Clinical Implementation of WSI

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Clinical Implementation of WSI

• Jonhan Ho, MD
• Pathology Informatics Fellow
• hoj_at_upmc.edu

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Disclosure Page

• This work was partially supported by funding from
  the U.S. Air Force administered by the U.S. Army
  Medical Research Acquisition Activity (USAMRAA),
  820 Chandler Street, Fort Detrick MD 21702-5014,
  Contract No. DAMD17-03-2-0017. The content of
  the information does not necessarily reflect the
  position or policy of the U.S. Government and no
  official endorsement should be inferred.
• I have no conflicts of interest, financial or
  otherwise with any of the vendors mentioned here

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Why are we implementing a clinical whole slide
image delivery system?
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Whole slide image clinical trials

• Whole slide images are ready for clinical use
• Clinical trials for validation
• Quality assurance
• Primary diagnosis
• Immunohistochemistry
• 3 pathologists
• 25 full cases, same workflow (3-24 slides)
• 200-500 whole slide images per study
• Project team
• Pathologists
• Project manager
• Imaging tech
• QA staff
• Evaluation team
• Significant logistical effort

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Before
Vendor machine
WSI Robot
WSI Presentation Server
Client Pathologist
WSI DB
WSI Storage
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Goal

• To create a whole slide image delivery system for
  pathologists for clinical sign-out
  responsibilities
• requires AP LIS integration, but workflow will
  reside in the AP LIS

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Before
Vendor machine
WSI Robot
WSI Presentation Server
Client Pathologist
WSI DB
WSI Storage
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After
X
WSI Server
WSI Robot
Pathology Informatics WSI Solution
WSI DB
X
X
WSI Storage
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Roles the system should play

• Microscope
• Slide
• Slide tray
• Medical technologist
• Deliver the right slides to the right pathologist
• Slide police
• Slide Repository

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Features

• Understand/integrate with the AP LIS
  infrastructure
• Support multiple vendors
• DICOM
• HIPAA
• DoD Information Technology Security Certification
  and Accreditation (DITSCAP)
• The usual
• Reliable
• Available
• Redundant
• Disaster recovery

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Our environments

• Pathology
• Development

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Pathology environment

• AP LIS (CoPath)
• Centers of Excellence (subspecialty signout)
• 4 imagers
• Aperio Scanscope
• Trestle - Interscope
• Trestle Robotic microscope
• Nikon Coolscope

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Development environment

• Pathology informatics
• CoPath development
• Imaging
• Information Services Department
• Radiology Informatics
• Creators of Stentor
• Sharing code
• Common backoffice and middleware architecture

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Nuts and Bolts

• Infrastructure
• Workflow integration

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Infrastructure
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What is a whole slide image?
Size 100,000x50,000 pixels Tiff 13.5 gb JP2
290 mb
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Image Capture
Barcode Thumbnail
WSI Robot
Base image
Pyramidal image
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Before
Client Pathologist
WSI Robot 1
Vendor Server 1
Client Pathologist
WSI Robot 2
Vendor Server 2
Client Pathologist
WSI Robot 3
Vendor Server 3
Client Pathologist
WSI Robot 4
Vendor Server 4
Client Pathologist
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After
CoPath
Client Pathologist
WSI Robot 1
Client Pathologist
WSI Robot 2
WSI Image Import Server
WSI Image Presentation Server
metadata
Client Pathologist
WSI Robot 3
Client Pathologist
Process 1
Process 2
WSI Robot 4
UPMC Domain Server
Client Pathologist
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CoPath
Process 1
Barcode elements
Patient/specimen elements
WSI Image Import Server
To Process 2
metadata
From WSI Robot
Looks for new whole slide images Pulls new
images Decodes the 2D barcode Verifies
slide/accession info with APLIS Fetches
specimen/patient info from APLIS Constructs XML
metadata wrapper Reconstructs file Sends file to
WSI Image server
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Unique slide problem

• Each produced glass slide is unique
• Each whole slide image corresponds to only 1
  glass slide
• The AP LIS does not enforce identity of each
  slide
• Inability to ensure that each whole slide image
  can be traced to a specific glass slide

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Metadata wrapper

• UID 1.2.840.152371.157.229.222.79.20050706.121311
  .30.1
• XML
• Patient level (last name, first name, med rec
  num, sex, birthdate)
• Accession level (Accession number, date, time,
  pathologist)
• Study level (Modality, date, time, manufacturer,
  IP address)
• Series level (whole slide image)
• Part
• Block
• Slide number
• Stain
• Components and descriptions (thumbnail, label,
  base image)
• Image level (describes each component)

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Example of metadata wrapper

• ltSeriesLevelgt
• A Series is effectively one slide imaged one
  time.
• A Series has multiple images usually in a TIFF
  container
• Some images are "real" optical images, others
  are sampled as part of a Pyramid
• ltS.1gt
• Series Identification
• ltUIDgt1.2.840.152371.157.229.221.31.200503
  22.112447.30.1lt/UIDgt
• ltPartNumbergt1lt/PartNumbergt
• ltBlockNumbergtAlt/BlockNumbergt
• ltSlideNumbergt1lt/SlideNumbergt
• ltPartDescriptiongtColon Resectionlt/PartDescriptio
  ngt
• ltBlockDescriptiongtProximal
  Marginlt/BlockDescriptiongt
• ltSeriesBeginTimegt143456lt/SeriesBeginTimegt
• ltSeriesEndTimegt144056lt/SeriesEndTimegt
• ltSeriesFileDescriptiongtWSI-TIFFlt/SeriesFileDescr
  iptiongt
• ltPixelSizegtN/Alt/PixelSizegt
• ltSeriesCommentgtNAlt/SeriesCommentgt
• ltPathsgt
• ltP.1gtC\Image Quality\Images\Focus
  Measure\Yukako Imageslt/P.1gt

• ltDICOMMetaTagsgt
• ltx00020002gt1.2.840.10008.5.1.4.1.1.7lt/x00020002gt
• ltx00020003gt1.2.840.152371.157.229.221.
  31.20050322.112447.30lt/x00020003gt
• ltx00020010gt1.2.840.10008.1.2.4.50lt/x00
  020010gt
• ltx00020016gtSimpleDICOMWraplt/x00020016gt
  
• ltx00080005gtISO_IR 100lt/x00080005gtlt!--
  specific character set --gt
• ltx00080008gtORIGINAL\\PRIMARYlt/x0008000
  8gtlt!-- Image type --gt
• ltx00080016gt1.2.840.10008.5.1.4.1.1.7lt/
  x00080016gtlt!-- SOP class UID --gt
• ltx00080018gt1.2.840.152371.157.229.221.
  31.20050322.112447.30.1.1lt/x00080018gtlt!-- SOP
  instance UID --gt
• ltx00080020gt20050322lt/x00080020gtlt!--
  Study Date --gt
• ltx00080023gt20050322lt/x00080023gtlt!--
  Content Date --gt
• ltx00080030gt112447lt/x00080030gtlt!--
  Study Time --gt
• ltx00080033gt112447lt/x00080033gtlt!--
  Content Time --gt
• ltx00080050gt1234lt/x00080050gtlt!--
  Accession Number --gt
• ltx00080060gtOTlt/x00080060gtlt!--
  Modality --gt
• ltx00080070gtOlympuslt/x00080070gtlt!--
  Manufacturer --gt
• ltx00080080gtUPMC Presbyterianlt/x0008008
  0gtlt!-- Institution Name --gt
• ltx00080090gtDr. John
  Kirkwoodlt/x00080090gtlt!-- Referring Physician's
  Name --gt
• ltx00081010gtOlympus CC12lt/x00081010gtlt!-
  - Station Name --gt

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Process 2
Client Pathologist
Process 2
WSI Image Import Server
WSI Image Presentation Server
Client Pathologist
metadata
Client Pathologist
CoPath

• Process 2
• Receives the image
• Parses metadata wrapper
• Writes database entry
• Stores the image
• Fetches images context
• Serves the image

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Software Framework
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Software Framework
UPMC Domain Server
WSI Robot
Client Pathologist
CoPath
Middleware (web services)
WSI Import Server
WSI Presentation Server
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Software Framework, Process 1
WSI Robot
Checks for new file
Pulls new file
CoPath
Middleware (web services)
Oracle/CoPath gateway
Recognizes file format Decodes barcode Constructs
metadata wrapper
Patient and Specimen metadata For wrapper
Sends whole slide image, CoPath data, components
WSI Import Server
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Software Framework, Process 2
UPMC Domain Server Users group
Checks permissions
Allows access
Client Pathologist
Clicks on link Sends credentials Sends link info
CoPath
Middleware (web services)
Sends link info
Receives context info
Sends image, context
Sends link info
Receives list of images
WSI Presentation Server
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UPMC Domain Server Users group
WSI Security Schema
User credentials
LDAP/NT authentication Group membership
restriction
Client Pathologist
CoPath Worklists
Middleware Security module
Oracle/CoPath gateway
User credentials
LDAP/NT authentication
Oracle authentication IP restriction
Server credentials
LDAP/NT authentication
WSI Server
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Pathologist Workflow
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Workflow Integration

• Designed for high volume evaluation of whole
  slide images
• Presents whole slide image in its context
• Specimen, slide info, other available slides
• Speed
• Only one area transferred at a time
• Intuitive
• Not extra work

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GUI

• Browser based
• Thin client with the look and feel of a rich fat
  client.
• ActiveX component
• .NET 2.0

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Final thoughts

• The real world
• Multiple vendors
• Multiple information systems to interface with
• Difficulties we encountered
• Unique slide problem
• Lack of standard for modality output format
• Lack of DICOM standards for whole slide images