Implementation of Subspecialty
Whole Slide Image Teaching Sets
for Residency Education
Bryan Dangott, M.D.
University of Utah
Hematopathology Fellow
The UPMC Health System
• Diversified environment ( academic hospitals,
community hospitals)
• 19 hospitals with another 18 affiliations
• 2 million + outpatient visits per year
University of Pittsburgh Medical Center
www.upmc.com
29 Western PA Counties
19 Hospitals
40 Cancer Center Locations
Pathology Centers of Excellence (COEs) at UPMC
UPMC Presbyterian
Dermatopathology
ENT/Thyroid Pathology
Gastrointestinal Pathology
Hematopathology
Neuropathology
Thoracic/Mediastinal Pathology
Transplant Pathology
UPMC Magee-Womens Hospital
Breast Pathology
Gynecologic Cytopathology
Obstetric/Gynecologic Pathology
UPMC Shadyside
Pathology Informatics
Genitourinary Pathology
Bone/Soft Tissue/Melanoma
Pathology
UPMC Childrens Hospital
Pediatric Pathology
Background
• UPMC is a multi-site institution
– Residents rotate at different facilities
• Problems with glass sets
– Only available to one person at any given time
– Missing slides
– Broken
– Disorganized
– Degradation (cover slip adhesion, stain quality)
Digital Teaching Material
• AP Teaching Site
(http://path.upmc.edu/cases/index.html)
• 700 cases
– Prepared by the residents
– Gross images, microscopic snap shots
– Comprehensive discussions
TELE-EDUCATION: Online Conferences
Creating Whole Slide Image Sets
• Scanning began in 2005 with GU
• Over 2900 whole slide images
– General Unknowns collection
– Genitourinary
– Head and Neck
– Thoracic
– Hematopathology
• Under Development
– GI, Bone and Soft tissue, Cytology
Infrastructure
• Storage space
– Storage Area Network for image files
• 20 terabytes.
– Supplemental file storage space.
– Web hosting space.
Servers
• Image server
– Aperio ImageServer
• Webscope, Flash viewer
• ImageScope, Desktop Application
– Zeiss, Java viewer
• Web servers
– Apache
– IIS
– ColdFusion
Database Backend
• Oracle
– Unknowns
– GU
– Thoracic
– Head and Neck
• Microsoft Access
– Hemepath
– Testing Interface
Front End Language
• ColdFusion
– Database searching
– Page presentation and formatting
• Javascript
– Used to selectively display portions of the page
– Selects the viewer to launch based on link
Basic Procedures
• Gather data
– Clinical Information
– Diagnostic Material
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•
•
•
Slides
Radiology
Gross Images
Flow, Cytogenetics, Molecular data
• De-identify data
Scan Hardware
•
•
•
•
Aperio Scanscope XT (120 slide loader)
Aperio Scanscope CS (5 slide loader)
Zeiss Mirax MIDI (12 slide loader)
Hamamatsu (210 slide loader)
Scanning Challenges
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•
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Tape style cover slips
Scratched / damaged slides
Uneven tissue sections
Very thin sections of fatty tissue.
Peripheral smears / Aspirate smears
Cytology specimens
Scanning Challenges
• Cytology and hematopathology
– Focus points
– Depth of field
• Scan time
– 40x hemepath
• 30 bone marrow aspirate slides (~24 hrs)
• Batch scanning
Personnel
•
•
•
•
•
Web Developer – Thomas Harper
Slide Scanning – Jon Duboy
Server Administration – Ishtiaque Ahmed
Project Coordinator – Doris Dayoub
Project Oversight – Anil Parwani, MD, PhD
Implementation by Subspecialty
Unknowns
Head and Neck
Genitourinary
Thoracic
Hemepath
Database
Oracle
Oracle
Oracle
Oracle
Access
Front End
ColdFusion
ColdFusion
ColdFusion
ColdFusion
ColdFusion
ImageServer
Aperio / Zeiss
Aperio
Aperio
Aperio
Aperio
Data Entry
Web Interface
Web Interface
Web Interface
Web Interface
Direct Entry
Updates
Weekly
One Time Batch
Continuous
Continuous
Continuous
Clinical History
Limited
Moderate
Moderate
Extensive
Extensive
Stats by Subspecialty
Unknowns
Head and
Neck
Genitourinary
Thoracic
Hemepath
Total
Total Cases
340
130
300
806
173
1,749
Total Slides
400
158
340
983
1083
2,964
Slides per Case
1.18
1.22
1.13
1.22
6.26
Uncompressed
Total Data (GB)
2,122
897
3,141
6,266
20,450
32,876
Compressed
Data /Storage
Space (GB)
98
66.2
79.9
282
1520
2,046
Overall
Compression
Ratio
21.67
13.5
39.3
23.4
14.1
Capabilities
Unknowns Head and Neck
Whole Slide Links
8
Ancillary Image/File Links
3
Free Text Fields
1
8
7
Genitourinary
Thoracic
Hemepath
8
5
Unlimited
10
Unlimited
7
14
7
Other Data Fields
12
Diagnosis
X
X
X
X
Discussion
X
X
X
X
ICD-O Codes
X
X
X
X
X
Challenges
• Managing images, web page code, clinical
data sources.
• Customization of individual sites
– Each of the subspecialties has different needs
From Template to Flexible
• Hemepath vision
– More slides
– Higher magnification (40x minimum)
– More slide area (smears)
– More data types
Two Projects at a Time
• Hemepath teaching set was built
simultaneously with a testing interface.
– Required architecture flexibility
– Required more involvement with the developers
Hemepath Data Types
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•
•
•
•
•
CBC
Differential counts
Molecular data
Immunophenotyping
Flow Cytometry
Cytogenetics
Hemepath Database Design
• Access
– Up front design required a lot of interaction
– Hemepath wanted to manage the database
• This eliminated building a web interface for data entry
– Allowed additional development to enhance data
entry
Work Flow Improvements
• Batch data download from APLIS
– Tab delimited text file
• Batch data processing
– Vbscript
– Notepad++ vs Excel
• Data Entry
– Copy and paste data fields
– Link integration
Hemepath File Naming
• File naming conventions
–CASE# - TYPEID - FREETEXT
– WSI
• 001-CBX-HE
– Supplemental Files
• 001-FLO-CD2,CD3,CD4,CD8
Hemepath File Naming
Slide_Type
Slide_Abbv
aspirate
ASP
clot
CLT
core
core touch prep
cytogenetics
CYT
CBx
flow
FLO
CTP
molecular
MOL
other
OTH
reference
REF
static slide image
SSI
whole slide
WSI
lymph node
LN
lymph node touch
prep
LNTP
other
OTH
peripheral blood PB
soft tissue
LinkType_Name Link_Abbv
ST
Special Features
Unknowns Head and Neck
Testing Interface
X
Genitourinary
X
Thoracic
Hemepath
X
Auto Import WSI Links
X
Auto Import Ancillary
Files
X
Link Sorting
X
Naming Convention
X
Multiplatform Scans
X
Testing Interface
Future Goals
• Cross site searching
• Expansion of the testing interface to other
sites
• Further development of other subspecialties
Credits
•
Contributors
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–
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Jon Duboy
Li Li
Joseph Sirintrapun
Gaurav Sharma
Doris Dayoub
Ishtiaque Ahmed
Thomas Harper
Christine Garcia
Fiona Craig
E. Leon Barnes
Samuel Yousem
– Project Oversight
– Anil Parwani, Liron Pantanowitz, Trevor Macpherson