Digital Pathology Across Continents

Digital Pathology Across Continents

Humphrey Gardner MD FCAPDirector, Oncology Translational LaboratoriesNovartis

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

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

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

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

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

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

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

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

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.

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\2008-05-16\27695.svs *....

Place batch file in target drive, run• and wait….

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

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

Case pulled upAnd diagnose/score etc

And you can work anywhere

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……

The desktop platform

The iPerio

Documents

Digital Pathology Across Continents