High Volume Slide Scanning Architecture and Applications

Dr. André Huisman Department of pathology UMC Utrecht, The Netherlands [email protected]

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

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

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

Aim (2007)

Digitize all diagnostic slides we have (prospectively)

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

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

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)

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

Linking systems

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

Scanner workflow Scanning Database

LIS Image / Data server U-DPS Other images (e.g. macro) Order form scanner Speech recognition

HSM Storage 120 TB on tape 6 TB fast disks

pathology users

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

Preliminary results validation GI tract (%) Skin (%)

Same Similar Discrepant 1 92 7 94 5 1 • GI tract discrepancy • Different interpretation of abnormality • Glass slide and WSI contained same information • Skin discrepancy • Clinical information not used for interpreting digital slide

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

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

Teleconsultation

• Place (small) slide scanners at different labs • Upload digital slides to UMC Utrecht • Aurora mScope Clinical

Upload new media

• www.pathoconsult.com

Digital slide panel discussions

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

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

Discussion

• Limitations current system •

Cytology

• • •

Speed Magnification (20x / 40x incidental) Backup

•

Quality Control

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?

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 [email protected]