1 / 18

Digital Pathology Across Continents

Digital Pathology Across Continents. Humphrey Gardner MD FCAP Director, Oncology Translational Laboratories Novartis. Why Digital pathology. Image management Multisite access We still keep the slide as the image of record Aperio is unsurpassed for convenience

evita
Download Presentation

Digital Pathology Across Continents

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  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 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

  6. 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

  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 can’t 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 > 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.

  11. 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….

  12. How to pull slides to goSvs files moved to loval hard drive

  13. How link svs files to cases Create hyperlinks to local files in spreadsheet

  14. Case pulled upAnd diagnose/score etc

  15. And you can work anywhere

  16. 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……

  17. The desktop platform

  18. The iPerio

More Related