Acquisition & Storage of Digitized Whole Slide Images The

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Transcript Acquisition & Storage of Digitized Whole Slide Images The

APIII 2006
Advancing Practice, Instruction, and Innovation through Informatics
Acquisition & Storage of
Digitized Whole Slide Images
The Radiology Perspective
John S. Koller & Garrett W. Lindemann, Ph.D.
Copyright 2006 by KAI-LRC Resources
Created for & Licensed to APIII 2006
Introduction & Disclosures
• Garrett W. Lindemann Ph.D.- President of Lindemann Research
Consulting, Inc.
– 17+ years of Research & Development in the Biotechnology and
Pharmaceutical Industries.
– Employment and Consulting Relationships
• Roche Chief Technology Office
• Histatek Pharmaceuticals Inc.
• Large and small Pharmaceutical companies (North America and
Europe)
• Large and small Biotechnology companies (North America and
Europe)
• Venture Capital Firms
• M & A firms
• Pharmaceutical and Biotechnology Business Development Firms
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Introduction & Disclosures
• John S. Koller - President of KAI Consulting
– 25+ years experience in secure, highly available IT solutions.
– Employment & Consulting relationships
•
•
•
•
Philips Medical Systems
EMC Corporation
Multiple Imaging & Informatics Vendors
Multiple IT Technology Vendors
– Other Relationships
• Contributing Editor – Imaging Technology News
• Board of Directors
– HealthSphere Corporation
• Advisory Board Member
– Bycast, Inc
– Imaging Technology News
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Agenda
• Part 1 – John Koller
– Introduction to the Digital Healthcare Enterprise
– Introduction to the Radiology Imaging Model
• Part 2 – Dr. Lindemann
– Introduction to the Pathology Imaging Model
– Compare & Contrast Pathology to Radiology
• Part 3 – John Koller
– The Enterprise Perspective of the Storage &
Management of Healthcare Image Data
• Summary & Questions
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Introduction to the
Digital Healthcare Enterprise
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The Digital Healthcare Enterprise (DHE)
• Enterprise Systems
– Business Centric
•
•
•
•
Billing
Accounts Payable
HR, Payroll
Supply-Chain Management
– Patient Centric
• Hospital Information System
(HIS)
• Electronic Medical Record
(EMR, EPR, EHR)
• Clinical Information System
(CIS)
• Computerized Physician
Order Entry (CPOE)
• Departmental Systems
– Radiology
• RIS (data)
• PACS (images)
– Cardiology
• CVIS (data & waveforms)
• PACS (images)
– Radiation Oncology
• Treatment planning systems
(images)
– Pathology
– Pharmacy
– Laboratory
– Etc.
The Typical Healthcare Enterprise has an average of 100 to 175 Applications.
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The Challenges of the DHE
• Business
– Cost control vs. quality
patient care
– Regulatory compliance
– BC/DRP - Time to recover
– Access to data across
applications
• Clinical
– Information when & where
required
– Loss or corruption is
unacceptable
– Impact on patient care
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• Technical
– Lack of qualified technical
professionals
– Integration & interoperability
with increasing numbers of
applications
– Manage & protect increasing
amounts of data
– 100% data integrity &
availability
– Security for data storage and
distribution
– Standards vs. proprietary
solutions
Traditional Healthcare Infrastructure
Hospital Data
Physician Practice Data
Ambulatory Data
Network
Server/OS
E-Medical
Records
Database
Application
Pharmacy, Laboratory
and Ancillary Data
Imaging
Center
Financial
Records
CPR
Financials
Legato to
DLT
ADSM
to
3490s
Patient Care
Billing
Billing
e-commerce
OLTP
Backup by
FDR Upstream
STK
Silos
Backup by
tar—8mm
Exchange
Lotus
Notes
Cheyenne to
4mm
Disaster Recovery plan
(mainframe only)
Proactive
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Reactive
HR
DK tape
Test
Disaster
Recovery
Employee Data
Batch
CICS
Storage
Backup
Radiology
Cyclic Process
OmniBack
Data Types in the DHE
• Data Information Systems
– Contain Variable Content Files (VCF) or transactional
files
– Transactions are small - typically less than 10 KB
– Transaction rates are high
• Image Information Systems
– Contain Fixed Content Files (FCF)
– Files & Transactions are usually large
• typically 100 KB to 1 GB plus
– Transaction rates are low
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Importance of Standards in the DHE
• HL7 (Health Level 7)
– Simple protocol to exchange
information
– Usually requires an interface
between applications
– Current version of HL7 is
Version 2.x
– Version 3.x compliant with
XML – Extensible Markup
Language
• CCOW (Clinical Context
Working Group)
– Simplify and improve workflow
and functionality between
applications
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• DICOM (Digital Image and
Communication in Medicine)
– A true standard dealing with
objects – images > series >
study>patient
– Deals with images, waveforms
and structured reports
– Includes many clinical
specialties in addition to
radiology
– Ensures interoperability of
images, etc. generated by
modalities and devices
manufactured by different
vendors
Introduction to the
Radiology Imaging Model
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History & Timeline
• Introduced in 1984
• Cost of Entry
– 1985 ACR/NEMA Ver.1.0
– 1988 ACR/NEMA Ver. 2.0
– GE/IBM Demonstrate @
RSNA
– AT&T and Philips
Demonstrate
– RSNA 1992 DICOM 3.0
– 1992 – Madigan Army
Hospital goes Film-less
– Quad 2K Workstation
• 1992 - $250K
• 2002 - $115K (flat-panel)
• 2004 - $90K
– (2) 5Mp flat-panel & 1 clr
– 350 Bed Facility
• 1992 - $6M
• 2002 - $3M
1st Film-less Hospital
DICOM 3.0
1st PACS 1st Army ACR/NEMA ACR/NEMA MDIS
WS-$250K,
PACS-$6M
Conference TeleRad
Awarded
V2
V1
1982 1983
1985
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1988
1991
1992
WS - $115K
PACS - $3M
2002
WS - $115K
PACS - $3M
2004
Evolving Imaging Architectures
• Film & Processors
• Proprietary Interfaces
• Dedicated Print
Networks
• Closed Mini-PACS
• Enterprise PACS
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xIS
PACS
Radiology Workflow is User Driven
Information Unit
has its
Prime User
ORDER:
A request for imaging service
(Accession Number)
CLINICIAN
OR REFERING DOC:
The Imaging Dept Customer
REQUESTED PROCEDURE :
Units of work resulting in one Report
RADIOLOGIST :
In Charge of producing
the Report
with associated codified, billable acts
(Requested Procedure ID)
PROCEDURE STEP :
The smallest unit of work
in the workflow
(modality worklist entry)
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TECHNOLOGIST
(and RADIOLOGIST)
In charge of acquiring
images, etc.
Normal Workflow
Typical workflow: One Order – One Procedure – One Report
Radiology Department
ORDER
A request for
Radiologic
Requested
Service
Procedure
Performed
Procedure
Step
Report
One or
more series
of images
Set of
Codifiable,
Billable,
Acts
Acquisition Modality
Chart courtesy of Integrating the Healthcare Enterprise (IHE)
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Multiple Modality Steps
ORDER
A request for
Radiologic
Service
DICOM
Modality Worklist Radiology Department
Scheduled
Procedure
Step A
Requested
Procedure
1
Scheduled
Procedure
Step B
DICOM
Modality Worklist
Performed
Procedure
Step P1
One or
more series
of images
Report
Set of
Codifiable,
Billable, Acts
Performed
Acquisition
Procedure
Step P2 Modality
One or
more series
of images
Acquisition
Modality
Chart courtesy of Integrating the Healthcare Enterprise (IHE)
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Integrated Healthcare Environment (IHE)
• Voluntary technical definition of functionality that
enhances interoperability
• Integration profiles – e.g. scheduled workflow
– establishes consistency and integrity of
radiological data crossing a RIS/PACS
(HL7/DICOM) boundary
• Many RFPs require vendor to specify which
integration profiles they support and with whom
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IHE Integration Profiles
Scheduled Workflow
Admit, order, schedule, acquire images, notify of completed steps
Patient
Information
Reconciliation
Unknown
patients and
unscheduled
orders
Consistent
Presentation of
Images
Hardcopy and
softcopy
grayscale and
presentation state
Access to
Radiology
Information
Consistent
access to
images and
reports
Presentation of
Grouped Procedures
Subset a single acquisition
Key Image
Notes
Exchange flagging
significant images
Simple Image and
Numeric Reports
Exchange simple
reports with image
links and, optionally,
measurements
Chart courtesy of Integrating the Healthcare Enterprise (IHE)
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Scheduled Workflow Profile
report
report
Registration
report
HIS
Report
Repository
patient
information
Film
Diagnostic
Lightbox
Workstation
images
retrieved
PACS
Orders Placed
examination orders
RIS
Orders Filled
procedure
scheduled
Prefetch any relevant
prior studies
Acquisition images
modality
Modality stored
worklist
acquisition
in-progress
completed
Chart courtesy of Integrating the Healthcare Enterprise (IHE)
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Image
Manager
& Archive
acquisition
completed
Modality
images
printed
Film
Folder
Film
Lessons & Landmines
• Modality <-> PACS - Standards “Grey” Areas
– Limited inter-vendor compatibility in early years
• Installation of RIS prior to or with PACS
– The installation of Image Management prior to
Workflow Management introduces potential for
errors and lost studies.
• The 2nd PACS Challenge
– Was it truly stored in a standard format?
– How is all the data migrated?
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20
Introduction to the
Pathology Imaging Model
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Pathology Imaging Models
Current Consultation Models: Sneaker Management
Manual
Specimen
Tissue
Processing
Preprocessing &
Staining / Detection
Mounted
Section
Gross
Pathology
1.
2.
3.
4.
5.
Sectioning
Fixation
1.
2.
3.
Preprocessing
Alcohol
Urea
Citric Acid
Microwave
Heat
Staining / Detection
OCT
Formaldehyde
Paraffin
1.
2.
3.
4.
5.
Blocking
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Finished
Slide
Sectioning
Mounting
Normal Stains
Special Stains
Immuno Histochemistry
In Situ Hybridization
FISH
Pathology Imaging Models
Current Consultation Models: Sneaker Net
Finished
Slide
Report
Transportation
Pathologist
Second Opinion
Review by Specialist
Transportation
Pathologist
Transportation
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Pathology Imaging Models
Near Future consultation Models: Image Acquisition & Workflow
Management
Near Full Automation
Partial Automation
Digital Image
Automated
Specimen
Tissue
Processing
Gross
Pathology
Preprocessing &
Staining / Detection
Mounted
Section
1.
2.
3.
4.
5.
Sectioning
Fixation
1.
2.
3.
Preprocessing
Alcohol
Urea
Citric Acid
Microwave
Heat
Staining / Detection
OCT
Formaldehyde
Paraffin
1.
2.
3.
4.
5.
Blocking
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Finished
Slide
Sectioning
Mounting
Normal Stains
Special Stains
Immuno Histochemistry
In Situ Hybridization
FISH
Pathology Imaging Models
Current Consultation Models: Image Acquisition & Workflow Management
Image Acquisition & Display Chain
Analog-Digital
Conversion in
Scanner
(Camera)
Physical
Slide
Digital-Analog
Conversion in
Display (LCD)
Digital Image
Storage &
Management
Diagnostic
Workstation
Image Server
Slide
Scanning
Whole Slide
Imaging Scanner
Digital
Image
Digital
Image
(WSI)
Finished
Slide
WSI Analog to Digital Acquisition
1.
2.
3.
4.
Automated
Preparation
System
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System Calibration
Robotic slide positioner
Special light & filters (Fluorescence)
Camera for Digital Image acquisition
Storage
Laboratory Information System (LIS)
Archive
Pathology and Radiology:
Fraternal Twin Medical Specialties
• Similarities and Differences
• PACs Models
• TelePathology and Whole Slide Imaging
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Pathology and Radiology:
Fraternal Twin Medical Specialties
• Similarities
– Highly trained and skilled Physicians.
– Image based and focused on evaluation of tissues.
– Sub-specialized along technologies, tissues and
organ systems.
– Apply a range of different technologies and
procedures to provide alternative methods for
visualization and characterization of tissues.
– Typically hospital based and commonly function as
consulting Physicians.
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Pathology and Radiology:
Fraternal Twin Medical Specialties
• Differences
– Radiology is the younger of the two specialties.
– Pathologist use microscopes and have contact with
fresh tissue specimens.
– Pathologists diagnosis and Radiologists provide
opinions'.
– The primary data set for the Pathologist is the
specimen, slide and the corresponding block. While,
the primary data set for the Radiologist is the study.
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Pathology and Radiology:
Fraternal Twin Medical Specialties
• Similarities exist and the differences are not so
vast as not to use the history of Digital Radiology
as a guide path for the implementation of Digital
Pathology.
– The experiences of Digital Radiology can be used to
construct a backbone for guiding the implementation
of Digital Pathology.
• Regulatory and Standards issues
• Image management and archiving
• Integration issues
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Pathology and Radiology:
Fraternal Twin Medical Specialties
• PACs systems
– Digital Radiology started with small, proprietary, self
contained, vendor specific image archiving systems.
• The “mini PACs” mind set
– Digital Radiology eventually moved to Department
based modality vendor independent systems and the
migration to enterprise, whole hospital, systems has
been the normal for several years.
– Currently, several Tele- and Digital Pathology
software and modality vendors sell self contained
proprietary vendor specific image archiving systems
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Current Digital Pathology Imaging Concepts
• Technology Groupings
– TelePathology
• Static
• Streaming
– Whole Slide Imaging
• Strip
• Tile
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Current Digital Pathology Imaging Concepts
• Devices
– TelePathology
• Static
– Transmission of a single image over a distance
– Transmission of another frame or field of view requires
sending another image
• Streaming
– Transmission of a video signal over a distance
– Ability for remote access to microscope
– Ability for visualization of the whole slide through the
video camera
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Current Digital Pathology Imaging Concepts
• Devices
– Whole Slide Imaging
• Strip
– Slide is scanned one strip at a time.
– Viewing of the whole slide requires assembling the strips
into a complete image of the slide.
• Tile
– Slide is scanned one Field of View at a time.
– Viewing of the whole slide requires assembling the tiles
into a complete image of the slide.
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Current Digital Pathology Imaging Concepts
• Image Management
– TelePathology
• Computer Storage (Hard drive, servers, DVDs,
CDs, …)
• Path-PACs system
– Whole Slide Imaging
• Computer Storage (Hard drives, servers, DVDs,
CDs, …)
• Proprietary storage systems, formats and software.
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Current Digital Pathology Imaging Concepts
• Data Size
– TelePathology
• Dependent on static or video
– Whole Slide Imaging
• Dependent on strip or tile
• Dependent on size of section
• Dependent on magnification and number of
magnifications used
• Dependent on usage of Island/Ocean view
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Current Digital Pathology Imaging Concepts
• Data Size
– Examples from the VIIIth European
Conference on Telepathology and 2nd on
Virtual Microscopy (July 2006, Budapest
Hungary)
• 50 T-Bytes per year (3 years)
– Department of Pathology, Semmelweis University,
Budapest Hungary
• 1000 T-Bytes per year (estimated)
– Department of Pathology, Charite University, Berlin
Germany
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The Future is Now 1
• Into the telepathology trenches at Henry Ford;
CAP Today, May 2006
– Dr. Tuthill (Pathology Informatics Director)
interviewed by Ed Finkel
– Henry Ford is a geographical disperse four hospital,
26-clinic network.
– Annual Specimen Load
• 50,000 Surgical
• 100,000 to 150,000 Cytology Specimens
The Future is Now 1
• Costs
– Before Implementation
• Direct:
– $30,000 to $50,000 on digital imaging and $600 per 100
slide PowerPoint presentations.
• Indirect:
– Time and inconvenience of travel between different sites
– Lost wait time
The Future is Now 1
• Costs
– Implementation
• $125,000
• Benefits
– Improved workflow
– Improved Intra-Institutional support
– Increased efficiency and support for clinical conferences and
education
– Support Pathologists in outlying hospitals and clinics
• Return on Investment
– Three to five years
The Future is Now 1
• Dr. Tuthill comments:
– “Understand current costs that relate to
implementation”
– “To be effective, digital imaging has to be an integral
part of your process. It’s not an ad hoc, maybe we
will, maybe we won’t. To make that so, you need to
have the appropriate equipment to allow for
streamlined and efficient acquisition of images without creating workflow challenges that slow the
process down.”
The Future is Now 2
• Dr. Dunn (Milwaukee Department of Veterans
Affairs Medical Center, Milwaukee, Wisconsin).
– Implemented a routine Surgical Telepathology service
in 1996 between the Iron Mountain and Milwaukee
Veterans Affairs Medical Centers, a separation of 220
miles.
– In 2000, implemented a network between 8 Regional
Veterans Hospital Laboratories (VISN-12) located in
the States of Michigan, Wisconsin, Illinois, and
Indiana.
The Future is Now 2
• Costs
– Test-bed suggests:
• “…more cost effective than maintaining an on-site
Pathologist at a remote site with limited workload”
• “…annual cost of telepathology is likely greater
than that of transporting specimens from Iron
Mountain to be processed and diagnosed in
Milwaukee”
The Future is Now 2
• Benefits
– Implementation of a WAN system saves
VISN-12 $200,000 Monthly.
– Decreased specimen turn around time (TAT)
is decreased as compared to transportation.
– Increased clinical satisfaction
– Increased efficiency
What Now?
• The History of Digital Imaging in Radiology
• The Workflow of Standard Pathology
• The Future Workflow of Digital Pathology
• How do we manage all this data?
The Enterprise Storage &
Management of Healthcare
Imaging Data
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Evolution of DHE – Common Infrastructure
Patient
Accounts
Billing
Radiology and Cardiology
All Ancillary Dept. Data
Financial
Data
E-Medical
Records
High Availability
High Performance
Centralized
Management
Consolidated
Backup/Restore
Prod
Non-Intrusive
Data Loads &
Data Mining
Common
Disaster
Recovery
.
Data
Mart
Staff Data
and Records
Test
Standardized
Testing & Change
Control
.
Proactive
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Reactive
Cyclic Process
Challenges of Image Management
(The Pathology Perspective)
• Very Large Datasets
– Storage
– Communications
• Very Large Annual Volumes
– Data Protection Requirements
• Variable Retention Periods
– Lifecycle Management
• Variable Locations
– Communication Delays
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Imaging - Backup Vs. Archiving
Backup
Archiving
• When to Use?
• When to Use?
– Variable Content Data
– Commercial Database
• Examples
– RIS / LIS Databases
– Image Pointer Database
• Backup Management
– Create Regular Backups
– Manage & Rotate Multiple
Generations (Grandfather,
Father, Son)
– Database Snapshots &
Replication
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– Fixed Object Based
Content
– Long-term Retention
Requirements
– Large Volume of Objects
• Example
– PACS Image Database
• Archive Management
– Create Data Protection &
Retention Policies
– Automate Everything
Possible
The Healthcare Enterprise Archive (HEA)
Why an HEA?
• Eliminate isolated silos of
departmental storage
• Provide an integrated
storage and storage
management system
• Reduce cost of hardware,
software, licensing and
maintenance fees and
personnel, i.e. minimize
TCO
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– Divorce storage
component from clinical
applications
– Allow clinical
departments to acquire
applications that optimize
workflow and
visualization
– Minimize risk and cost of
information migration
– Independence from
clinical application
vendor
49
The Healthcare Enterprise Archive (HEA)
Why an HEA?
• Integrated and uniform security solution
• Provide high availability and redundancy
• Satisfy state and federal statutory
retention periods for medical information
• Satisfy HIPAA as cost effectively as
possible
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50
Types & Costs of Storage
Increased
Cost & Speed
•
•
•
•
•
•
Enterprise Disk (Fiber Channel)
Mid-range Disk (Fiber Channel / SAS)
Archive Disk (SATA)
Optical Disk
MAID (Massive Array of Idle Disks)
Tape
Higher
Density
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Image Data Management
How can your image data be managed?
•
Let your Imaging vendor decide.
– Dependent on vendor for all storage & future migration.
•
Use an all disk solution with multiple copies managed by storage vendor.
– No real intelligence
– Not responsive to conditions affecting individual data objects
– Still dependent on vendor for future migration.
•
Use an HSM to archive your images.
– Better control, but minimal metadata for policy-based automation.
– Requires Linkages Back to Requesting System
– Still dependent on vendor for future migration.
•
Use an Information Lifecycle Management (ILM) strategy.
ILM – What is it?
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Definition of ILM
Information Lifecycle Management is comprised
of policies, processes, practices and tools
used to align the business value of information
with the most appropriate and cost effective IT
Infrastructure from the time information is
conceived through its final disposition…
Source: SNIA Data Management Forum
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ILM – What is it?
• What ILM is not!
– Hardware,
– Software,
– A product!
• Policies, Processes and Technologies for Storing
Data Objects on the Most Appropriate & Cost
Effective Platforms / Media
–
–
–
–
–
Performance
Frequency of Access
Cost
Retention Requirements
Data Protection / Integrity Requirements
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ILM – What is it? (cont)
• Depends on the Vendor – ILM? DLM? xLM?
– Information Lifecycle Management (ILM)
– Data Lifecycle Management (DLM)
• True ILM is Dependent on the Ability to Apply
Intelligent Data Management based on the Richness
of Metadata and Application Awareness
• All Solutions Should be Standards-based (if
possible)
• The Entire Life of a Information Object is Predestined at Time of Creation, But
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ILM vs. DLM
• Data Lifecycle Management
– Focus is to make efficient use of storage
resources
– Based on basic characteristics of the
data and data access
– Basic Metadata
Application &
Business Process
ILM
Processing
• Date/Time, Last Access
• Object Size, System Watermark
• Information Lifecycle Management
– Requires information about business
processes (application aware)
– Holistic view of managing information
– Robust Metadata
• DICOM, Derived from HL-7, Other
DLM
Storage
Tier 1
Storage
Tier 2
Storage
Tier 3
– Uses functions of data lifecycle
management
Excerpted from Storage Industry Primer by Dennis Martin
RMWTUG – Fall ‘05
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DLM vs. ILM – An Imaging Example
Cardio
PACS
WSI
SACS
On-line
Near-line
Redundant Archive
Fast Disk
Slow Disk
Tape / Optical
Key Images –
7 yrs
Rad
PACS
7 days
30 days
30
days
1 yr.
6 mo.
2 yr.
7 yrs.
+++ yrs.
DLM (Typical HSM)
ILM – Negative
Lifecycle
MGR
xIS
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ILM – Positive
ILM – Pathology
Summary
• PACS for Radiology has been successful
because:
–
–
–
–
–
–
Increased productivity
Streamlined workflow
Increased efficiency of referring physicians
Excellent marketing tool
Can result in reduction in hospital stay
Can result in a POSITIVE ROI
• Will these results be repeated if Pathology
implements PACS?
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Summary
• Pathology Imaging
– Tele-Pathology is being successfully used in several locations and is
a reality.
– WSI has the capacity to provide significant value to the patient and
Pathologist.
– Standards and Interoperability need to be developed and applied.
• Enterprise Archiving
–
–
–
–
Enterprise vs. Department Solutions
Standards are Critical to Enterprise Interoperability.
Addresses Security & Regulatory requirements
ILM can help make imaging solutions more manageable & affordable.
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Questions?
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• Contact Information
– John S. Koller
• Email: [email protected]
• Office: 303.681.2854
– Garrett W. Lindemann
• Email: [email protected]
• Office: 307.655.5109
• APIII 2006 Support Page (Private Event Page)
– www.kaiconsulting.com/conferences/apiii2006/index.htm
– Password given at conference
(c)2006 KAI-LRC Resources