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Re: TCGA / Microscopy Imaging Use Case

From: Scott Serich <sserich@opengeospatial.org>
Date: Thu, 12 Mar 2015 04:39:33 -0400
To: Joshua Lieberman <jlieberman@tumblingwalls.com>, Phil Archer <phila@w3.org>
CC: "frans.knibbe@geodan.nl" <frans.knibbe@geodan.nl>, "public-sdw-wg@w3.org" <public-sdw-wg@w3.org>
Message-ID: <D126C75B.9F01%sserich@opengeospatial.org>
Hi Josh. A quick follow-up question. Is your recommendation that this
subject remain out-of-scope because the communities who tend to face
coordinate tensor complexities donıt have the requirement for web spatial
data interoperability in the first place? Or is it that they have the
requirement but tend to address it in their own specialized, parochial
manner? Or (likely) something Iım not even contemplating in my proposed
multiple-choice answers? Thanks.

Scott Serich, Ph.D., JD
Director, Interoperability Programs, Open Geospatial Consortium (OGC)
+1 (703) 283-3432
Skype: scott.serich.ogc
The OGC: Making Location Count.

From:  Joshua Lieberman <jlieberman@tumblingwalls.com>
Date:  Tuesday, March 10, 2015 at 9:05 AM
To:  Phil Archer <phila@w3.org>
Cc:  "frans.knibbe@geodan.nl" <frans.knibbe@geodan.nl>,
"public-sdw-wg@w3.org" <public-sdw-wg@w3.org>
Subject:  Re: TCGA / Microscopy Imaging Use Case
Resent-From:  <public-sdw-wg@w3.org>
Resent-Date:  Wed, 11 Mar 2015 16:59:52 +0000

Certainly any space with multiple basis vectors can be "spatial" and it's
great to think broadly about this in terms of data representation. However,
it doesn't just depend on forming the right coordinate reference system,
which can be challenging enough for non-Cartesian frames of reference such
as the earth's surface or composition spaces.. If coordinate and physical
frames of reference diverge sufficiently, we can also end up with coordinate
tensors and other rather complex issues such as SEDAC tried to deal with. We
should tread lightly there in terms of scope.


Joshua Lieberman, Ph.D.
Interoperability Engineering Without Barriers
+1 (617) 431-6431

On Mar 10, 2015, at 03:53, Phil Archer <phila@w3.org> wrote:

> Historical note: Erich's use cases are why this is the Spatial Data on the Web
> WG, not the Geospatial Data on the Web WG :-)
> On 10/03/2015 01:30, Simon.Cox@csiro.au wrote:
>> Materials science also has overlapping use cases.
>> Perhaps closer to home for the geo-spatial community would be geology, where
>> the practitioners span the scales routinely, particularly in petrological
>> investigations. So we should not dismiss this too quickly.
>> Caveat lector - Sent from a tablet using TouchDown
>> ________________________________
>> From: Frans Knibbe | Geodan
>> Sent: Tuesday, 10 March 2015 12:42:11 AM
>> To: public-sdw-wg@w3.org
>> Subject: Re: TCGA / Microscopy Imaging Use Case
>> Wow, that is an interesting use case. Maybe this may calls for a better
>> definition of what we mean by 'spatial data'?
>> I remember the time when geographers started switching from using the
>> adjective 'geographic' to using 'spatial', implying a broadening of scope and
>> a higher relevance. But still the actual topics were macroscopic objects,
>> things that you can plot on a map. And the reference systems still are earth
>> based.
>> Taken literally, 'spatial' covers a lot more than 'geographic'. It includes
>> concepts from all scales, from quantum particles to the universe itself. Are
>> we ready to take on all these scales?
>> Related to the issue of the scope of scale is the relationship between space
>> and time. I think that on the human/macroscopic/geographical level space and
>> time can be kept separate, in the sense that a model or ontology for space
>> does not really need time concepts, and vice versa. But it could well be that
>> such a separation is not possible for very small things (like elemental
>> particles) and very big things (like galaxies). On such levels time and space
>> tend to be more entangled.
>> Greetings,
>> Frans
>> On 2015-03-03 21:52, Erich Bremer wrote:
>>   Studying the morphology of disease at the cellular and sub-cellular levels
>> using high resolution tissue images is extremely important to help understand
>> the nature of various cancers. The Cancer Genome Atlas (TCGA)
>> (http://cancergenome.nih.gov/) contains over 32,000 de-identified whole-slide
>> microscopy images (WSI) of over two dozen cancer types. These images can
>> contain between 100K-1M nuclei each.  Biomedical informatics researcher have
>> developed (and continue to develop) software to automatically segment nuclei
>> for study.  The spatial features of each nucleus and groups of nuclei as it
>> relates to other nuclei combined with other linked data such as other
>> morphological features (crypts, ducts, etc) and/or patient lab results are
>> used in analyzing and categorizing tissues and patients into groups and in
>> comparing such groupings to understand disease mechanisms in a particular
>> cancer type as well as across cancer types.
>> Representing nuclear segmentations is often done with binary masks or through
>> polygon representations (e.g., the use of Well Known Text (WKT)
>> representations) and also by leveraging work from the Geospatial community.
>> However, in the case of nuclear segmentations, coordinate systems are 2D & 3D
>> Cartesian based.  Although the majority of work is this area is 2D-based, a
>> growing segment of microscopy is also 3D-based as the technology develops and
>> become more sophisticated.  As living tissue can change over time through
>> growth, infection, cancer, damage, etc, (as well as its associated organismıs
>> various properties) it is important that spatial locations of features such
>> as nuclear segmentation be also represented in a temporal aspect for proper
>> comparisons.
>> Samples of TCGA WSI data can be viewed at:
>> http://cancer..digitalslidearchive.net
>> <http://cancer.digitalslidearchive.net>
>> --
>> ==========================================================
>> Erich Bremer, M.Sc.
>> Director for Cyberinfrastructure
>> Health Sciences Division of Applied Informatics
>> Stony Brook Medicine
>> Tel. : 1-631-444-3560
>> Fax  : 1-631-444-8873
>> Cell : 1-631-681-6228
>> erich.bremer@stonybrook.edu<mailto:erich.bremer@stonybrook..edu
>> <mailto:erich.bremer@stonybrook.edu> >
>> Office Location/Mailing Address
>> HSC, L3: Room 119
>> Stony Brook, NY 11794-8330
>> ________________________________
>> Frans Knibbe
>> Geodan
>> President Kennedylaan 1
>> 1079 MB Amsterdam (NL)
>> T +31 (0)20 - 5711 347
>> E frans.knibbe@geodan.nl<mailto:frans.knibbe@geodan.nl>
>> www.geodan.nl <http://www.geodan.nl> <http://www.geodan.nl> |
>> disclaimer<http://www.geodan.nl/disclaimer>
>> ________________________________
> -- 
> Phil Archer
> W3C Data Activity Lead
> http://www.w3.org/2013/data/
> http://philarcher.org
> +44 (0)7887 767755
> @philarcher1
Received on Thursday, 12 March 2015 09:37:51 UTC

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