Integrating whole slide images into clinical workflow

1. Integrating whole slide images into clinical workflow Jonhan Ho, MD Dermatopathology Fellow, UPMC APIII 2006 Vancouver Breakout Session A2

2. Purpose How do we integrate whole slide images into a pathologist’s workflow? APIII 2006 Vancouver Breakout Session A2

3. Objectives • Present an overview of current pathology workflow • Discuss the steps needed to fit a scanner and its output into clinical anatomic pathology workflow • Present a working example of integrated clinical WSI APIII 2006 Vancouver Breakout Session A2

4. Diagram of pathology workflow APIII 2006 Vancouver Breakout Session A2

5. Pathologist’s workflow Inflow Paperwork Pt. demographics Surgeon Clinical history Specimen information Gross description Previous accessions Accession number Outflow Final Report Microscope Objective Slide Accession number Part Block Stain Slide description Slide preview Diagnostic visual information APIII 2006 Vancouver Breakout Session A2

6. Pathologist’s workflow with WSI Inflow Paperwork (APLIS) Pt. demographics Surgeon Clinical history Specimen information Gross description Previous accessions Accession number Outflow Final Report Microscope (WSI) Objective Slide (APLIS/WSI) Accession number Part Block Stain Slide description Slide preview Diagnostic visual information APIII 2006 Vancouver Breakout Session A2

7. Sources of information using WSI APIII 2006 Vancouver Breakout Session A2

8. Manual WSI implementationSteps required to import WSI (not vendor specific) • Scan the slide • Open the image • Look at the label image • Open the APLIS • Find the case • Match up part/block/stain/instance of slide • Rename the image • Move the image • Repeat for each image APIII 2006 Vancouver Breakout Session A2

9. Manual WSI implementationSteps required to view WSI (not vendor specific) • Open application • Browse to proper folder • Browse to proper file • Open the image APIII 2006 Vancouver Breakout Session A2

10. A working prototype of WSI clinical workflow integration The “Back End” APIII 2006 Vancouver Breakout Session A2

11. Automatic WSI Implementation • Microsoft .NET 2.0 • Microsoft IIS 6.0 • SQL Server 2005 • AJAX (Asynchronous Javascript and XML) APIII 2006 Vancouver Breakout Session A2

12. Automatic WSI implementationSteps required to import WSI • Scan the slides • Import the images • Read/decode the barcode • Query the APLIS for a match • Query the APLIS for patient metadata • Query the APLIS for specimen metadata • Query the scanner for image metadata • Wrap metadata as XML wrapper around image • Writes WSI database entry • Move the image • Rename the image to Unique ID • Repeat for next image APIII 2006 Vancouver Breakout Session A2

13. Automatic WSI implementationSteps required to import WSI • Scan the slides Web service monitors folder for new images • Import the images • Read/decode the barcode (2D, Datamatrix) Accession number – SYS04-123456 Part – 1 Block – A Stain – H&E Slide Label – “FS” (frozen section) Query scanner for decoded barcode information • Query the APLIS for a match “A match exists, proceed” APIII 2006 Vancouver Breakout Session A2

14. Automatic WSI implementationSteps required to import WSI • Query the APLIS for patient metadata Last name, first name Gender Social security number Medical record number Birthdate • Query the APLIS for specimen metadata Ordering physician Clinical history Accession number, date/time Assigned pathologist Part, block, stain slide description Part description APIII 2006 Vancouver Breakout Session A2

15. Automatic WSI implementationSteps required to import WSI • Query the scanner for image metadata Study/series dates/times Image info (pixels, h/w, compression, x-y, etc.) Scanner info (make, model, serial number, IP address, spatial sampling, lens, etc.) And many others… • Rename the image to Unique ID <UID>1.2.840.152371.157.229.221.31.20050322.112447.332.1 • Wrap metadata as XML wrapper around image • Writes database entry Includes all metadata • Move the image • Repeat for next image APIII 2006 Vancouver Breakout Session A2

16. A working prototype of WSI clinical workflow integration The “Front End” APIII 2006 Vancouver Breakout Session A2

17. Human computer interaction • How ‘useful’ is an application? • How intuitive is the software? • Fosters user loyalty • iPod • Stentor APIII 2006 Vancouver Breakout Session A2

18. Workflow integration APIII 2006 Vancouver Breakout Session A2

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22. Pathologist scanning behavior • Highly repetitive actions • Slow panning • Changing objectives • Concentration is maintained on the subject at hand • Usually is in center of optical field APIII 2006 Vancouver Breakout Session A2

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26. Issues • Lack of a ‘unique slide identifier’ • Requires a change to the APLIS (additional fields and relationships) • Lack of barcode support • Restricts large scale use • ‘Moving target’ • File format changes • Software updates APIII 2006 Vancouver Breakout Session A2

27. Moving forward • Establishing standards • Known, predictable output format • DICOM WG26 • LDIP • Investigating ‘workflow accelerators’ • Offer pathologists better ways to examine tissue • Workflow for pathologists and for histology already exists, software must accommodate this workflow (and not vice versa) APIII 2006 Vancouver Breakout Session A2