Digital Pathology Clinical Interface Issues:
The CHOP Experience
Alexander R. Judkins, M.D., Division of Neuropathology, Department of Pathology &
Laboratory Medicine, Children’s Hospital of Philadelphia, University of Pennsylvania
School of Medicine, Philadelphia PA
History
 1855 - Dr. Francis West Lewis,
visits to the Great Ormond Street
Hospital for Sick Children in
London (founded 1852)
 Along with Drs. T. Hewson Bache
and R.A.F. Penrose founds the
first children's hospital in North
America.
 In 1855, Philadelphia had a
population of about 460,000

10,507 deaths

Leading causes of death were
smallpox, typhoid, and scarlet
fever.

In one month in 1855, 300
children under 12 years old died,
primarily of infectious diseases.
History
Department of Pathology
How many?
 Technical and clerical staff: 230 clinical FTE
 Professional staff: 29 pathologists and
laboratorians (MD, PhD, MD/PhD)
 42,000 sqf
 > 1,700,000 billable tests
 24/7: chemistry, hematology, blood bank,
microbiology
 Research Faculty and Staff: ~100
Clinical Labs Test Volume
(# samples in 1,000,000)
2
1.8
1.6
1.4
1.2
1
0.8
0.6
0.4
0.2
0
1995 1997 1999 2001 2003 2005 2007
Lab Expenses & Charges
(in $1,000,000)
*
350
300
250
200
Expenses
Charges
150
100
50
0
1995
1998
2001
2004
2007
Digital pathology project
 Goal: implement digital pathology in an
academic center for pediatric pathology
 Long-term strategic commitment
• Phase I - Scanning and integration
• Phase II - Implementation for
subspecialty (NP, HP) service work
– Transient material (consults, blood smears)
– Autopsy pathology (less time sensitive)
• Phase III - Implementation for
general pediatric pathology diagnostic
work
Digital pathology project
 Phase I - Scanning and integration
 Hardware (ScanScope XT, 4TB DSR - fall 2007)
 Key goals:
• Train operator and develop workflow to
support scanning
• Begin scanning daily clinical volume for NP
division (S, CS, AN, CA, CF)
• Format Spectrum to reflect clinical reporting
• Support key academic collaborations:
– Virtual slide conferencing
– Tissue BioBanking
Digital pathology project
Mayor Nutter
 Phase I - Train operator and
develop workflow to support
scanning

“Taylor”
Medical photographer

Filing slides

Everything else …

3 months
• Aperio Handbook
–
–
Too technical
Needed the “Idiot’s Guide to
ScanScope”
• Susan Schmitt (x2)
–
–
Hands on training to setup
scanning runs
Observe our workflow and
adapt Spectrum to reflect it
• Aperio Seminars
• Technical support
–
Many calls
Digital pathology project
 Phase I - Scanning and integration
 Scanning workflow: 10% of slides needed to be returned to
lab or required additional handling prior to scanning
• Bubbles
• Misaligned coverslips
• Dirty / fingerprints
• Glued on labels
• Slides need to be dry (ScanScope XT)
Digital pathology project
 Phase I - Scanning and integration
 Key steps:
• Develop an appropriate data hierarchy
• Obtain and optimize HL7 feed
• Bar coding (won’t be discussing …)
Digital pathology project
 Phase I - Scanning and integration
 Key steps:
• Develop an appropriate data hierarchy
Digital pathology project
 Phase I - Scanning and integration
 Understanding workflow …
Digital pathology project
 Phase I - Scanning and integration
 Configuring Spectrum to reflect workflow …
• Case (me) = a surgical or autopsy specimen
• Case (Aperio) = highest level data element,
ie patient level information
QuickTime™ and a
decompressor
are needed to see this picture.
Digital pathology project
 Phase I - Scanning and integration
 Configuring Spectrum to reflect workflow …
QuickTime™ and a
decompressor
are needed to see this picture.
X
X
X
X
X
X
X
Digital pathology project
 Phase I - Scanning and integration
 Configuring Spectrum to reflect workflow …
QuickTime™ and a
decompressor
are needed to see this picture.
Digital pathology project
 Phase I - Scanning and integration
 Key steps:
• Develop an appropriate data hierarchy
• Obtain and optimize HL7 feed
Digital pathology project
 Phase I - Scanning and integration
Digital pathology project
Digital pathology project
 Phase I - Scanning and integration
 Whole slide imaging means scanning, and
scanning means storage
How much data do we
make?
 CHOP experience,
extrapolated
 Typical slide = 506MB
(JPEG compression)
 CHOP lab: One year =
55,374 slides
 = 27TB (1TB can hold
2,070 slides)
 X $2600 / TB =
$69,551/yr
 = $1.27 / slide storage
cost
 Maximum limit for DSR
DAS is 80TB = 3 years!!!
(assuming no growth in
volume)
How much data do we
make?
Source: UC Berkeley, School of Information Management and Systems
More Data Over the Last 3 Years
Than Previous 40,000 years
Combined
Introduction
Why Grid Storage System?
Before Grid
Site 1
App 1
Site 3
Site 2
App 2
App 3
After Grid
Site 1
...
App 4
App 10
App 1
Site 3
Site 2
App 2
App 3
App 4
...
App 10
Grid Storage Platform
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“Siloed” Traditional architecture:
• Difficult & expensive to administer
• Low utilization of hardware & storage
• Vulnerable to failure and downtime
• Bandwidth inefficient
• Block level replication
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“Virtualized” Grid infrastructure:
• Smaller, shared & more cost effective
storage environment
• Adaptive, self healing & self managing
• High availability & speed
• Enables infrastructure to be managed
independent of the application
Think Outside the PACS – Enterprise Medical Imaging Storage Solutions
IBM Healthcare & Life Sciences
Radiology
Digital Pathology
Cardiology
AcuoMed Image Manager
IBM GMAS Storage Manager
Configuration Architecture
Acuo Workflow
Cache
Radiology
Acuo DSG Server
PACS Server
Migration Server
ControlNode
StorageNode 1
Virtualized & Automated
Smart File System
StorageNode 2
Main
Datacenter
25
LAN WAN
/
Other
Fixed Content
Server
GMAS
HA Gateway
Administrative
Node
Aperio Spectrum
ArchiveNode
TSM Server
Tape
Library
Norristown Datacenter
The Children’s Hospital of Philadelphia
IBM Healthcare
IBM Medical GRID Archive for Digital Pathology
Transparent Actions Performed by the GRID
Aperio Spectrum
Application
Dual Read/Write

Each file is protected with digital fingerprint

Validated on access, replication and rebuild

Proactively verified in background

Corrupted files are quarantined and replaced
with a known good file

Grid is both content-aware and resource-aware
4 TB DAS
CIFS mount protocol
TCP/IP NAS attachment
GMAS
2 TB Cache in GMAS Gateway Node
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111000
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SATA
Disk
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Storage
Node #1
SATA
Disk
Storage
Node #2
The Children’s Hospital of Philadelphia
© 2008 IBM Corporation
Digital pathology project
 Phase I - Scanning and integration
 DICOM and digital pathology (whole slide images)
 Round hole (DICOM)
• Built around two assumptions:
– Storage architecture designed for working with relatively small file
sizes
– Designed for store-and-forward access
 Square peg (WSI)
• Designed to support pathologist workflow
– WSI data sizes tend to be quite large
– Designed for pathologist access patterns - pan, zoom, focus
Digital pathology project
 Enterprise storage
advantages
 Enterprise storage
disadvantages

Complex

New relationships are
required
 Potential for data

Cost (est. 10K/TB) for
enterprise storage
 Shared costs

Potential for data integration
(no silos) - are radiologists
really our friends?

Customization
 Scalable
 Secure
integration (no silos)
• DICOM
• Spectrum configured
to interface with
enterprise storage
Digital pathology project
 Lessons learned (CHOP)
 Clinical samples can
present challenges for
scanner technology
 Invest in training
• Initially 1 FTE -> 0.5
FTE when trained
 Know your LIS
 Understand your
workflow from a digital
POV
 Time (Q/A > Scanning)
 Use barcoding
 Data storage
• Compression &
Quality
• Enterprise storage
• DICOM
 Lessons learned (Aperio)
 Vendor cooperation is
important.
• Hijacking an
existing HL7
interface is hard
 Prototype the field
mapping.
• A lot of thought is
required to get
data from the LIS
mapped effectively
into the Spectrum
Plus hierarchy.
 Time. Working out all
the details takes time.
Acknowledgements
 Mark Wrenn
 Susan Schmitt
 John Banks
 Joanne Taylor
 Michelle Dennis
 CHOP NP Colleagues