High Volume Slide Scanning
Architecture and Applications
Dr. André Huisman
Department of pathology
UMC Utrecht, The Netherlands
a.huisman-4@umcutrecht.nl
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
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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
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1D Barcodes
U-DPS: reporting system
LMS: Laboratory Management System
Spectrum: Aperio’s image management solution
Storage system
• Own development: integration layer
Scanner workflow
Other images
(e.g. macro)
Scanning
Database
Order form
scanner
LIS
Image / Data server
U-DPS
HSM
Storage
6 TB fast disks
120 TB on tape
pathology users
Speech
recognition
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
92
94
Similar
7
5
Discrepant
1
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
a.huisman-4@umcutrecht.nl