Links to Image Archive Resources
This list links the various components and interests of the National Cancer Institute Cancer Imaging Program Image Archive Committee, and related websites. There are special sections on image archive formats and standardization.
- General References on Biomedical Image Archives
- Image Archive Technology
- Image Archive Standards
- Image Archive Applications - Clinical Trials
- Image Archive Applications - General
- Imaging in Clinical Trials
- Clinical Trials Image Archive Technology
- NIH Information Standards
- Other Federal Agencies
- XML and DICOM
- Implementation of Biological Databases
- Cancer Image Archives
- Biological Databases
General References on Biomedical Image Archives
NCI
Image Archive Committee Listserver
A listserver for medical image
archive technology, applications, standards, and related topics sponsored by
the National Cancer Institute Cancer Imaging Program.
NCI
Image Archive Management Workshop Report - August 2000 [PDF File]
The
National Cancer Institute (NCI)
workshop entitled "Image
Archive Management" that was presented on August 28 and 29, 2000, at the
Natcher Conference Center on the National Institutes of Health (NIH) campus is
summarized. The purpose of this workshop was to solicit expert input for the
planned development of an archival system to make imaging databases readily
accessible by the broad scientific community. This PDF file is the workshop
report published in Academic Radiology.
BIRN - Biomedical Informatics
Research Network
The BIRN is a National Center for Research Resources
(NCRR) initiative iaimed at creating a
testbed to address neuroscience researchers' need to access and analyze data at
a variety of levels of aggregation located at diverse sites throughout the
country. The BIRN testbed will bring together hardware and develop software
necessary for a scalable network of databases and computational resources.
Issues of user authentication, data integrity, security, and data ownership
will also be addressed. BIRN initiative has created consortiums of biomedical
technology and clinical research centers that are working together to address
two fundamental biomedical research issues: 1) integrating data across
modalities and scales; and 2) merging difficult to acquire data with
heterogeneous collection attributes from multiple research sites. These
initiatives are only first steps in creating the infrastructure to support the
synergistic approaches needed to solve challenging biomedical problems. The
BIRN Coordinating Center has a separate
website
Bristol Biomedical Image
Archive
The Bristol Biomedical Image Archive is an online collection of
about 8500 medical, dental, and veterinary images for use in teaching and
learning. All the images have been donated by academics working in the
biomedical fields in different countries. Hosted at the Institute for Learning
and Research Technology, University of Bristol, UK.
Global Image
Database
The Global Image Database (GID) is a web-based structured
central repository for scientific annotated images. The GID was designed to
manage images from a wide spectrum of imaging domains ranging from microscopy
to automated screening. The annotations in the GID define the source experiment
of the images by describing who the authors of the experiment are, when the
images were created, the biological origin of the experimental sample and how
the sample was processed for visualization. A collection of experimental
imaging protocols provides details of the sample preparation, and labeling, or
visualization procedures. In addition, the entries in the GID reference these
imaging protocols with the probe sequences or antibody names used in labeling
experiments. The GID annotations are searchable by field or globally.
The BioImage Homepage
A
European initiative for a database of multidimensional biological images. The
BioImage database project, funded by the European Union, is a collaboration
between eight European groups. Its aim is to provide the general scientific
community with a flexible and searchable database of multi-dimensional
biological images.
Open Archives
Initiative
The Open Archives Initiative develops and promotes
interoperability standards that aim to facilitate the efficient dissemination
of content. The Open Archives Initiative has its roots in an effort to enhance
access to e-print archives as a means of increasing the availability of
scholarly communication. The fundamental technological framework and standards
that are developing to support this work are, however, independent of the both
the type of content offered and the economic mechanisms surrounding that
content, and promise to have much broader relevance in opening up access to a
range of digital materials. As a result, the Open Archives Initiative is
currently an organization and an effort explicitly in transition, and is
committed to exploring and enabling this new and broader range of applications.
As we gain greater knowledge of the scope of applicability of the underlying
technology and standards being developed, and begin to understand the structure
and culture of the various adopter communities, we expect that we will have to
make continued evolutionary changes to both the mission and organization of the
Open Archives Initiative.
Back to
TopImage Archive Technology
David Clunie's Medical Image Format
Site
This website includes FAQs on medical image data, applications, and
formats. It was assembled and is sponsored by a key expert and advocate from
the DICOM community.
Very Large Data Base Endowment
Inc.
The Very Large Data Base Endowment Inc. (VLDB Endowment) is
non-profit organization incorporated in the United States for the sole purpose
of promoting and exchanging scholarly work in databases and related fields
throughout the world. The contents of the VLDB journal are available. An annual
VLDB Conference schedule and many PDF files with extended abstracts are
available.
Digital Medical Image
Archive Technology
An effective, low cost, long term archive is critical
to the successful implementation of a PACS system and any filmless plan.
Performance and capacity requirements must be carefully understood and
cost/performance tradeoffs must be made in light of these requirements.
Provided by StorageTech Corp.
Microsoft
Research - Scalable Servers
Microsoft is exploring techniques to build
large servers as arrays of commodity processors, disks, and interconnects -
Scalable Networks and Platforms (SNAP). The resulting computer cluster should
be as easy to program, manage, and use as a single system. In addition, by
using spare modules and redundant storage, the cluster should mask component
failures and so provide highly-available services. This work combines the
expertise of the NTclusters group to help define the requirements for clusters
and the SQLserver database team to add fault-tolerance, scalability, and
parallelism to SQLserver.
Terra-server™
A
one-node terabyte geo-spatial database server (the Terra-Sever™ ), and a
45-node cluster doing a billion transactions per day. There were also SAP + SQL
+ NT-Cluster failover demos, a 50 GB mail store, a 50k user POP3 mail server, a
100 million-hits-per-day web server, and 64-bit addressing SQL Server were also
shown. The TerraServer started as a joint research project between Aerial
Images, Inc., Microsoft, the USGS, and Compaq. The TerraServer concept grew out
of the convergence of two needs. Aerial Images, Inc. wanted to sell imagery
online and Microsoft Research needed a large database to demonstrate the
capabilities of its new database software.
Teradata
Corp.
Teradata, a division of NCR Corporation, offers powerful
analytical solutions that help businesses drive growth. Teradata solutions
include the Teradata warehouse, along with analytical applications for customer
relationship management, operations/financial management, business performance
management and e-business. NCR Corporation (NYSE: NCR) is a leader in providing
Relationship Technology™ solutions to customers worldwide. In addition to
Teradata solutions, NCR offers store automation systems and automated teller
machines (ATMs). NCR employs over 33,000 people in more than 100 countries, and
is a component stock of the Standard Poor's 500 Index.
Archive Builders
Corp.
Archive Builders assists organizations with their plans for
document management, document imaging systems and digital libraries. One
valuable service has proven to be advice and discussion of document management
plans drawn up by organizations considering a system installation. They offer
onsite systems analysis, requirements planning and assistance in writing system
specifications. Whitepapers and presentation materials used in the document
management class taught by Archive Builders are available free for download.
Please include a reference to http://www.ArchiveBuilders.com if you
make reference to these materials or distribute them. The papers are updated
periodically.
My SQL - Open Source Relational
Database
MySQL is the world's most popular Open Source Database,
designed for speed, power and precision in mission critical, heavy load use.
MySQL AB is the company that develops, supports and markets the MySQL database
server globally. Their mission is to make superior data management available
and affordable for all, and to contribute to building the mission-critical
high-volume systems and products of tomorrow. The product is available at zero
price under the GNU General Public License (GPL), and it is sold under a
commercial license to those who do not wish to be bound by the terms of the
GPL. The MySQL database server embodies an ingenious software architecture that
maximizes speed and customizability. Extensive reuse of code within the
software and minimal but functionally rich features have resulted in a database
management system unmatched in speed, compactness, stability and ease of
deployment. The unique separation of the core server from the table handler
makes it possible to run MySQL under strict transaction control or with
ultrafast transactionless disk access, whichever is most appropriate for the
situation. Today MySQL is the most popular open source database server in the
world with more than 2 million installations powering websites, data
warehouses, business applications, logging systems and more. Customers such as
Yahoo! Finance, MP3.com, Motorola, NASA, Silicon Graphics, and Texas
Instruments use the MySQL server in mission-critical applications.
Image Archive Standards
DICOM - Digital Imaging and
Communications in Medicine
DICOM Standards Committee exists to create
and maintain international standards for communication of biomedical diagnostic
and therapeutic information in disciplines that use digital images and
associated data. The goals of DICOM are to achieve compatibility and to improve
workflow efficiency between imaging systems and other information systems in
healthcare environments worldwide. DICOM is a cooperative standard. Therefore,
connectivity works because vendors cooperate in testing via scheduled public
demonstration, over the Internet, and during private test sessions. Every major
diagnostic medical imaging vendor in the world has incorporated the standard
into their product design and most are actively participating in the
enhancement of the standard. Most of the professional societies throughout the
world have supported and are participating in the enhancement of the standard
as well. DICOM is used or will soon be used by virtually every medical
profession that utilizes images within the healthcare industry. These include
cardiology, dentistry, endoscopy, mammography, ophthalmology, orthopedics,
pathology, pediatrics, radiation therapy, radiology, surgery, etc. DICOM is
even used in veterinary medical imaging applications.
Health Level Screen
(HL7)
Founded in 1987, Health Level Seven, Inc. is a not-for-profit,
ANSI-accredited standards developing organization that provides standards for
the exchange, management and integration of data that supports clinical patient
care and the management, delivery and evaluation of healthcare services. Its
2,200 members represent over 500 corporate members, including 90 percent of the
largest information systems vendors serving healthcare. HL7's endeavors are
sponsored, in part, by the support of its benefactors: CAP Gemini Ernst &
Young U.S. LLC, Eclipsys Corporation, Eli Lilly & Company, IDX Systems
Corporation, Johnson & Johnson, McKesson Information Solutions, Microsoft
Corporation, Philips Medical Systems, Quest Diagnostics Inc., Siemens Medical
Solutions Health Services, Sun Microsystems and the U.S. Department of Veterans
Affairs.
NCI Information
Technology Standards (External)
Various information technology standards
relevant to the National Cancer Institute
(NCI) and the NCI Center for Bioinformatics (NCICB). This table provides
links to many of the standards, standard development groups or standards-based
tool developers' sites, especially XML, SXL, SOAP and related sites.
Cancer
Bioinformatics Infrastructure Objects (caBIO)
The
caBIO
[Microsoft Word File] object modeling effort is an on-going effort to model
the domains of cancer research. The caBIO objects simulate the behavior of
actual components in biomedicine such as genes, chromosomes, sequences, agents,
trials, ontologies, etc. They provide access to a variety of data sources
including GenBank, Unigene, LocusLink, Ensemble, GoldenPath (through DAS), and
NCICB's CGAP (Cancer Genome Anatomy Project) data repositories. The current
object model was designed via the interaction of domain experts and IT
professionals. The object model is designed using an iterative software
development approach to accommodate new requirements for modeling genomic
information. Details of each object were identifed during domain analysis and
include information provided by domain experts as well as industry standards.
caBIO is an "open source" software project.
XML
Standards for Biology and Medicine
A set of links to diverse XML
standards in biology and medicine are provided, including clinical trial data,
gene expression, taxonomy, documents, and cell biology.
CODATA - Committee on Data for
Science and Technology
CODATA, the Committee on Data for Science and
Technology, is an interdisciplinary Scientific Committee of the International
Council for Science (ICSU). CODATA was established over 30 years ago and its
secretariat is located in Paris, France. CODATA seeks: 1) improvement of the
quality and accessibility of data, as well as the methods by which data are
acquired, managed, analyzed and evaluated, with a particular emphasis on
developing countries; 2) facilitation of international cooperation among those
collecting, organizing and using data; 3) promotion of an increased awareness
in the scientific and technical community of the importance of these
activities; and 4) consideration of data access and intellectual property
issues.
National
Informatics Standards in Cancer [PDF File]
The National Cancer Institute
(NCI) has been building a compendium of cancer-related vocabulary and the
technical resources to maintain and to disseminate the vocabulary. Standard
vocabulary is an aspect of a larger set of standards that will be needed to
provide cancer-related information and services in a structured form readily
interpretable by people and computers. NCI must become a much more active voice
in setting technical standards and promulgating cancer-related vocabulary.
SANE -
Scanner Access Now Easy Image Data Format
SANE stands for "Scanner Access Now
Easy" and is an application programming interface (API) that provides
standardized access to any raster image scanner hardware (flatbed scanner,
hand-held scanner, video- and still-cameras, frame-grabbers, etc.). The SANE
API is public domain and its discussion and development is open to everybody.
SANE is a universal scanner interface. The value of such a universal interface
is that it allows writing just one driver per image acquisition device rather
than one driver for each device and application. So, if you have three
applications and four devices, traditionally you'd have had to write 12
different programs. With SANE, this number is reduced to seven: the three
applications plus the four drivers. Of course, the savings get even bigger as
more and more drivers and/or applications are added.
Cancer
Informatics
"Cancer Informatics: Essential Technologies for Clinical
Trials" is a book published in January 2002 that describes the National Cancer
Institute's vision of a Cancer Informatics Infrastructure (CII). By exploring
the best that the Internet and information technology have to offer, the CII
will facilitate clinical trials, for all who are involved, including the
patient along with the Myriad of health professionals involved in cancer
trials.
NIH
Home Page on Sharing Research Data
NIH is developing a new statement on
sharing research data that will expect and support the timely release and
sharing of final research data from NIH-supported studies for use by other
researchers. Investigators submitting an NIH application will be required to
include a plan for data sharing or to state why data sharing is not possible.
This is an extension of NIH policy on sharing research resources. There is a
link to a list of
Frequently
Asked Questions on data sharing.
Open Source Health
Care Resources
Open source refers to software that comes with the source
code in a form that customers can modify for their own needs and resell or give
away to others under the same terms. Software
in the Public Interest has registered the phrase "open source" as a
certification mark and www.opensource.org contains a detailed
definition of what open source means. An open
source computed tomography (CT) simulator is available, for example.
Image Archive Applications - Clinical Trials
CDISC - Clinical Data Interchange
Standards Consortium
CDISC is an open, multidisciplinary, non-profit
organization committed to the development of industry standards to support the
electronic acquisition, exchange, submission and archiving of clinical trials
data and metadata for medical and biopharmaceutical product development. The
mission of CDISC is to lead the development of global, vendor-neutral, platform
independent standards to improve data quality and accelerate product
development.
FDA
Electronic Submissions and Review
The Food
and Drug Administration (FDA) regulates drugs, biologics and
medical devices. The FDA Center for Drug
Evaluation and Research's Electronic Regulatory Submissions and Review (ERSR)
web page provides information about the electronic submission of regulatory
information to the Center and the review of it by CDER staff.
QARC - Quality Assurance Review
Center
The Quality Assurance Review Center (QARC) is a Global Data and
Review Center, providing Radiotherapy Quality Assurance and Diagnostic Imaging
data management programs for several
National Cancer Institute
(NCI) supported Cooperative Groups and International Pharmaceutical
Companies. QARC is a research program within the
University of Massachusetts Medical
School. It is an established research resource for clinical investigators
around the world.
RCET - Resource
Center for Emerging Technologies
The Resource Center for Emerging
Technologies (RCET) at the University of Florida (UF) provides advanced
technical resources necessary to support radiotherapy. The use of medical
informatics is expected to facilitate education, collaboration, and peer
review, as well as provide an environment in which clinical investigators can
receive, share, and analyze voluminous multimodality clinical data.
Image Guided Therapy Center
at Washington University
The Image-Guided Therapy Center (ITC) (formerly
known as the 3DQA Center) WWW server at Washington University School of
Medicine in St. Louis, Missouri supports image-based 3D conformal radiotherapy
(CRT) multi-institutional trials.
ACRIN - American College of
Radiology Imaging Network
The American College of Radiology Imaging
Network (ACRIN) is a National Cancer Institute-funded cooperative group.
ACRIN's overarching goal is - through clinical trials of diagnostic imaging and
image-guided therapeutic technologies to generate information that will
lengthen and improve the quality of the lives of cancer patients.
NIH CIT Medical
Image Repository
At the NIH Center
for Information Technology (CIT), in collaboration with
NINDS, the
Computational Methods and Applications Group
(CMAG) has developed a Web-based medical image archive system for the
archive of imaging and clinical data from the Suburban Hospital study. This
archive system provides secure Web interfaces for clinical data entry, data
upload, database query, and data download. CMAG is currently developing a
separate archive system for the GAIN study.
Image Archive Applications - General
USF Digital
Mammography Database
The Digital Database for Screening Mammography
(DDSM) is a resource for use by the mammographic image analysis research
community. The primary purpose of the database is to facilitate sound research
in the development of computer algorithms to aid in screening. Secondary
purposes of the database may include the development of algorithms to aid in
the diagnosis and the development of teaching or training aids. The database
contains approximately 2,500 studies. Each study includes two images of each
breast, along with some associated patient information (age at time of study,
ACR breast density rating, subtlety rating for abnormalities, ACR keyword
description of abnormalities) and image information (scanner, spatial
resolution, ...). Images containing suspicious areas have associated
pixel-level "ground truth" information about the locations and types of
suspicious regions. Also provided are software both for accessing the mammogram
and truth images and for calculating performance figures for automated image
analysis algorithms.
Mouse Brain
Library
The MBL (http://mbl.org/) consists
of high-resolution images and databases of brains from many
genetically-characterized strains of mice. There are numerous uses of the MBL,
but the developers' mission is to systematically map and characterize genes
that modulate architecture of the mammalian CNS (for a complete description of
projects refer to the P20
Human Brain Project award: Informatics Center for Mouse Neurogenetics). MBL
databases also include detailed information on genomes of many strains of mice.
The collection now consists of images from approximately 800 brains and
numerical data from just over 8000 mice. MBL can be searched for cases by
strain, age, sex, body or brain weight. Images of the slide collection are
available at a series of resolutions. The base resolution is 24.5 ± 0.5
µm per pixel in the XY plane with a 150 µm interval between
sections (300 µm on each slide, 2 slides per case). Significantly higher
resolution images of single sections-4.5 µm/pixel-have been acquired for
over a hundred cases marked with a blue "hi-res" button. They are now
collecting 1 µm/pixel images for specific parts of the brain-at present,
the neocortex, hippocampus, and the dorsal lateral geniculate nucleus. Very
high resolution images (<0.2 µm/pixel) are available for C57BL/6J
using the iScope, a web-controlled microscope equipped with DIC optics.
List of Image
Database and Image Collection Sites
Assembled for the AMIA Fall Congress
while Mark E. Shelton was a postdoctoral fellow at the University of
Missouri-Columbia, this list gives a summary of many websites, some of which
are no longer active.
RSNA
Databases and Teaching Files: Medical Images
A set of links to
web-accessible medical image collections, primarily at academic institutions,
is included in the RSNA Education Portal. These sites comprise most
radiological subspecialty areas and modality types, especially case-based
teaching files.
CMU Computer
Vision Test Images
The
Computer Vision Homepage
was established at Carnegie Mellon University in 1994 to provide a central
location for World Wide Web links relating to computer vision research. The
emphasis of the Computer Vision Homepage is on computer vision research
rather than on commercial products. A comprehensive set of links to publicly
accessible websites with computer vision test images is offered.
ECVNet Image
Data Bases List
This page contains pointers to sites offering public
access to image collections via the Internet. There you can find color and
grayscale still images, medical images, textures, sequences, stereo pairs,
range images, etc.
Computer
Vision, Machine Learning, and Image Databases
A list of web links for
computer vision, machine learning, and image databases is provided by Kelly at
the University of Iowa. This list includes journals & conferences,
organizations, courses, laboratories, bibliographies, content-based retrieval
systems, image databases, image data mining, context-based indexing papers, and
other resources.
MedPix™
Medical Image Database
MedPix™ is a fully web-enabled and
cross-platform database, integrating images and textual information. The
primary "target audience" includes resident and practicing physicians, medical
students, graduate nursing students and other post-graduate trainees. The
material is organized by disease category, disease location (organ system), and
by patient profiles. The database can be searched through multiple internal
text search engines. In addition, search formulations can be sent directly to
PubMed, or to other outside search engines with just ONE CLICK. Registered
users may browse the image database through a "slide sorter" module.
Contributed content may be © copyrighted by the original
author/contributor, and is used with permission.
BRAID: Brain Image
Database
The BRAID project is developing database technology for the
manipulation and analysis of 3-dimensional brain images derived from MRI, PET,
CT, etc. BRAID is based on the Illustra server, an object/relational or SQL3
DBMS, which allows a standard relational DBMS to be augmented with
application-specific datatypes and operators. The BRAID project is adding
operations and datatypes to support querying, manipulation and analysis of 3D
medical images, including: image datatypes, image operators, statistical
operators, and a web interface.
Gastrolab Image
Library
Gastrolab
Endoscopy Pictures Archive
This website is an image library that will
eventually contain pictures of every disease that make visible changes in the
digestive system. Most of the endoscopic pictures are taken with Olympus
videoendoscopes. The picture quality in this library is not as good as in the
original pictures - the original quality would have made transmission times too
long. In this image library typical x-ray-findings in gastroenterologic
diseases are illustrated. This website is provided as a free service by
The Wasa Workgroup on Intestinal
Disorders, GASTROLAB, Vasa, Finland.
The
Stanford Visible Female
"The Stanford Visible Female is an Academic
Project sponsored by the Division of Anatomy and SUMMIT. Central to the project
is a series of 95 photographed cryosections of a reproductive-age female
cadaveric pelvis acquired in 1993. From these cross-sectional data, several
research projects have arisen. These range from 2D imaging correlations with
independent MR data to 3D models developed for anatomically accurate surgical
simulation."
Visible Human
Project
It is creating a complete, anatomically detailed,
three-dimensional representations of the male and female human body. The
current phase of the project is collecting transverse CT, MRI and cryosection
images of representative male and female cadavers at one millimeter intervals.
Includes an extensive collection of links to projects based upon the Visible
Human data.
Visible Human
Server
"...a virtual anatomic construction kit on the web using the
Visible Human dataset." Features include: "Extract slices, curved surfaces, and
slice animations from both datasets (male and female)" ; "Interactively
navigate by slicing through the male dataset in real-time" ; "Construct 3D
anatomical scenes using combinations of slices and 3D models of internal
structures from the male dataset, and extract 3D animations" ; "Add voice
comments to video sequences generated using the applets. Peripheral Systems Lab
(Prof. Hersch and his team), Computer Science Dept., Ecole Polytechnique
Fédérale de Lausanne
NIDCR -
Craniofacial and Skeletal Diseases Branch
The NIDCR imaging web page
will allow the NIH research and clinical community to collaborate on imaging
studies through the internet. All authorized users on the NIH campus and abroad
will be able to display and review the studies posted on the imaging web page
with the NIH developed imaging tool
Medical Image Processing,
Analysis and Visualization (MIPAV).
Imaging in Clinical Trials
Image
Collection in Clinical Trials [PDF File]
From the Image Guided Therapy
QA Center, Washington University in St. Louis, this is W.B. Harms, Sr.
presentatio at the Society of Clinical Trials meeting in Denver, CO on 20 May
2001. The PowerPoint file has been converted to PDF.
How does CDISC work with the
FDA?
First, the FDA has identified and assigned three liasons to CDISC:
Dr. Randy Levin (CDER), Michael Fauntleroy (CBER) and Sham Gupta (CBER). These
individuals work with CDISC on a regular basis in terms of reviewing output of
CDISC teams and suggesting future direction. They attend CDISC conference calls
and meetings. CDISC also has several other FDA representatives who work with us
by providing feedback, attending meetings with CDISC at the FDA and joining us
in sessions and presentations at industry conferences.
Multidisciplinary
Approach to Data Standards for Clinical Development [PDF File]
This
article originally appeared in APPLIED CLINICAL TRIALS, Volume 11, Number 4,
pages 35-44, April 2002, by Rebecca Kush, PhD who is president of CDISC. A
common interchange standard for clinical data is described that will save time,
effort, and money for everyone involved—and CDISC continues to develop new
functional models to prove it.
Clinical Trials Image Archive Technology
CardioNow,
Inc.
CardioNow's service, which is specifically designed to handle the
large file sizes (greater than 200 megabytes) associated with DICOM cardiology
images, enables study investigators to send complete trial images from their
cath lab to the angiographic core lab in near real-time. All cases sent via the
CardioNow network are transmitted and archived in native DICOM so the original
image quality is preserved. Furthermore, cases associated with clinical trials
are coded and anonymized to protect patient confidentiality. By facilitating
the secure, electronic transmission of cases, CardioNow eliminates the
unnecessary delays and expenses associated with copying, shipping and storing
CDs and cine films.
DICOM 3.0
Implementation Workshop
The Washington University Image-Guided Therapy
Center (ITC) held a workshop on the clinical implementation of the DICOM 3.0
standard for participation in advanced technology radiation therapy
multi-institutional trials. The workshop reviewed the DICOM 3.0 objects
required for multi-institutional trial participation as well as
ITC's DICOM
3.0 Conformance Statement [PDF File] or all of those objects. Additional
items to be covered are the use of Part 10 file sets, media of exchange of the
DICOM data, patient confidentiality issues, and assitance the ITC can provide
to those vendors who are planning to implement DIMSE (networked) communications
but not (Part 10) file set creators. The DICOM objects discussed include Image
Sets (CT, MRI and ultrasound), Structure Sets (region of interest contours:
critical structures, tumor and target volumes), Plans (external beam and
permanent prostate seed), Doses (both dose matrices and dose-volume histograms)
and RT Images (e.g. DRRs, on-line images, digitized films, etc.). This workshop
was held on Saturday, March 16, 2002.
NIH Information Standards
NIH Computer
Security Requirements
The Department of Health and Human Services (DHHS)
Automated Information Systems Security Program (AISSP) Handbook gives us
guidelines for determining the sensitivity of information and the criticality
of data processing capabilities as they pertain to the mission of an office.
All NIH data has some degree of sensitivity, even data that is intended for
unrestricted access by many and varied individuals and groups. Further
information is available from http://www.cio.gov/.
NCICB Plans
and Priorities - Standards-Based Repository (SBR)
NCICB is building a
repository to comprehensively store the data used by NCI programs in adherence
with the international standards used by many other Federal organizations. This
keystone effort will ensure that all data from NCICB supported programs can be
easily shared, whether from clinical trials, animal model programs, basic
research, or any other discipline. NCICB is collaborating to create a unified
national repository of health-related meta-data to describe much of the data
held by NCI. The repository will be compliant with international standards and
will make finding and using data held by NCI much easier.
NCI
Common Data Elements
A repository of terms called Common Data Elements
(CDEs) that medical providers may use to collect patient information for
clinical trials or for cancer care. NCI hopes to facilitate uniform standards
for both cancer clinical trials and patient care by assembling and maintaining
this information on-line for all interested caregivers. The CDEs are compliant
with the ISO 11179 standard. Of particular interest are “Medical
Imaging” CDEs, especially those developed for lung cancer CT
screening.
ISO 11179:
Specification and Standardization of Data Elements
ISO 11179 is a
standard for describing data elements used in databases and documents that
specifies basic aspects of data element composition, including metadata. The
standard applies to the formulation of data element representations and meaning
as shared among people and machines; it does not apply to the physical
representation of data as bits and bytes at the machine level. This standard is
used as the basis for the NCI Common Data Elements.
Dublin Core Metadata
Initiative
The Dublin Core Metadata Initiative is an open forum engaged
in the development of interoperable online metadata standards that support a
broad range of purposes and business models. DCMI's activities include
consensus-driven working groups, global workshops, conferences, standards
liaison, and educational efforts to promote widespread acceptance of metadata
standards and practices.
NLM Communications
Engineering Branch
Projects in the Communications Engineering Branch
focus on R&D in image engineering: the capture, storage, processing, online
retrieval, transmission and display of both biomedical documents (mainly
journals) and medical imagery. The data repositories available from the NLM
Communications Engineering Branch have been collected from a variety of
sources. This collection contains digitized versions of radiographs and rare
manuscripts. Data Repositories include the
National
Health and Nutrition Examination Surveys (NHANES) with collateral data and
x-ray images.
Other Federal Agencies
DARPA Information Processing
Technology Office
DARPA IPTO will create Information Processing
Technology for new generation intelligent systems, transforming our national
infrastructure to enhance global stability. The IPTO has a 4-part mission: 1)
Create transformational information technologies to anticipate and meet
National Security imperatives; 2) Validate technologies with prototypes of real
National Security solutions; 3) Lead, stimulate, and complement commercial
technology; and 4) Transition technologies to National Security users, via
partnerships with other DARPA offices, industry, armed services, and government
agencies.
NIST
Fingerprint Image Software (NFIS)
A new public domain software release
from the Image Group of the National Institute of Standards and Technology
(NIST). NIST Fingerprint Image Software (NFIS) contains software technology,
developed for the Federal Bureau of Investigation (FBI), designed to facilitate
and support the automated manipulation and processing of fingerprint images.
Source code for over 50 different utilities and an extensive User's Guide are
distributed on CD-ROM free of charge without licensing and usage restrictions.
A listing of
test
data produced by the NIST Image Group for use in evaluating automated OCR,
fingerprint classification/matching, and face recognition systems is available.
In addition, NIST offers image
databases that constitute standard reference data for a variety of
applications.
CDC Health
Information and Surveillance Systems Board
The Centers for Disease
Prevention and Control (CDC) Health Information and Surveillance Systems Board
(HISSB) website lists organizations and resources related to development of
health information standards. These include Coordinators/Promoters of Standards
Development, Standards Development Organizations, and
Classification/Nomenclature Systems.
Public
Health Data Standards Consortium
In November 1998, the National Center
for Health Statistics (NCHS) of the Centers for Disease Control and Prevention
(CDC), in conjunction with the Agency for Healthcare Research and Quality
(AHRQ) and the National Committee on Vital and Health Statistics (NCVHS),
convened a workshop to examine the implications of the Health Insurance
Portability and Accountability Act of 1996 (HIPAA) for the practice of public
health and health services research. The workshop, "The Implications of HIPAA's
Administrative Simplification Provisions for Public Health and Health Services
Research," brought together 85 leaders in health statistics, research, and
informatics to examine the challenges and opportunities presented by HIPAA.
This resulted in creation of a new consortium, officially established in
January 1999 as the Public Health Data Standards Consortium, that serves as a
mechanism for ongoing representation of public health and health services
research interests in HIPAA implementation and other data standards-setting
processes.
NASA ESAD
Scientific Data Purchase Program
The Scientific Data Purchase (SDP) is a
demonstration program developed in response to the President's Space Policy,
directing NASA to purchase remote sensing data from the private sector.
Initiated in fiscal year 1997, the SDP was funded under the
Earth Science Enterprise (ESE) Program
to provide scientific data to the ESE science community. The $50 million
program is an opportunity to advance global-systems research, to strengthen the
U.S. economy through development of remote sensing technologies, and to test a
new way of doing business. The NASA Earth Science Applications Directorate
(ESAD) at the John C. Stennis Space Center in Mississippi manages the SDP.
NASA EOSDIS Core System
Information for Scientists = ECS Info
The
Earth
Observing System Data and Information System (EOSDIS) is designed to
archive unprecedented amounts of Earth observing data from a wide range of
instruments collecting information over decades. Its diverse user community can
search, retrieve, and analyze any of these observations, also over a period of
decades. EOS data products need descriptive information, or metadata, to enable
users and data providers to locate and use the information. Over several years,
numerous teams of scientists, computer scientists, and information engineers
have collaborated to develop the data model, with its metadata attributes and
how they are organized, to meet these needs. A
catalog of EOSDIS
related information has been prepared.
Astronomy Digital Image
Library (ADIL)
ADIL collects astronomical, research-quality images and
makes them available to the astronomical community and the general public.
Patrons access the Library through the World Wide Web to search for and browse
images. Once images are located in the Library, users may download them to
their local machines in FITS format for further analysis. The Library provides
a number of benefits not only to those looking for images, but also to those
who add images to the Library's growing collection. The Library is being
developed and maintained by the Radio
Astronomy Imaging Group at the National
Center for Supercomputing Application (NCSA) on the campus of the
University of Illinois at Urbana-Champaign
(UIUC) with support from:
- the National Aeronautics and Space Administration (NASA) through Project Horizon, a cooperative agreement with UIUC.
- the National Science Foundation (NSF) High Performance Computing and Communications (HPCC) program.
- Project 30, Applied Information Science Research Program sponsored by the NASA Office of Space Science.
- and the National Center for Supercomputing Applications.
XML and DICOM
What is
XML?
A markup language is a mechanism to identify structures in a
document. The XML specification defines a standard way to add markup to
documents. In order to appreciate XML, it is important to understand why it was
created. XML was created so that richly structured documents could be used over
the web. The only viable alternatives, HTML and SGML, are not practical for
this purpose. This is the 1st part of a
technical introduction to
XML.
Why
is XML so important? and
What
is metadata?
XLML allows us to focus the problem on metadata, and
metadata is the key to interoperability. Metadata is one of the critical
success factors to sharing information. Metadata also is one of the critical
success factors to storing information cost-effectively. Metadata can make
information sharing and storage efforts great successes, or great failures.
Metadata costs money and has its own ROI. There are many specific
recommendations on XML and metadata by the
Federal Council of Chief Information Officers.
Transcoding
DICOM to XML
Supplement 23 to DICOM (Digital Imaging and Communications
for Medicine), Structured Reporting, is a specification that supports a
semantically rich representation of image and waveform content, enabling
experts to share image and related patient information. DICOM SR supports the
representation of textual and coded data linked to images and waveforms.
Nevertheless, models that work as bridges between the DICOM relational model
and open object-oriented technologies are needed. An object-oriented model to
represent the DICOM SR standard and generate XML-exchangeable representations
using World Wide Web Consortium specifications was developed. [ABSTRACT] A
distributed database course project on the
exchange of
DICOM-compatible medical images using XML was done at the University of
Waterloo.
XML for
Molecular Biology
A list of XML resources compiled by Paul Gordon that
may be of use to the bioinformatician. If you don't think XML is where it's at,
count how many times the word appears in
EU/US Workshop on Large
Scientific Databases report.
Object
Management Group (OMG)
The OMG was formed to create a component-based
software marketplace by hastening the introduction of standardized object
software. The OMG's charter includes the establishment of industry guidelines
and detailed object management specifications to provide a common framework for
application development. Conformance to these specifications will make it
possible to develop a heterogeneous computing environment across all major
hardware platforms and operating systems. The nearly 800 member companies of
the Object Management Group produce and maintain a suite of specifications that
support distributed, heterogeneous software development projects from analysis
and design through coding, deployment, runtime, and maintenance. These
include:
- Model Driven Architecture (MDA)
- Unified Modeling Language (UML)
- MetaObject Facility (MOF)
- XML Metadata Interchange (XMI)
- Common Warehouse Metamodel (CWM)
- Common Object Request Broker Architecture (CORBA)
- Object Management Architecture (OMA)
XML
- CORBA - DICOM
What Digital Imaging and Communication in Medicine
(DICOM) could look like in common object request broker (CORBA) and extensible
markup language (XML). [ABSTRACT]
CDISC
Operational Data Model (ODM)
The final version 1.1 Specification for the
Operational Data Model (ODM) was released by CDISC on 9 May 2002. The XML-based
Operational Data Model "provides a format for representing the study metadata,
study data, and administrative data associated with a clinical trial. It
represents only the data that would be transferred among different software
systems during a trial, or archived after a trial. It need not represent any
information internal to a single system, for example, information about how the
data would be stored in a particular database." The version 1.1 release
includes the text of the specification, with XML DTDs and supporting
documentation. ODM v1.1 Final "represents the culmination of more than three
years of effort by a multi-disciplinary team of pharmaceutical and
biotechnology sponsors and technology vendors; the development team believes
the CDISC 1.1 DTD is now ready for widespread adoption among sponsors, vendors
and CROs to facilitate the interchange of clinical trial data.
DARPA Agent Markup Language
(DAML)
The World Wide Web (WWW) contains a large amount of information
and is expanding at a rapid rate. Most of that information is currently being
represented using the Hypertext Markup Language (HTML), which is designed to
allow web developers to display information in a way that is accessible to
humans for viewing via web browsers. While HTML allows us to visualize the
information on the web, it doesn't provide much capability to describe the
information in ways that facilitate the use of software programs to find or
interpret it. The World Wide Web Consortium
(W3C) has developed the Extensible Markup
Language (XML) which allows information to be more accurately described
using tags. As an example, the word Algol on a web site might represent a
computer language, a star or an oceanographic research ship. The use of XML to
provide metadata markup, such as Algol, makes the meaning of the work
unambiguous. However, XML has a limited capability to describe the
relationships (schemas or ontologies) with respect to objects. The use of
ontologies provides a very powerful way to describe objects and their
relationships to other objects. The DAML language is being developed as an
extension to XML and the Resource Description
Framework (RDF). The latest release of the language (DAML+OIL) provides a rich
set of constructs with which to create ontologies and to markup information so
that it is machine readable and understandable.
XML
Multimedia Radiology Report
The clinical display of radiologic
information as an interactive multimedia report is accomplished using a
multimedia report model based on Extensible Markup Language (XML), rather than
a traditional workstation model. XML does not replace existing standards (i.e.,
Digital Imaging and Communications in Medicine [DICOM], Transmission Control
Protocol/Internet Protocol [TCP/IP]). Instead, it provides a powerful framework
that is used in combination with existing standards to allow system designers
to modify display characteristics based on user need. The application of XML to
the clinical display of radiologic information is described. [ABSTRACT]
Review/Tutorial
on Standards for Radiology Networks
Medical communication standards,
i.e., HL 7, DICOM, and in the near future the migration towards XML, support
the interoperability between the IT subsystems and pave the way to patient
information systems with access to unified and complete electronic medical
records (EMR). Furthermore, with standardized communication techniques, such as
CORBAmed [PDF
File], an object-oriented design of Healthcare applications will be possible in
the near future. [ABSTRACT]
MIMOS:
A framework for exchanging medical image processing results
DICOM
presently supports structured reporting of image studies, but does not
accommodate semantics in the image handling domain. This can impede the
exchange and the interpretation of processing results. To overcome this
limitation, a framework based on a formal grammar was developed, with documents
encoded using XML. [ABSTRACT]
Implementation of Biological Databases
SIDB - Scientific
Image Data Base (SIDB)
A web-driven open source database for 2-D and 3-D
images (http://sidb.sourceforge.net/),
specifically designed for (confocal) microscopy units, but applicable wherever
groups of users collaborate with images.
OpenHealth™ --
Open source software in health care
Electronic medical records and
networks are the solutions to the technical issues around coordinating the work
of diverse health care professionals caring for a single person across multiple
sites. Open source software has potential to overcome some of the obstacles now
being encountered in this transition: 1) Open source reference implementations
of medical record standards could speed their adoption and increase
interoperability in practice. The differences in adoption between TCP/IP and
ISO network protocols illustrate the importance of reference implementations.
2) Open source software could reduce the issue of "Who pays?" in community
health networks by eliminating per user and per site license costs and
unbundling implementation and support charges.
ASN.1 - Abstract
Syntax Notation One
ASN.1, or Abstract Syntax Notation One, is an
International Standards Organization (ISO) data representation format used to
achieve interoperability between platforms. The
National Center for Biotechnology
Information (NCBI) uses ASN.1 for the storage and retrieval of data such as
nucleotide and protein sequences, structures, genomes, and MEDLINE records. It
permits computers and software systems of all types to reliably exchange both
the data structure and content. The
NCBI Software Development
ToolKit (known as the 'NCBI Toolbox') is a set of software and data
exchange specifications used by NCBI to produce portable, modular software for
molecular biology. The software in the Toolbox is primarily designed to read
ASN.1 format records. It is freely available to the public, and can be used in
its own right or as a foundation for building tools with similar
properties.
VISIM:
Information Retrieval and Exploration in Large Medical Image
Collections
Visual information systems in medicine (VISIM) are emerging
capable of retrieving items from large collections of images and exploring
connections between them to discover new insights, confirm hypotheses, or
search for similar findings. The advance of these systems is at the crossroads
of computer vision, man-machine interaction and image database technology,
invoking many novel issues that need to be addressed. This one day workshop was
held in Utrecht, NL on October 18, 2001.
Biological
Databases: Information Retrieval
Author/Sponsor: David Landsman (NCBI,
NIH) - Videocast
lecture [PDF File] from the current topics in genome analysis
course.
Biological
Databases: Content and Submission
Author/Sponsor: Francis Ouellette
(Canadian Center for Molecular Medicine and Therapeutics) - Videocast
lecture
[PDF File] from the current
topics in genome analysis course.
NCSA Emerge
Emerge
is an National Center for Supercomputer
Applications (NCSA) effort to develop middleware components of a new
distributed search infrastructure which addresses the scale and heterogeneity
of scientific data. The components enable search services to interoperate
across scientific domains by providing user-configurable tools for mapping
between metadata schemas, performing search queries against multiple data
sources, and performing query pre- and post-processing. Access to our search
services is through platform-neutral standard and emerging-standard tools such
as Z39.50,
Open Archives,
XML, and Java. This work was done in collaboration with
the National Cancer Institute.
Micromine, Corp.
Chris
Barnes's consultant services company in Powder Springs, GA has processed
mammograms (and many other types of imagery) using multimedia data warehouses
and data mining that combine pixel-searchable image archives with linkable
descriptive data.
PEIPA -- the Pilot European
Image Processing Archive
PEIPA is an archive of material relating to the
processing of images, with an emphasis on image analysis and computer vision.
The archive is supported from the British
Machine Vision Association, the University of Essex, and the EU-funded
project Performance Characterization in Computer Vision.
Cancer Image Archives
National Digital
Mammography Archive (NDMA)
The National Digital Mammography Archive (NDMA
[PDF File]) represents a collaborative effort between the University of
Pennsylvania Medical Center (including the
National Scalable Cluster Project -
NSCP), the University of Chicago Department of Radiology, the University of
North Carolina - Chapel Hill School of Medicine, the Department of Radiology -
Breast Imaging - Sunnybrook and Women's College Health Sciences Centre of the
University of Toronto, and Advanced Computing Technologies Division of BWXT
Y-12 L.L.C. in Oak Ridge Tennessee. This is a
Next Generation
Internet project sponsored by the National Library of Medicine. NDMA seeks
to develop a testbed that demonstrates the feasibility of a
national breast
imaging archive and network infrastructure [PDF File] to support digital
mammography using Next Generation Internet (NGI) technologies.
Virtual
Cancer Image Data Warehouse
At the National Cancer Center (Tokyo,
Japan), more than 100 virtual cancer images from CT or MR data of individual
patients with cancer (Cancer Edutainment Virtual Reality Theater: CEVRT). These
images can be used to help explain procedures, findings, etc. to the patient,
to obtain informed consent, to simulate surgery, and to estimate cancer
invasion to surrounding organs. A
web-based
object-oriented database [PDF File] was created to access these cancer
images and to register medical images at international research sites via the
Internet.
Mammographic
Image Analysis Society - Mammographic Database
The original MIAS
Database (digitised at 50 micron pixel edge) has been reduced to 200 micron
pixel edge and clipped/padded so that every image is 1024 pixels x 1024 pixels.
There are 322 cases. Reference: J Suckling et al (1994) "The Mammographic Image
Analysis Society Digital Mammogram Database" Exerpta Medica. International
Congress Series 1069, pp 375-378.
UCSF
Digital Mammography Warehouse
The design and development of a digital
mammography data warehouse to facilitate clinical and research activities is
described (SPIE Medical Imaging 2002 meeting). A data warehouse is a complete
and consistent integration of data from many information sources. It enables
users to explore the warehouse for various analyses and decision support
purposes. The information system incorporates breast imaging data from a
diversity of existing clinical systems, into a digital data warehouse. Various
types of breast imaging data, including patient demographics, family history,
digital mammography and radiological reports, will be acquired for the
University of California San Francisco
digital
mammography PACS modules, as well as Radiological Information System.
UCSF Neuroimaging
Data Warehouse
An image data warehouse infrastructure containing a broad
array of biomedical imaging and clinical data is built on a Picture Archiving
and Communication Systems (PACS) environment. Up to now, the primary purpose of
most database systems and tools was to meet the needs of operational systems,
which are typically transactional in nature. In contrast, an object-oriented
analysis and design (OOAD) process was used for epilepsy research and patient
care.
The
implementation is based on a Java CORBA (Common Object Request Broker
Architecture) and Web-based architecture that separates the graphical user
interface presentation, data warehouse business services, data staging area,
and backend source systems into distinct software layers.
Biological Databases
Molecular Biology
Database Collection
The Molecular Biology Database Collection is an
online resource listing key databases of value to the biological community.
This Collection is intended to bring fellow scientists' attention to
high-quality databases that are available throughout the world, rather than
just be a lengthy listing of all available databases. As such, this up-to-date
listing is intended to serve as the initial point from which to find
specialized databases that may be of use in biological research. The databases
included in this Collection provide new value to the underlying data by virtue
of curation, new data connections or other innovative approaches. Short,
searchable summaries and updates for each of the databases included in the
Collection are available through the Nucleic Acids Research Web site at
http://nar.oupjournals.org.
Nucleic
Acids Research - Special Database Issue (2002)
The 2002 Database Issue
of Nucleic Acids Research is the ninth in a series dedicated to factual
biological databases. These databases have become an essential resource for
working biologists and the aim of this compilation is to provide descriptions
of the most important of these databases and especially to introduce newly
compiled databases that provide specialist information in the biological area.
In the current issue (Jan 2002), there are descriptions of 2112 databases.
Last Updated: March 2003