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Re: TCGA / Microscopy Imaging Use Case

From: Erich Bremer <erich.bremer@stonybrook.edu>
Date: Tue, 10 Mar 2015 10:26:23 -0400
Message-ID: <CAGR3=-_f+=fpjZFQ81DH8Nx53f73fFD5gjHHvRHGXM6-ghFpLQ@mail.gmail.com>
To: Phil Archer <phila@w3.org>
Cc: frans.knibbe@geodan.nl, public-sdw-wg@w3.org
Heh, I had noticed the name change a few days after the W3C AC meeting
where I was inquiring about my use case (and where I had first heard of the
then Geospatial Data on the Web new WG).  I didn't want to presume ;-)  -
Erich

On Tue, Mar 10, 2015 at 3:53 AM, 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 organism’s 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
>>
>>
>> --
>> ==========================================================
>> 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>
>> 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> | 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
>
>


-- 
==========================================================
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
Office Location/Mailing Address
HSC, L3: Room 119
Stony Brook, NY 11794-8330
Received on Tuesday, 10 March 2015 14:26:50 UTC

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