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PROJECTS:
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A Metadata Framework for Digitized Pathologic Images (July 1,
2008 to Current) Click here for more information about IMLS; here
to read the press release about the Grant Award)
Project description: Due to a number of advantages over traditional
glass slides, digital pathologic images are increasingly used for clinical
diagnosis, scientific research, and biomedical education. However, a
standardized and complete method for describing these digitized images does
not yet exist. With the increased use of digital imaging in pathology, it is
crucial that a standardized metadata framework be developed so virtual
microscopic image information can be efficiently stored, managed, retrieved
and shared. To develop this framework, the project team will examine and
analyze four existing data standards, none of which, individually, provide a
collection of data elements that adequately describe pathologic images.
Potential data elements will be collected, merged, and evaluated to determine
those that provide the best metadata set for these complex digital images.
Experts in the fields of pathology, ontology, library science, and imaging
will be interviewed to determine relevant test image descriptions and to
construct a standard that can effectively represent image information
contained in the set. This project will involve extensive collaboration with
the UK Markey Cancer Center, UK College of Health Sciences, and Massachusetts
General Hospital, with the goal of providing a single standard to enable
seamless querying across different pathologic imaging systems.
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The Human Tissue Image Database (HTIDB) (July 1,2008 to
Current):
Available at http://128.163.118.36/HTIDB/welcome.do
Project Description: A web-based application supporting the storage,
annotation, and searching of human breast cancer specimens. This database is
designed primarily for pathologists; providing them with a forum to upload
digital pathologic images and assign detailed specimen and
morphological-related information to the images. Pathologists and registered
researchers can also use this database to make notes on specific specimens or
to search for tissue samples matching a particular set of attributes.
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Mouse and Rat Tissue Image Database (MRTIDB) (July 1,2008 to
Current):
Available at
Project Description: A web-based database providing access to images
of mouse and rat tissue specimens. This application allows registered users
to search cases, view animal information, upload specimens, search specific
specimen information, and annotate images.
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OMERO Server (August 1, 2008 to Current):
Available at http://128.163.118.39/WebAdmin
Project Description: This system, a Java-based set of software tools
developed by Open Microscopy Environment (OME), is comprised of three
different client applications which together provide users the ability to
view, annotate, organize, archive and import microscopic images and metadata.
These applications are OMERO.insight, allowing for the viewing, management,
and annotation of images to the OMERO server; OMERO.importer, providing the
ability to upload a number of different image file formats to the server; and
OMERO.editor, allowing for scientists and researchers to record experimental
metadata.
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caTISSUE Core Server (August 1, 2008 to Current):
Available at University of Kentucky Tissue Bank XML
database (January 2007 to Current):
Available at: http://128.163.118.139:8080/XMLDB/welcome.do
Project description: The system is to integrate heterogeneous tissue
bank data in XML-encoded format so that web databases that are written in
different application languages can be searchable through a centralized
web-based XML database.
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Microscopic Image Annotation Engine (May 2007 to Current):
Project description: This project is to develop a web-based
microscopic image database that allows to annotate microscopic images with pre-defined
data elements (from standards such as DICOM and OME) and to make them
searchable through a seamless search engine.
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University of Kentucky Mouse Tissue Bank Information System
development(University
of Kentucky, Center for Reproductive Health Sciences, 2006 to date).
Available at: http://128.163.118.123:8080/UKMTB/welcome.do
Project description: Engineered mice are often discarded once they are
used for a single project. In this project, we developed a web-based mouse
tissue tracking system so that people can register and request mouse samples,
otherwise discarded
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University of Kentucky biospecimen repository system
development(University
of Kentucky Medical Center, 2004 to date). Available at: http://128.163.118.123:8080/UKTB/welcome.do
Project description: University of Kentucky Markey Center runs a
tissue bank so that tissue resources can be shared among UK research
community. In this database project, we developed a web-based tissue tracking
system that can be accessible through a secure Kentucky Cancer Registry’s web
server.
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Lung Frozen Tissue Bank Inventory System Prototype Development (National Korea Frozen Lung Tissue
Bank, Seoul, Korea, and University of Pittsburgh Medical Center, 2003 to
date) Available at: http://128.163.118.123:8080/BIS-JS/signIn.do
Project description: Over 18 lung tissue banks are located in diverse
regions in Korea. Through this project, we connected these branch tissue
banks in a centralized location so that they can register, search, and
request human frozen lung tissue samples.
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Biomedical Researchers’ Information Seeking Behavior Study(University of Pittsburgh Medical
Center, 2001 to 2003)
Project description: People in system development field are easy to
ignore what end-users would like to collect from the system they design. This
project was to understand about what information biomedical researchers
(especially those who require human biological samples) require for their
research.
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Consistency Study for Concept based Image Indexing of
Microscopic Prostate Cancer Images (University of Pittsburgh Medical Center, 1999 to
2000)
Project description: When indexing biomedical images, Indexers
produced inconsistent terms for the same images. This project is to
investigate the inconsistency rate of the microscopic images of prostate
cancers.
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Tissue Bank Information System Prototype (University of Pittsburgh Medical
Center, under Dr. John Gilbertson and Rajnish Gupta, 1999)
Project description: Prostate Cancer Tissue Bank at the University of
Pittsburgh Medical center collected paraffin tissue samples for further use
in biomedical research, however, there was not database that can
systematically track the availability of tissue samples. We designed a
web-based tissue tracking system and this system became a prototype of tissue
bank information system.
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Content Based Image Retrieval Project for Prostate Microscopic
Image Collection
(University of Pittsburgh Medical Center, under direction of Dr. Mike Becich
and Art Wetzel from Pittsburgh Super Computing Center, 1998)
Project description: Images annotation can have various attributes
that describe contents of microscopic images. This project is to investigate
whether the digitized microscopic images could be able to retrieve similar
images based on the contents -- such as distance between cell, color, shape,
etc.-- indexed.
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