DefiningImageAccess/ScenarioNotes
From ImageWeb
Scenarios, use-cases and requirements
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Gene expression images
Our image web work is motivated by problems in post-genomic life science research.
Gene expression experiments involve creating microscopic images of parts of organisms to which genetic techniques have been applied to make visible those regions in which a chosen gene is active (expressed). This information, in turn, helps researchers to understand how the genetic mechanisms interact with other life processes to guide the development of an organism, for example by showing how gene expression patterns vary between different mutations of a given reference organism. Producing these in situ gene expression images can be very time consuming, and a single image might be used in different lines of research. We anticipate that in the near future, such images generated in the course of a research project will be published online with sufficient metadata to interpret the image (e.g. organism, genetic strain, observed gene, developmental stage, etc.).
A researcher exploring factors causing sterility in Drosophila may create a number of in situ images of gene expression in the testes, with a primary goal of studying sperm development. Another researcher may be interested in distribution patterns of gene expression products within a cell for study of internal cell transport mechanisms, for which some of the same images might contain useful information. But how is such a researcher to discover that the image even exists? Our Image Data Web aims to support using a single search operation to find, say, images of expression patterns for aly genes in Drosophila melanogaster that may be stored in various repositories with different but overlapping descriptive metadata. To do this requires some mechanisms to access and partially match metadata from different images sources, and locate those images that have associated metadata meeting some given criteria.
Requirements:
- Essential metadata includes strain of drosophila, anatomical region viewed, name of expressed gene, description of localization of gene expression
- Annotations are gathered using controlled vocabulary terms, with minimal free text.
See also: Protein trap project, Flannotator (http://www.flyprot.org/).
Collections of medical images for teaching
(Notes from discussion with Vivien Sieber, Peter Robinson, Damian (?) and Tang? (?), 2007-04-19)
Currently using a combination of Magnolia Web CMS and Photospace image management. Magnolia is used to create virtual collections of images in Photospace. FCKedit (Javascript rich text editor) in Magnolia page provides web interface to Photospace for image browsing to locate images for a coillection. Original system by Phil Reese.
Currently have about 2000 images in Photospace, of uncertain provenance. Organized into a directory structure corresponding to MESH taxonomy terms (http://www.nlm.nih.gov/mesh/). About 350 MESH terms are currently used in this way. Additional metadata (category terms) is "wedged" into Photospace-defined fields.
Current areas of pain are:
- very poor usability of image browse interface
- concern about copyright restricting freedom to access collections (dependent on various factors: can a patient be identified? Has permission been obtained? Who is the requester?
- concern about patient confidentiality: lack of fine-grained access control
- Matadata entry isn't always consistent: different submitters use terms in different ways, with varying levels of care
Some of the access control concerns could extend to migration between local/departmental/institutional/national repositories.
Requirements for image storage element:
- easy browse/search interface for finding images
- on-the-fly arbitrary rescaling of images
- flexible storage and access to additional metadata with search over metadata terms
- generation of thumbnail display (in browse interface)
(Follow-up top vivien.sieber at medsci.ox.ac.uk)
