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RE: TCGA / Microscopy Imaging Use Case

From: <Simon.Cox@csiro.au>
Date: Tue, 10 Mar 2015 01:30:56 +0000
To: <public-sdw-wg@w3.org>, <frans.knibbe@geodan.nl>
Message-ID: <2A7346E8D9F62D4CA8D78387173A054A600D9785@exmbx04-cdc.nexus.csiro.au>
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.


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 organismís 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
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Frans Knibbe
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Received on Tuesday, 10 March 2015 01:31:42 UTC

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