object. The objects ROI and features can be linked using the
"TimePoint, StackNum, FieldNum, ObjectType, ObjectID".

Finally for the Acapella code to make the polygons/chain codes? I would
like to share it, but need to ask our lawyers for permission first. We
can take this off-line. Also, I have also have some java code for it,
which I was planning to put into bioformats, to convert turn a bunch of
points into a polygon/chaincode. This only works if the object does not
have non adjacent parts (if you have one multipart object only the top
left object is returned as an ROI), and for objects with holes, only the
outer shell is returned as a polygon. Hopefully, this could be worked on
a little more by the community, to provide support for more complex
objects! 

Best,

Ghislain Bonamy, PhD
__________________________________________
Research Investigator

Genomic Institute of the
Novartis Research
Foundation
Department of Molecular & Cell Biology, room G214
10675 John Jay Hopkins Drive
San Diego CA 92121
USA

+1 (858) 812-1534 (W & F)
+1 (757) 941-4194 (H)
+1 (858) 354-7388 (M)
www.gnf.org

Hudson-Alpha Institute for Biotechnology
www.hudsonalpha.org

-----Original Message-----
From: ome-devel-bounces at lists.openmicroscopy.org.uk
[mailto:ome-devel-bounces at lists.openmicroscopy.org.uk] On Behalf Of
Cornelissen, Frans [PRDBE]
Sent: Wednesday, June 10, 2009 5:40 AM
To: ome-devel at lists.openmicroscopy.org.uk
Subject: Re: [ome-devel] ome-devel Digest, Vol 63,Issue 4 - message 1 :
ROI's-> give them a LABEL?

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)

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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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