Wednesday

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Integrating whole slide images into clinical
workflow

• Jonhan Ho, MD
• Dermatopathology Fellow, UPMC

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Purpose

• How do we integrate whole slide images into a
  pathologists workflow?

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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

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Diagram of pathology workflow
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Pathologists 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
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Pathologists workflow with WSI
Inflow
Paperwork (APLIS) Pt. demographics Surgeon Clinica
l history Specimen information Gross
description Previous accessions Accession number
Outflow
Final Report
Microscope (WSI) Objective
Slide (APLIS/WSI) Accession number Part Block Stai
n Slide description Slide preview Diagnostic
visual information
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Sources of information using WSI
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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

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Manual WSI implementationSteps required to view
WSI (not vendor specific)

• Open application
• Browse to proper folder
• Browse to proper file
• Open the image

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A working prototype of WSI clinical workflow
integration

• The Back End

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Automatic WSI Implementation

• Microsoft .NET 2.0
• Microsoft IIS 6.0
• SQL Server 2005
• AJAX (Asynchronous Javascript and XML)

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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

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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 HE
• Slide Label FS (frozen section)
• Query scanner for decoded barcode information
• Query the APLIS for a match
• A match exists, proceed

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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

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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
• ltUIDgt1.2.840.152371.157.229.221.31.20050322.112447
  .332.1
• Wrap metadata as XML wrapper around image
• Writes database entry
• Includes all metadata
• Move the image
• Repeat for next image

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A working prototype of WSI clinical workflow
integration

• The Front End

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Human computer interaction

• How useful is an application?
• How intuitive is the software?
• Fosters user loyalty
• iPod
• Stentor

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Workflow integration
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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

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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

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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)