Stack or Trash? Quality assessment of virtual slides. Anatomic pathology & collaboration
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1 11th European Congress on Telepathology 5th International Congress on Virtual Microscopy 6-9 June 2012, Venice, Italy Stack or Trash? Quality assessment of virtual slides David Ameisen Christophe Deroulers, Valérie Perrier, Jean-Baptiste Yunès, Maxime Baptistella, Fatiha Bouhidel, Luc Legrès, Anne Janin, Philippe Bertheau Université Paris Diderot - Paris 7 Hôpital Saint-Louis Institut Universitaire d Hématologie Department of Pathology - INSERM U728 Anatomic pathology & collaboration 3 major issues - Asynchroneus viewing - Simultaneous viewing - Viewing of the whole slide, at multiple magnification levels
2 Medical Imagery Various types of images Various acquisition and visualization devices
3 1.7 Giga pixels 6589 tiles Virtual slides now essential in teaching, research and diagnostics Teaching: Practical work slides for third year students Breast, Cutaneous lymphomas, mouse pathology atlases Research: Morphometrics, image analysis Diagnostics: Second opinion consultations Integration to the hospital s laboratory results server AUTOMATED QUALITY ASSESSMENT?
4 What can a computer find out about this image? Size: 341 kilobytes Dimensions (in pixels) : 1376x1038 Color space : 8bit RGB Color profile : srgb IEC Main colors: Brightness: [25% ; 100%] : OK Saturation: [1% ; 100%] : OK Contrast: 60% : OK Focus:? Is this image in focus?
5 It s easy to compare. It s easy to compare. But most of the tim
6 Using edge detection Laplacian convolution m Definition of the scores core1: Maximum intensity of the edge detection image (rangi etween 0% and 100%). Score1 = 100%, the image contains at least one edge maximum intensity (ie. one sharp region)
7 Definition of the scores core2 = S2b / S2a Value S2a: sum of intensities of all the pixels of the edge detection image (each rang tween 0% and 100%). Value S2b: similar to Value S2a, but with pixels whose intensity is above a given value rightness (10% in our experiments). core2 describes the overall intensity of the edges in an image. core2 describes the overall sharpness of the image. No-reference blur assessment: Absolute assessment, whichever the image To each of these scores associate a threshold, configurable and customi for different types of imag selected for analysis. Score 1 : 40% Threshold score 1 = 98% Score 2 : 52.35% Threshold score 2 = 70% Out of focus Score 1 : 100% Threshold score 1 = 98% Score 2 : 98.03%
8 Survey: 100 images Survey: 100 images
9 1.7 Giga pixels 6589 tiles 1.25x
10 2.5x 5.0x
11 10x 20x
12 Survey: 100 Virtual Slides Survey: 100 Virtual Slides
13 Survey: 100 Virtual Slides Survey: 100 Virtual Slides
14 Survey: 100 Virtual Slides Survey: 100 Virtual Slides
15 An ultra fast process Blur analysis on a single computer: 34Mpx / second 2Gpx / minute 2 patent applications: D. Ameisen, P. Bertheau. Method of blur detection and assessment in a digital image. PCT/FR2011/052951, priority date 2010 Dec 13. D. Ameisen, P. Bertheau. Process of quality assessment of a virtual slide of an object. FR/2011/ , 2011 Mai 10. How to make it even better? Present: J2EE = Compatible, Portable... Next version: C++: Faster Open MP (Open Multiprocessing): Multi-threaded Open MPI (Open Message Passing Interface): Multi-node = Processing clusters Web API (Application Programming Interface): Interoperability
16 Applications: saving time, increasing the quality uring the digitization Reacquisition of blurred tiles during the scan Reacquisition of the whole slide with more suitable profile ust after the digitization Notification sent to reacquire the slide ontinuous quality assurance Notification sent to recalibrate the scanner n 2012, FDA declared WSI systems as Class III medical devic ality assessment is a Key issue given the digitization of med a and the increasing importance of digital imaging for Acknowledgements and thanks SERM U728! titut Universitaire d Hématologie! iversité Paris Diderot! pital Saint-Louis, APHP! Philippe Bertheau Jean-Baptiste Yunès Anne Janin François Sigaux Mathieu Desrues Christophe Deroulers Valerie Perrier Robert Claude Maltais Nicolas Fournier Antoine Lemieux Stack or Trash? Quality assessment of virtua David A
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