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Implementation of Subspecialty Whole Slide Image Teaching Sets for Residency Education Bryan Dangott, M.D. University of Utah Hematopathology Fellow.

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Presentation on theme: "Implementation of Subspecialty Whole Slide Image Teaching Sets for Residency Education Bryan Dangott, M.D. University of Utah Hematopathology Fellow."— Presentation transcript:

1 Implementation of Subspecialty Whole Slide Image Teaching Sets for Residency Education Bryan Dangott, M.D. University of Utah Hematopathology Fellow

2 The UPMC Health System Diversified environment ( academic hospitals, community hospitals) 19 hospitals with another 18 affiliations 2 million + outpatient visits per year

3 University of Pittsburgh Medical Center 29 Western PA Counties 19 Hospitals 40 Cancer Center Locations

4 Pathology Centers of Excellence (COEs) at UPMC UPMC Presbyterian Dermatopathology ENT/Thyroid Pathology Gastrointestinal Pathology Hematopathology Neuropathology Thoracic/Mediastinal Pathology Transplant Pathology UPMC Shadyside Pathology Informatics Genitourinary Pathology Bone/Soft Tissue/Melanoma Pathology UPMC Magee-Womens Hospital Breast Pathology Gynecologic Cytopathology Obstetric/Gynecologic Pathology UPMC Childrens Hospital Pediatric Pathology

5 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)

6 Digital Teaching Material AP Teaching Site ( 700 cases – Prepared by the residents – Gross images, microscopic snap shots – Comprehensive discussions

7 TELE-EDUCATION: Online Conferences

8 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

9 Infrastructure Storage space – Storage Area Network for image files 20 terabytes. – Supplemental file storage space. – Web hosting space.

10 Servers Image server – Aperio ImageServer Webscope, Flash viewer ImageScope, Desktop Application – Zeiss, Java viewer Web servers – Apache – IIS – ColdFusion

11 Database Backend Oracle – Unknowns – GU – Thoracic – Head and Neck Microsoft Access – Hemepath – Testing Interface

12 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

13 Basic Procedures Gather data – Clinical Information – Diagnostic Material Slides Radiology Gross Images Flow, Cytogenetics, Molecular data De-identify data

14 Scan Hardware Aperio Scanscope XT (120 slide loader) Aperio Scanscope CS (5 slide loader) Zeiss Mirax MIDI (12 slide loader) Hamamatsu (210 slide loader)

15 Scanning Challenges Tape style cover slips Scratched / damaged slides Uneven tissue sections Very thin sections of fatty tissue. Peripheral smears / Aspirate smears Cytology specimens

16 Scanning Challenges Cytology and hematopathology – Focus points – Depth of field Scan time – 40x hemepath 30 bone marrow aspirate slides (~24 hrs) Batch scanning

17 Personnel Web Developer – Thomas Harper Slide Scanning – Jon Duboy Server Administration – Ishtiaque Ahmed Project Coordinator – Doris Dayoub Project Oversight – Anil Parwani, MD, PhD

18 Implementation by Subspecialty UnknownsHead and NeckGenitourinaryThoracicHemepath DatabaseOracle Access Front EndColdFusion ImageServerAperio / ZeissAperio Data EntryWeb Interface Direct Entry UpdatesWeeklyOne Time BatchContinuous Clinical HistoryLimitedModerate Extensive







25 Stats by Subspecialty Unknowns Head and Neck GenitourinaryThoracicHemepathTotal Total Cases3401303008061731,749 Total Slides40015834098310832,964 Slides per Case1. Uncompressed Total Data (GB) 2,1228973,1416,26620,45032,876 Compressed Data /Storage Space (GB) 9866.279.928215202,046 Overall Compression Ratio 21.6713.539.323.414.1

26 Capabilities UnknownsHead and NeckGenitourinaryThoracicHemepath Whole Slide Links8885Unlimited Ancillary Image/File Links310Unlimited Free Text Fields177714 Other Data Fields12 DiagnosisXXXXX DiscussionXXXX ICD-O CodesXXXX


28 Challenges Managing images, web page code, clinical data sources. Customization of individual sites – Each of the subspecialties has different needs

29 From Template to Flexible Hemepath vision – More slides – Higher magnification (40x minimum) – More slide area (smears) – More data types

30 Two Projects at a Time Hemepath teaching set was built simultaneously with a testing interface. – Required architecture flexibility – Required more involvement with the developers

31 Hemepath Data Types CBC Differential counts Molecular data Immunophenotyping Flow Cytometry Cytogenetics

32 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

33 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

34 Hemepath File Naming File naming conventions – CASE# - TYPEID - FREETEXT – WSI 001-CBX-HE – Supplemental Files 001-FLO-CD2,CD3,CD4,CD8

35 Hemepath File Naming LinkType_NameLink_Abbv cytogeneticsCYT flowFLO molecularMOL otherOTH referenceREF static slide imageSSI whole slideWSI Slide_TypeSlide_Abbv aspirateASP clotCLT coreCBx core touch prepCTP lymph nodeLN lymph node touch prepLNTP otherOTH peripheral bloodPB soft tissueST






41 Special Features UnknownsHead and NeckGenitourinaryThoracicHemepath Testing InterfaceXXX Auto Import WSI LinksX Auto Import Ancillary Files X Link SortingX Naming ConventionX Multiplatform ScansX

42 Testing Interface











53 Future Goals Cross site searching Expansion of the testing interface to other sites Further development of other subspecialties

54 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

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