Digital Pathology Across Continents

1
Digital Pathology Across Continents

• Humphrey Gardner MD FCAP
• Director, Oncology Translational Laboratories
• Novartis

2
Why Digital pathology

• Image management
• Multisite access
• We still keep the slide as the image of record
• Aperio is unsurpassed for convenience
• Rapid recall for internal conferences
• Can usually pull real time data from a laptop on
  campus
• Image recovery on demand for presentations
• Speed
• Chromatic consistency
• Portability
• A key advantage of good images

3
Aperio Experience

• 10K scans per year on one instrument (last 3
  years)
• Overnight runs, typically, are reserved for array
  slides
• Failure rate/rescan rate
• 1 in 2008
• 5 prior to snapshot
• Favorable comparable to some other hardware
• Could still work to get seamless data transfer
  from login through Ventana and Aperio by barcode

4
Aperio Reliability

• Overall Downtime
• Breakdowns managed remotely 30 /year, typical
  downtime 2 hours each
• Breakdowns managed by site visit 2yr
• Overall, 6 days/ year unanticipated and 4 days
  per year for periodic maintenance and upgrades

5
Matching workflow to Aperios strengthsRegular
by day, TMA by night.

• Daytime
• Prescan 20-80 slides by snapshot 1 min/slide
• Review snapshots and correct a few minutes
• Scan 3 min/slide
• Round up gripper failures (a few a week) and
  rerun
• Nightime
• Prescan a few TMA slides, several minutes per
  slide
• Corrections, a few minutes
• Scan up to an hour a slide

6
Multisite dataA major part of Aperios value to
us

• Pathologists based in US and Europe
• Slides made in one place and read in another
• Remote conferencing for calibration
• Database architecture for maximum access
• Use of overnight file pulls for efficiency

7
Multisite data architecture in OTL One solution
of many speedy and effective
Scanscope controller PC
Basel DSR
Basel Scanscope
send request for image and serve image
Client PC
phusca-s6659
MS SQL server Apache Web server Spectrum Image
Server
image meta data and svs file path
Client PC
Cambridge Scanscope
Cambridge DSR L drive
Scanscope controller PC
8
Day to day usePathologists are many species

• Pathologist preference
• 1 uses glass only 2 use both one uses aperio
  only
• Getting to image lists
• Custom links in case spreadsheet
• Search function in Spectrum
• Desirable upgrades to search function, eg case
  sets

9
Work for a pathologist on the goYou cant pull
out a microscope on the plane

• Filling a hard drive using custom scripts
• Portable drive 320GB 600-1000 slides 40
  trays

10
How to pull a slide list to goExample
generalizable to any annotation scheme

• The method via Microsoft SQL server on host
  machine
• SELECT im.ImageId, im.CompressedFileLocation,
  im.BarcodeId, s.BlockId, st.ShortName, im.CaseId,
  c.ExternalId, prj.Name
• FROM Image im
• LEFT JOIN Slide s ON (im.ParentId s.Id AND
  im.ParentTable 'Slide')
• LEFT JOIN Stain st ON (s.StainId st.Id)
• LEFT JOIN Specimen sp ON (s.ParentId sp.Id AND
  s.ParentTable 'Specimen')
• LEFT JOIN Case c ON (sp.ParentId c.Id AND
  sp.ParentTable 'Case')
• LEFT JOIN Project prj ON (sp.ParentId prj.Id
  AND sp.ParentTable 'Project')
• WHERE
• im.ImageId gt 15000 AND
• im.BarcodeId LIKE '164' OR im.BarcodeId LIKE
  '244' OR im.BarcodeId LIKE '212' OR
  im.BarcodeId LIKE '211' OR im.BarcodeId LIKE
  '264' OR im.BarcodeId LIKE '792' OR
  im.BarcodeId LIKE '272' OR im.BarcodeId LIKE
  '273' OR im.BarcodeId LIKE '707' OR
  im.BarcodeId LIKE '174' OR im.BarcodeId LIKE
  '226' OR im.BarcodeId LIKE '276' OR
  im.BarcodeId LIKE '274' OR im.BarcodeId LIKE
  '189' OR im.BarcodeId LIKE '277' OR
  im.BarcodeId LIKE '788' OR im.BarcodeId LIKE
  '789' OR
• The first number 15000 is simply to speed up the
  search by restricting the domain to the image ids
  most likely to contain your project.
• The numbers in the '' are the unique parts of
  the TBG ids.

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How to pull a slide list to goCreate a batch
file from the sql query

• Create a batch file
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-04-30\27445.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-04-30\27446.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-04-30\27447.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-04-30\27448.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-04-30\27449.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-09-02\30394.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-09-02\30391.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-05-16\27704.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-05-16\27703.svs
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\ima
  ges\2008-05-16\27695.svs ....
• Place batch file in target drive, run
• and wait.

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How to pull slides to goSvs files moved to loval
hard drive
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How link svs files to cases Create hyperlinks to
local files in spreadsheet
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Case pulled upAnd diagnose/score etc
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And you can work anywhere
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Prospects for the futureSuggestions for features

• Live tools at hand, eg Genie Proon the way?
• Markup masks which carry over from level to
  level/stain to stain?
• Data management/data capture for pathologists
  with portable and workstation synchronization?
• Touch screen platforms

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The desktop platform
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The iPerio