Implementation of Subspecialty Whole Slide Image Teaching Sets

for Residency Education

Bryan Dangott, M.D.

University of UtahHematopathology 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 Centerwww.upmc.com

29 Western PA Counties19 Hospitals40 Cancer Center Locations

Pathology Centers of Excellence (COEs) at UPMC

UPMC PresbyterianDermatopathology

ENT/Thyroid PathologyGastrointestinal Pathology

HematopathologyNeuropathology

Thoracic/Mediastinal PathologyTransplant Pathology

UPMC ShadysidePathology Informatics

Genitourinary PathologyBone/Soft Tissue/Melanoma

Pathology

UPMC Magee-Womens HospitalBreast Pathology

Gynecologic CytopathologyObstetric/Gynecologic Pathology

UPMC Childrens HospitalPediatric 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

• 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

• 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 SubspecialtyUnknowns 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 SubspecialtyUnknowns 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

Ratio21.67 13.5 39.3 23.4 14.1

CapabilitiesUnknowns Head and Neck Genitourinary Thoracic Hemepath

Whole Slide Links 8 8 8 5 Unlimited

Ancillary Image/File Links 3 10 Unlimited

Free Text Fields 1 7 7 7 14

Other Data Fields 12

Diagnosis X X X X X

Discussion X X X X

ICD-O Codes 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

• 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 NamingLinkType_Name Link_Abbv

cytogenetics CYT

flow FLO

molecular MOL

other OTH

reference REF

static slide image SSI

whole slide WSI

Slide_Type Slide_Abbv

aspirate ASP

clot CLT

core CBx

core touch prep CTP

lymph node LNlymph node touch prep LNTP

other OTH

peripheral blood PB

soft tissue ST

Special Features

Unknowns Head and Neck Genitourinary Thoracic Hemepath

Testing Interface X X 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

– 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