2007- SSVS for hand held microscopes
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Whole slide of small size. SSVS (small size virtual slide)
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2007- SSVS for hand held microscopes
- 1. Telepathology and Distant DiagnosisTelepathology and Distant Diagnosis with SMALL SIZEVIRTUAL SLIDESwith SMALL SIZEVIRTUAL SLIDES (SSVS)(SSVS) Eng. Marcano, Fco & Prof. Dr. O. Ferrer-RocaEng. Marcano, Fco & Prof. Dr. O. Ferrer-Roca 20072007.. UNESCO Chair in TelemedicineUNESCO Chair in Telemedicine University of La LagunaUniversity of La Laguna Quality Control in Telemedicine - BiobankingQuality Control in Telemedicine - Biobanking CATAI - XVI Winter CourseCATAI - XVI Winter Course ULL - XXI Image Analisys CourseULL - XXI Image Analisys Course http://www.teide.net/catai
- 2. ContentsContents • IntroductionIntroduction • VSVS • SSVSSSVS • SSVS quality assessmentSSVS quality assessment • ResultsResults • ConclusionsConclusions
- 3. Virtual SlidesVirtual Slides • Specimens converted to digitalSpecimens converted to digital imagesimages • Images are transmitted overImages are transmitted over networks, Internetnetworks, Internet • Remote Analysis, Diagnosis,Remote Analysis, Diagnosis, teaching purposesteaching purposes © Telemedicine Research Group - University of Udine, Italy Bone biopsy Area: 2.8x8.2 mm Pixels: about 290M
- 4. Virtual Slide Capture SystemsVirtual Slide Capture Systems High power VS (40x) Image size in the order of Gigabytes Expensive equipments 50000€ - 250000€
- 5. Virtual Slides SizeVirtual Slides Size • Demands aDemands a lot oflot of storagestorage • JPEG basedJPEG based imagesimages 20x20x compressioncompression © Department of Pathology. Clínica Universitaria. University of Navarra. Pamplona. Spain.
- 6. Virtual Slides Size - QCVirtual Slides Size - QC • Technique:Technique: linearlinear scanningscanning • ImageImage artifactsartifacts • EquipmentEquipment price vs.price vs. ImageImage qualityquality ?? © Department of Pathology. Clínica Universitaria. University of Navarra. Pamplona. Spain.
- 7. Virtual Slides Size - QCVirtual Slides Size - QC • GoodGood AlignmentAlignment © Department of Pathology. Clínica Universitaria. University of Navarra. Pamplona. Spain.
- 8. VS – High PowerVS – High Power Not alwaysNot always necessarynecessary to haveto have high-powerhigh-power imagesimages Images:Images: severalseveral GigabytesGigabytes 1.3X 3.9X 11.1X 40X
- 9. e-Slidese-Slides • Telemedicine Research Group - University of Udine, ItalyTelemedicine Research Group - University of Udine, Italy © Telemedicine Research Group - University of Udine, Italy Technique:Technique: stitching ofstitching of imagesimages CheaperCheaper approachapproach JPEG basedJPEG based imagesimages Size: stillSize: still very largevery large
- 10. e-Slides - QCe-Slides - QC © Telemedicine Research Group - University of Udine, Italy Stitching ofStitching of imagesimages more imagemore image artifactsartifacts
- 11. e-Slides - QCe-Slides - QC © Telemedicine Research Group - University of Udine, Italy ProblemsProblems with imagewith image alignmentalignment
- 12. Small Size Virtual Slides –Small Size Virtual Slides – SSVS©SSVS© • Novel TechniqueNovel Technique • Generates digital slides small in sizeGenerates digital slides small in size • High resolution cameras (8-12 Mpx)High resolution cameras (8-12 Mpx) • Excellent achromatic planapochromatic (infinite)Excellent achromatic planapochromatic (infinite) opticsoptics SSVS© 2008
- 13. Small Size Virtual Slides –Small Size Virtual Slides – SSVS©SSVS© • Uses Image-Compression format: JPEG2000Uses Image-Compression format: JPEG2000 (ISO 15444-1, Wavelet)(ISO 15444-1, Wavelet) • Take advantage of JPEG2000 Image format toTake advantage of JPEG2000 Image format to facilitate:facilitate: • navigation,navigation, • zooming,zooming, • transmission,transmission, • storagestorage SSVS© 2008
- 14. JPEG2000JPEG2000 • Created by theCreated by the JJointoint PPhotographichotographic EExpertsxperts GGroup committeeroup committee (2000)(2000) • Intended to supersede discrete cosine transform-based JPEGIntended to supersede discrete cosine transform-based JPEG standard (1991)standard (1991) • Standard Filename extension:Standard Filename extension: jp2 (ISO/IEC 15444-1 conforming files)jp2 (ISO/IEC 15444-1 conforming files) jpx (Extended part-2 specifications or ISO/IEC 15444-2)jpx (Extended part-2 specifications or ISO/IEC 15444-2) • Included in DICOM sup. 61 (Jan 2002)Included in DICOM sup. 61 (Jan 2002)
- 15. JPEG2000 Standard - PartsJPEG2000 Standard - Parts • Part 1, Core coding system (intended as royalty and license-fee free - NB NOT patent-free) • Part 2, Extensions (adds more features and sophistication to the core) • Part 3, Motion JPEG 2000 • Part 4, Conformance • Part 5, Reference software (Java and C implementations are available) • Part 6, Compound image file format (document imaging, for pre-press and fax-like applications, etc.) • Part 7 has been abandoned • Part 8, JPSEC (security aspects) • Part 9, JPIP (interactive protocols and API) • Part 10, JP3D (volumetric imaging) • Part 11, JPWL (wireless applications) • Part 12, ISO Base Media File Format (common with MPEG-4)
- 16. JPEG2000JPEG2000 • Complex algorithm for compression / decompression takes a long timeComplex algorithm for compression / decompression takes a long time Compressed Image decompression Source Image Color Transformation Tiling Wavelet Transform Quantization Tier-1 Encoder (Modeling & Arithmetic Coding) Tier-2 Encoder (Stream Creation) Rate Control 8 7 8 8 34 34 34 34 7 7 8 8 34 34 34 34 8 8 12 12 34 34 34 34 8 8 12 12 34 34 34 34 34 34 34 34 55 55 55 55 34 34 34 34 55 55 55 55 34 34 34 34 55 55 55 55 34 34 34 34 55 55 55 55 EBCOT - Embedded Block Coding with Optimal Truncation
- 17. JPEG2000JPEG2000 • Higher compression ratios, images get blurredHigher compression ratios, images get blurred 570k 57k 6k 2k
- 18. JPEG2000JPEG2000 Compression factor: 1:250Compression factor: 1:250 Jpeg2000 - blurred Jpeg - blocked
- 19. Distant Diagnosis - TEXCAN©-Distant Diagnosis - TEXCAN©- IIII • TEXCAN-II® implements SSVS technique, allowing: • Zoom-Focus© • Spatial resolution extreme digital zoom; • High quality focused image • Small size of compressed images • Fast & efficient distant consultation • Non-expensive digital virtual microscope
- 20. TEXCAN®-II Capture System Intel 3.4 GHz Pentium® 4 / Intel® Core™2 Duo, 4 Gb RAM CCD Camera 8Mpixels, firewire 1394.a 4x – 0.13 NA 20x – 0.46 NA (ROI’s)
- 21. TEXCAN®-II Assessment Tools Preparación Diagnóstico conocido Maligno Inflamación F.S.M.* 1 CITOLOGIA ORINA: Positivo para celulas malignas. Sugestivo de Carcinoma de celulas claras + 2 CITOLOGÍA ORINA: Citologia positiva para celulas tumorales malignas. Frotis sugestivo de Carcinoma. + 3 CITOLOGÍA DE LÍQUIDO PLEURAL. CITOLOGÍA SOSPECHOSA DE MALIGNIDAD. FROTIS CON INTENSA LINFOCITOSIS. + + 4 CITOLOGÍA DE LÍQUIDO PLEURAL: CITOLOGÍA POSITIVA PARA CÉLULAS TUMORALES MALIGNAS. Frotis sugestivo de Carcinoma. + 5 PUNCIÓN ASPIRACIÓN DE MAMA: Frotis sugestivos de mastopatía fibroquística con lesión epitelial proliferativa benigna intraquística. 6 CITOLOGÍA DE LAVADO PERITONEAL: CITOLOGÍA POSITIVA PARA CÉLULAS TUMORALES MALIGNAS. Frotis sugestivo de Carcinoma + 7 CITOLOGÍA DE LÍQUIDO PLEURAL: CITOLOGÍA SOSPECHOSA DE MALIGNIDAD. + + 8 Frotis con estimulo estrogenico mediano, algo inflamatorio, con espermatozoides, elementos cervicales asi como cambios celulares queratosicos y celulas pavimentosas con atipias nucleares moderadas. HSIL (High grade squamous intraepitelial lesion) + + + 9 Frotis pseudoluteal, algo inflamatorio, con elementos endocervicales sin anomalias. Hay cambios celulares queratosicos, asi como binucleaciones y elementos pavimentosos con atipias nucleares. LSIL-HPV? (Lesion escamosa intraepitelial de bajo grado-Human Papiloma Virus?) + + 10 Frotis mixto, moderadamente inflamatorio, con alteraciones celulares degenerativas, asi como escasos elementos pavimentosos con atipias ligeras, de probable origen reactivo. + 11 Estimulo estrogenico moderado, con citolisis, algo inflamatorio. Elementos cervicales bien conservados y escasos elementos pavimentosos con atipias ligeras. ASCUS (Atipical scamous cells of unknown significance). + 12 Estimulo estrogenico moderado, con citolisis, algo inflamatorio. Elementos cervicales bien conservados y celulas metaplasicas con atipias nucleares y algun pseudokoilocito, asi como cambios queratosicos. LSIL-HPV (Lesion escamosa intraepitelial de bajo grado-Human Papiloma Virus) + 13 Microcarcinoma papilar de tiroides. + 14 Adenoma tubular 15 Adenoma tubulovelloso (*) F.S.M.: Fase secretora Menstrual + : Positivo para el caso JPIP JPEG2000 www.cataibreezee.ull.es:81. V5.2 Samples Stat. Software Viewer & Transmissione-forms
- 22. SSVS CaptureSSVS Capture • SSVS captured with the 4x objectiveSSVS captured with the 4x objective • ROI’s (Region of Interest) selected byROI’s (Region of Interest) selected by technician, captured with the 20xtechnician, captured with the 20x objectiveobjective • Some clinical data included in eachSome clinical data included in each SSVSSSVS
- 23. SSVS – samplesSSVS – samples • Small powerSmall power enough forenough for having anhaving an image withimage with diagnosticdiagnostic qualityquality 53MB 68MB 7.8x 250x 1.6x 6.3x Digital zoom 500x
- 24. 6x 3x SSVS - samplesAreas identified by pathologist / technician Random captured areas 26Mb 16Mb 40x 40x
- 26. SSVS AssessmentSSVS Assessment • 10 pathologists, not trained in10 pathologists, not trained in TelepathologyTelepathology • 3 pathologists, trained in TelePathology3 pathologists, trained in TelePathology • 9 cytological/histological samples9 cytological/histological samples
- 28. Results – ROCResults – ROC SSVS - Validity for diagnosis:SSVS - Validity for diagnosis: • Area under the ROC curve ofArea under the ROC curve of 0.95 p<0.0010.95 p<0.001, (good diagnostic quality), (good diagnostic quality)
- 29. Results - KappaResults - Kappa Concordance and precision was high forConcordance and precision was high for telepathology trained pathologiststelepathology trained pathologists • k=0.73, p<0.001k=0.73, p<0.001 • Concordance and precision was low forConcordance and precision was low for pathologists non-trained in telepathologypathologists non-trained in telepathology • low k=0.4, p<0.001low k=0.4, p<0.001 • Comments of the users where mainly devoted toComments of the users where mainly devoted to improve the sampling area of the ROI.improve the sampling area of the ROI.
- 30. ConclusionsConclusions • The SSVS technique allows the technicians to digitize aThe SSVS technique allows the technicians to digitize a virtual slide easy to storage due to its small size.virtual slide easy to storage due to its small size. • SSVS is perfectly suitable for discussion and diagnosis atSSVS is perfectly suitable for discussion and diagnosis at distance through intranet and Internet providing a cheapdistance through intranet and Internet providing a cheap digital microscope and an online collaborative system.digital microscope and an online collaborative system. • For specimens that require high power to make diagnosis,For specimens that require high power to make diagnosis, the SSVS+ROI technique has been proved of value.the SSVS+ROI technique has been proved of value.
- 31. Thanks!Thanks!