Interactive Histology of large-scale biomedical image stacks

IEEE Transactions on Visualization and Computer Graphics

Volumn 16, Issue 6, 2010, Pages 1386-1395

  Jeong, Won Ki ^a   Schneider, Jens ^b   Turney, Stephen ^a   Faulkner Jones, Beverly E ^d   Meyer, Dominik ^c   Westermann, Rüdiger ^c   Reid, R Clay ^e   Lichtman, Jeff ^a   Pfister, Hanspeter ^a  

^a HARVARD UNIVERSITY   (United States)

^b KING ABDULLAH UNIVERSITY OF SCIENCE AND TECHNOLOGY   (Saudi Arabia)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d BIDMC Pathology and Harvard ^*  (United States)

^e HARVARD MEDICAL SCHOOL   (United States)

Author keywords

biomedical image processing; Gigapixel viewer; GPU; texture compression

Indexed keywords

BIO-MEDICAL IMAGE PROCESSING; BIOLOGICAL TISSUES; BIOMEDICAL IMAGES; DATA SETS; DIGITAL-IMAGING TECHNOLOGY; ELECTRON MICROGRAPH; GIGAPIXEL VIEWER; GPU; HIGH-RESOLUTION MICROSCOPY; IMAGE STACKS; INTERACTIVE TOOL; LARGE IMAGES; MEMORY BANDWIDTHS; MICROSCOPY TECHNIQUE; NANO SCALE; NEURAL STRUCTURES; ON-THE-FLY; PRE-PROCESSING; TEXTURE COMPRESSION; VISIBLE IMAGE; VISUALIZATION FRAMEWORK;

HISTOLOGY; IMAGE PROCESSING; IMAGING SYSTEMS; PROGRAM PROCESSORS; VISUALIZATION;

TEXTURES;

ARTICLE; COMPUTER GRAPHICS; HISTOLOGY; HUMAN; IMAGE PROCESSING; STATISTICS; TRANSMISSION ELECTRON MICROSCOPY;

COMPUTER GRAPHICS; HISTOLOGICAL TECHNIQUES; HUMANS; IMAGE PROCESSING, COMPUTER-ASSISTED; MICROSCOPY, ELECTRON, TRANSMISSION;

EID: 78149243509     PISSN: 10772626     EISSN: None     Source Type: Journal    
DOI: 10.1109/TVCG.2010.168     Document Type: Article

References (39)

1. A. C. Beers, M. Agrawala, and N. Chaddha. Rendering from compressed textures. In Proc. SIGGRAPH'96, pages 373-378, 1996.
2. D. Benson and J. Davis. Octree textures. In Proc. SIGGRAPH'02, pages 785-790, 2002.
3. M. J. Berger and J. Oliger. Adaptive Mesh Refinement for Hyperbolic Partial Differential Equations. Journal of Computational Physics, 53:484-512, Mar. 1984.
4. P. J. Burt and E. H. Adelson. The laplacian pyramid as a compact image code. IEEE Transactions on Communications, 31:532-540, 1983.
5. N. Fout and K.-L. Ma. Transform coding for hardware-accelerated volume rendering. IEEE Transactions on Visualization and Computer Graphics, 13(6):1600-1607, November 2007.
6. N. Fout, K.-L. Ma, and J. Ahrens. Time-varying, multivariate volume data reduction. In Proceedings of the ACM Symposium on Applied Computing, pages 1224-1230, 2005.
7. S. F. Frisken, R. N. Perry, A. P. Rockwood, and T. R. Jones. Adaptively sampled distance fields: a general representation of shape for computer graphics. In Proc. SIGGRAPH'00, pages 249-254, 2000.
8. A. Gersho and R. M. Gray. Vector Quantization and Signal Compression. Kluwer Academic Press, 1st edition, 1991.
9. M. H. Ghavamnia and X. D. Yang. Direct rendering of laplacian pyramid compressed volume data. In Proceedings of IEEE Visualization, pages 192-199, 1995.
10. GigaPan. http://www.gigapan.org/.
11. J. Gilbertson and Y. Yagi. Histology, imaging and new diagnostic workflows in pathology. Diagnostic Pathology, 3 (Suppl): S14, Jan 2008.
12. R. M. Gray and D. L. Neuhoff. Quantization. IEEE Transactions on Information Theory, 44(6):2325-2383, 1998.
13. S. Guthe and W. Straßer. Real-time decompression and visualization of animated volume data. In IEEE Visualization, pages 349-356, 2001.
14. S. Guthe, M. Wand, J. Gonser, and W. Straßer. Interactive rendering of large volume data sets. In IEEE Visualization, pages 53-60, 2002.
15. E. Haber and J. Modersitzki. Numerical methods for image registration. Inverse Problems, 24, 2004.
16. J. Ho, A. Parwani, D. Jukic, Y. Yagi, and L. Anthony. Use of whole slide imaging in surgical pathology quality assurance: design and pilot validation studies. Human pathology, 37:322-331, Jan 2006.
17. Aperio image scope. http://www.aperio.com/pathologyservices/imagescope- slide-viewing-software.asp.
18. J. Kopf, M. Uyttendaele, O. Deussen, and M. F. Cohen. Capturing and viewing gigapixel images. ACM Transactions on Graphics, 26(3):93:1-93:10, July 2007.
19. M. Kraus and M. Strengert. Pyramid filters based on bilinear interpolation. In Proceedings GRAPP 2007, pages 21-28, 2007.
20. Krieken, M. G. Rojo, I. Moreno, A. Ariza, and S. Tuzlali. A European network for virtual microscopy-design, implementation and evaluation of performance. Virchows Archiv, 454(4):421-429, Jan 2009.
21. E. Krupinski, A. Tillack, L. Richter, and J. Henderson. Eye-movement study and human performance using telepathology virtual slides. implications for medical education and differences with experience. Human pathology, 37:1543-1556, Jan 2006.
22. Y. Linde, A. Buzo, and R. Gray. An algorithm for vector quantizer design. IEEE Transactions on Communications, 28:84-94, 1980.
23. P. Ljung, C. Lundström, A. Ynnerman, and K. Museth. Transfer function based adaptive decompression for volume rendering of large medical data sets. In IEEE Symposium on Volume Visualization and Graphics, pages 25-32, 2004.
24. S. P. Lloyd. Least squares quantization in PCM. IEEE Transactions on Information Theory, 28:129-137, March 1982.
25. E. Lum, K.-L. Ma, and J. Clyne. Texture hardware assisted rendering of time-varying volume data. In IEEE Visualization, pages 263-270, 2001.
26. K.-L. Ma and H.-W. Shen. Compression and accelerated rendering of time-varying volume data. In Proceedings of the International Computer Symposium-Workshop on Computer Graphics and Virtual Reality, pages 82-89, 2000.
27. Microsoft HD view. http://research.microsoft.com/en-us/um/redmond/groups/ ivm/HDView/.
28. D. Nagayasu, F. Ino, and K. Hagihara. A decompression pipeline for accelerating out-of-core volume rendering of time-varying data. Computers & Graphics, 32(3):350-362, June 2008.
29. NDP.view. http://sales.hamamatsu.com/de/produkte/systemdivision/virtual- microscopy/products/software.php.
30. P. Ning and L. Hesselink. Vector quantization for volume rendering. In Proceedings of the Workshop on Volume Visualization, pages 69-74, 1992.
31. Oberhumer.com. LZO real-time data compression library. http://www.oberhumer.com/opensource/lzo/.
32. K. Sayood. Introduction to Data Compression. Morgan Kaufmann, 2nd edition, 2000.
33. J. Schneider. Kompressions-und Darstellungsverfahren für hochaufgelöste Volumendaten. Diploma thesis, RWTH Aachen, Germany, 2003. http://wwwcg.in. tum.de/Research (English).
34. J. Schneider and R. Westermann. Compression domain volume rendering. In Proceedings of IEEE Visualization, pages 293-300, 2003.
35. Seadragon. http://www.seadragon.com/.
36. H.-W. Shen and C. R. Johnson. Differential volume rendering: A fast volume visualization technique for flow animation. In IEEE Visualization, pages 180-187, 1994.
37. C. Wang, H. Yu, and K.-L. Ma. Application-driven compression for visualizing large-scale time-varying data. IEEE Computer Graphics and Applications, 30(1):59-69, 2010.
38. R. Westermann. Compression domain rendering of time-resolved volume data. In IEEE Visualization 1995, pages 168-175, 1995.
39. J. Wilhelms and A. V. Gelder. Multi-dimensional trees for controlled volume rendering and compression. In In Proceedings of the 1994 Symposium on Volume Visualization, pages 27-34, 1994.