REPLICATING A MODEL OF AVOIDANCES ACROSS CONTINENTS Bahattin Tolga Oztan and Douglas R. White.
Digital Pathology Across Continents
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Transcript of Digital Pathology Across Continents
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Digital Pathology Across Continents
Humphrey Gardner MD FCAPDirector, Oncology Translational LaboratoriesNovartis
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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
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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
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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
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Matching workflow to Aperio’s 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
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Multisite dataA major part of Aperio’s 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
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Basel Scanscope
Cambridge Scanscope
Scanscope controller PC
Scanscope controller PC
MS SQL serverApache Web server
SpectrumImage Server
phusca-s6659
Cambridge DSRL drive
Basel DSR
Client PC
Client PC
image meta data and svs file path
send request for image and serve image
Multisite data architecture in OTLOne solution of many: speedy and effective
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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
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Work for a pathologist on the goYou can’t pull out a microscope on the plane
Filling a hard drive using custom scripts
Portable drive: 320GB = 600-1000 slides = 40 trays
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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 > 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\images\2008-04-30\27445.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-04-30\27446.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-04-30\27447.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-04-30\27448.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-04-30\27449.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-09-02\30394.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-09-02\30391.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-05-16\27704.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\2008-05-16\27703.svs *
• copy \\phusca-s6003\inbox\usca-dev-axio-w20585\images\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 Pro…on 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