Optimal multiresolution blending of confocal microscope images

IEEE Transactions on Biomedical Engineering

Volumn 59, Issue 2, 2012, Pages 531-541

  Shao, Hao Chiang ^a   Hwang, Wen Liang ^b   Chen, Yung Chang ^a  

^a NATIONAL TSING HUA UNIVERSITY   (Taiwan)

^b INSTITUTE OF INFORMATION SCIENCE   (Taiwan)

Author keywords

Blending; confocal microscope image; mosaicing

Indexed keywords

BIOLOGICAL STUDIES; CONFOCAL FLUORESCENCE; CONFOCAL MICROSCOPES; FLUORESCENCE IMAGE; HIGHER RESOLUTION IMAGES; IMAGE PAIRS; MICROSCOPE IMAGES; MOSAICING; MULTI-RESOLUTIONS; MULTIPLE IMAGE; OPTIMAL SOLUTIONS; OPTIMIZATION APPROACH; OVERLAPPING REGIONS; QUADRATIC PROGRAMMING ALGORITHMS; RELATIVE IMPORTANCE;

BLENDING; FLUORESCENCE; IMAGING TECHNIQUES; MICROSCOPES; OPTIMIZATION;

QUADRATIC PROGRAMMING;

ALGORITHM; ANALYTICAL PARAMETERS; ARTICLE; BLENDING COEFFICIENT; CONFOCAL MICROSCOPE; FLUORESCENCE IMAGING; FLUORESCENCE MICROSCOPE; IMAGE PROCESSING; MICROSCOPE; NONHUMAN;

ALGORITHMS; ANIMALS; BRAIN; DROSOPHILA; IMAGE PROCESSING, COMPUTER-ASSISTED; MICE; MICROSCOPY, CONFOCAL; PANCREAS;

EID: 84862909598     PISSN: 00189294     EISSN: 15582531     Source Type: Journal    
DOI: 10.1109/TBME.2011.2175446     Document Type: Article

References (39)

1. X. Zhou and S. T. C. Wong, "Informatics challenges of high-throughput microscopy," IEEE Signal Process. Mag., vol. 23, no. 3, pp. 63-72, May 2006.
2. C. Vonesch, F. Aguet, J. K. Vonesch, and M. Unser, "The colored revolution of bioimaging," IEEE Signal Process. Mag., vol. 23, no. 3, pp. 20-31, May 2006.
3. H. Y. Shum and R. Szeliski, "System and experiment paper: Construction of panoramic image mosaics with global and local alighment," Int. J. Comput. Vis., vol. 36, no. 2, pp. 101-130, 2000.
4. S. E. Chen, "QuickTime VR-An image-based approach to virtual environment navigation," in Proc. SIGGRAPH, 1995, pp. 29-38.
5. J. Jia and C.-K. Tang, "Eliminating structure and intensity misalignment in image stitching," in Proc. 10th IEEE Int. Conf. Comput. Vis. (ICCV 2005), pp. 1651-1658.
6. A. Zomet, A. Levin, S. Peleg, and Y. Weiss, "Seamless image stitching by minimizing false edges," IEEE Trans. Image Process., vol. 15, no. 8, pp. 969-977, Apr. 2005.
7. M. Brown and D. G. Lowe, "Automatic panoramic image stitching using invariant features," Int. J. Comput. Vis., vol. 74, no. 1, pp. 59-73, 2006.
8. J. Kopf, M. Uyttendaele, O. Deussen, and M. F. Cohen, "Capturing and viewing gigapixel images," ACM Trans. Graph., vol. 26, no. 3, article 93, 2007.
9. P. Pérez, M. Gangnet, and A. Blake, "Poisson image editing," ACMTrans. Graph., vol. 22, no. 3, pp. 313-318, 2003.
10. P. Viola and W. M. Wells, III, "Alignment by maximization of mutual information," Int. J. Comput. Vis., vol. 24, pp. 137-154, 1997.
11. F. Maes, A. Collignon, D. Vandermeulen, G. Marchal, and P. Suetens, "Multimodality image registration by maximization of mutual information," IEEE Trans. Med. Imag., vol. 16, no. 2, pp. 187-198, Apr. 1997.
12. J. B. A. Maintz and M. A. Viegever, "A survey of medical image registration," Med. Image Anal., vol. 2, no. 1, pp. 1-36, 1998.
13. A. Gholipour, N. Kehtarnavaz, R. Briggs, M. Devous, and K. Gopinath, "Brain functional localization:Asurvey of image registration techniques," IEEE Trans. Med. Imag., vol. 26, no. 4, pp. 427-451, Apr. 2007.
14. G. Yang, C. V. Stewart, M. Sofka, and C.-L. Tsai, "Registration of challenging image pairs: Initialization, estimation, and decision," IEEE Trans. Pattern Anal. Mach. Intell., vol. 29, no. 11, pp. 1973-1989, Nov. 2007.
15. A. Eden, M. Uyttendaele, and R. Szeliski, "Seamless image stitching of scenes with large motions and exposure differences," in Proc. IEEE Conf. Comput. Vis. Pattern Recognit. (CVPR 2006), pp. 2498-2505.
16. P. Thévenaz and M. Unser, "User-friendly semiautomated assembly of accurate image mosaics in microscopy," Microsc. Res. Techn., vol. 70, no. 2, pp. 135-146, 2007.
17. P. J. Burt and E. H. Adelson, "A multiresolution spline with application to image mosaics," ACM Trans. Graph., vol. 2, no. 4, pp. 217-236, 1983.
18. P. J. Burt and E. H. Adelson, "The Laplacian pyramid as a compact image code," IEEE Trans. Commun., vol. COM-31, no. 4, pp. 532-540, Apr. 1983.
19. M. S. Su, W. L. Hwang, and K. Y. Cheng, "Analysis on multiresolution mosaic images," IEEE Trans. Image Process., vol. 3, no. 7, pp. 952-959, Apr. 2004.
20. Y. C. Liu and A. S. Chiang, "High-resolution confocal imaging and threedimensional rendering," Methods, vol. 30, pp. 86-93, 2003.
21. A.-S. Chiang, "Aqueous tissue clearing solution," U.S. Patent 6 472 216, 2002.
22. E. R. Dowski and W. T. Cathey, "Extended depth of field through wavefront coding," Appl. Opt., vol. 43, no. 11, pp. 1859-1866, 1995.
23. R. Ng, M. Levoy, M. Bredif, M. Horowitz, and P. Hanrahan, "Light field photography with a hand-held plenoptic camera," Dept. Computer Science, Stanford Univ., Stanford, CA, Tech. Rep. CSTR 2005-02, 2005.
24. F. Aguet, D. Van De Ville, and M. Unser, "Model-based 2.5-D deconvolution for extended depth of field in brightfield microscopy," IEEE Trans. Image Process., vol. 17, no. 7, pp. 1144-1153, Jul. 2008.
25. J. Rigaut and J. Vassy, "High-resolution 3D images from confocal scanning laser microscopy: Quantitative study and mathematical correction of the effects from bleaching and fluorescence attenuation in depth," Anal. Quant. Cytol., vol. 13, pp. 223-232, 1991.
26. R. Ghauharali, J. Hofstraat, and G. Brakenhoff, "Fluorescence photobleaching-based shading correction for fluorescence microscopy," J. Microsc., vol. 192, pp. 99-113, 1998.
27. J. Markham and J. Conchello, "Artefacts in restored images due to intensity loss in 3D fluorescence microscopy," J. Microsc., vol. 204, pp. 93-98, 2001.
28. S. Negahdaripour and C.-H. Yu, "A generalized brightness change model for comupting opticl flow," in Proc. 4th Int. Conf. Comupt. Vis., 1993, pp. 2-11.
29. S. Gopinath, N. Thakoor, J. Gao, and K. Luby-Phelps, "A statistical approach for intensity loss compensation of confocal microscopy images," in Proc. IEEE 14th Int. Conf. Image Process. (ICIP 2007), pp. VI-249-VI-252.
30. C. Kervrann, D. Legland, and L. Pardini, "Robust incremental compensation of the light attenuation with depth in 3d fluorescence microscopy," J. Microsc., vol. 214, no. 3, pp. 297-314, 2004.
31. H. H. Lin, Jason S. Y. Lai, A. L. Chin, Y. C. Chen, and A. S. Chiang, "A map of olfactory representation in the drosophila mushroom body," Cell, vol. 128, pp. 1205-1217, 2007.
32. Y.-Y. Fu, C.-W. Lin, G. Enikolopov, E. Sibley, A.-S. Chiang, and S.-C. Tang, "Microtome-free 3-dimensional confocal imaging method for visualization of mouse intestine with subcellular-level resolution," Gastroenterology, vol. 137, no. 2, pp. 453-465, 2009.
33. A. S. Chiang, C. Y. Lin, C. C. Chuang, H. M. Chang, C. H. Hsieh, C. W. Yeh, C. T. Shih, J. J. Wu, G. T. Wang, Y. C. Chen, C. C. Wu, G. Y. Chen, Y. T. Ching, P. C. Lee, C. Y. Lin, H. H. Lin, C. C. Wu, H. W. Hsu, Y. A. Huang, J. Y. Chen, H. J. Chiang, C. F. Lu, R. F. Ni, C. Y. Yeh, and J. K. Hwang, "Three-dimensional reconstruction of brain-wide wiring networks in Drosophila at single-cell resolution," Curr. Biol., vol. 21, no. 1, pp. 1-11, 2010.
34. I. Daubechies, Ten Lectures noWavelets. Philadelphia, PA: SIAM, 1994.
35. A. Ravindran, K.M. Ragsdell, and G. V. Reklaitis, Engineering Optimization Methods and Applications, 2nd ed. New York: Wiley, 2006.
36. E. K. P. Chong and S. H. Zak, An Introduction to Optimization, 2nd ed. New York: Wiley, 2001.
37. T. F. Coleman and Y. Li, "A reflective newton method for minimizing a quadratic function subject to bounds on some of the variables," SIAM J. Optim., vol. 6, no. 4, pp. 1040-1058, 1996.
38. R. Fletcher, Practical Methods of Optimization. New York: Wiley, 1987.
39. G.B. Dantzig, Linear Programming and Extensions. Princeton, NJ: Princeton Univ. Press, 1963.