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High Volume Slide Scanning Architecture and Applications

Dr. André Huisman Department of pathology UMC Utrecht, The Netherlands a.huisman-4@umcutrecht.nl. High Volume Slide Scanning Architecture and Applications. Department of pathology UMCU. UMC Utrecht >1,000 beds >10,000 employees Department of pathology: 20.000 surgical pathology cases

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High Volume Slide Scanning Architecture and Applications

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  1. Dr. André Huisman Department of pathology UMC Utrecht, The Netherlands a.huisman-4@umcutrecht.nl High Volume Slide ScanningArchitecture and Applications

  2. Department of pathology UMCU • UMC Utrecht • >1,000 beds • >10,000 employees • Department of pathology: • 20.000 surgical pathology cases • 156.000 glass slides (histology, cytology, IHC) • 15 pathologists, 10 residents

  3. Digital pathology - advantages • Digital Archiving • Instant access from multiple locations by multiple people • No searching for slides • Constant quality • Telepathology • Consultations, revisions and panels • Education • Research • Automated image processing

  4. Project background Clinico pathological conferences: • 900 meetings every year • No (multi headed) microscope needed • Quicker preparation of meetings • No retrieval of glass slides from archive

  5. Aim (2007) Digitize all diagnostic slides we have (prospectively)

  6. Challenges • Scanners • Image size: up to 1 GB x 500 slides per day • No existing infrastructure present for storage of this size at our facility • Image presentation and software integration • Logistics

  7. Scanners • Different manufacturers: • Speed • Focusing method • Acquisition technique • z-stack acquisition • File format policy • Application integration • 2007: 3D Histech (Zeiss), Aperio, Hamamatsu, Olympus (US: Dmetrix, BioImagene) • 2010: Leica, Menarini, Philips, Omnyx, BioImagene

  8. Scanning logistics • 3 Aperio XT scanners (120 slides per scanner) • Morgue assistants • Mark slides after scanning • 6 Hours per run at 20x magnification (~3 minutes/scan)

  9. Storage – HSM • HSM = Hierarchical Storage Management • Sun Microsystems (Oracle) • 6 TB available on very fast fibre channel disks • 120 TB available on tape (750 GB each) • 2 Tape drives • Completely transparent archiving and retrieval (robot) • Access time from tape: 1 - 3 minutes

  10. Linking systems • 1D Barcodes • U-DPS: reporting system • LMS: Laboratory Management System • Spectrum: Aperio’s image management solution • Storage system • Own development: integration layer

  11. Scanner workflow Other images (e.g. macro) Scanning Order form scanner Database LIS Image / Data server Speech recognition U-DPS HSM Storage 6 TB fast disks 120 TB on tape pathology users

  12. Validation • Aim: validate diagnostic use of digital slides • Method: reevaluate diagnosis with same pathologist on scanned slide after washout period (1 year) for several organs • Gold standard: original diagnosis using ‘traditional’ microscopy

  13. Preliminary results validation • GI tract discrepancy • Different interpretation of abnormality • Glass slide and WSI contained same information • Skin discrepancy • Clinical information not used for interpreting digital slide

  14. Pitfalls of digital archive • Costs • Huge storage needs – 40 TeraByte per year (over 57,000 CDs) • Largest storage in the UMCU • Logistics of scanning up to 500 slides per day • Currently scanning almost 24 / 7 • Place of scanning in process • Speed of image retrieval • Image compression (JPEG 2000?) • Backup

  15. Education • All students view the same “best slide” • Slide images can be integrated with • Annotations • Questions • Macroscopic images • Other multimedia • Most UMCU microscopy practical sessions are digital • Student satisfaction is high

  16. Teleconsultation • Place (small) slide scanners at different labs • Upload digital slides to UMC Utrecht • Aurora mScope Clinical • www.pathoconsult.com Upload new media

  17. Digital slide panel discussions

  18. Image processing research Image processing applications on virtual slides: • Detecting mitotic figures in breast cancer slides • Use texture features • Establishing histological grade in breast cancer • Segmentation of individual nuclei (on H&E stained slides) • Detect points of interest • Use marker-controlled watershed segmentation • Post processing

  19. Conclusions • Routine scanning is possible and makes sense • Future of pathology is digital • Digital pathology is expensive • Digital pathology is just starting.. Together we are shaping Pathology 2.0

  20. Discussion • Limitations current system • Cytology • Speed • Magnification (20x / 40x incidental) • Backup • Quality Control

  21. Discussion • Archive heavily used • Educational use still growing • Teleconsultation network growing (www.slideconsult.com) • Need for standards • DICOM / JPEG 2000 • Images, annotations and reports • Mixing scanners and integration with other software platforms (middleware?) • Image management central in workflow for pathologist?

  22. Questions?! Huisman et al., Creation of a fully digital pathology slide archive by high-volume tissue slide scanning, Human Pathology, 2010 May; 41(5): 751-7 a.huisman-4@umcutrecht.nl

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