An adaptive non-local means filter for denoising live-cell images and improving particle detection

Journal of Structural Biology

Volumn 172, Issue 3, 2010, Pages 233-243

  Yang, Lei ^a   Parton, Richard ^b   Ball, Graeme ^b   Qiu, Zhen ^a   Greenaway, Alan H ^a   Davis, Ilan ^b   Lu, Weiping ^a  

^a HERIOT WATT UNIVERSITY   (United Kingdom)

^b UNIVERSITY OF OXFORD   (United Kingdom)

Author keywords

Denoising; Drosophila; Feature extraction; Microtubules; Non local means filter; Particle detection

Indexed keywords

BINDING PROTEIN; END BINDING PROTEIN 1; UNCLASSIFIED DRUG;

ARTICLE; ARTIFACT; CELL VIABILITY; DENOISING; DROSOPHILA; FILTER; FLUORESCENCE IMAGING; IMAGE ANALYSIS; MICROTUBULE; NONHUMAN; PHOTOSENSITIVITY; PRIORITY JOURNAL; SIGNAL NOISE RATIO;

ALGORITHMS; ANIMALS; DROSOPHILA; MICROSCOPY, FLUORESCENCE; MICROTUBULES; SIGNAL PROCESSING, COMPUTER-ASSISTED;

EID: 77958165104     PISSN: 10478477     EISSN: 10958657     Source Type: Journal    
DOI: 10.1016/j.jsb.2010.06.019     Document Type: Article

References (33)

1. Becalska A.N., Gavis E.R. Lighting up mRNA localization in Drosophila oogenesis. Development 2009, 136:2493-2503.
2. Boulanger J., Sibarita J.B., Kervrann C., Bouthemy P. Non-parametric regression for patch-based fluorescence microscopy image sequence denoising. 5th Int. Symp. Biomed. Imaging 2008, 748-751.
3. Boulanger J., Kervarann C., Bouthemy P., Elbau P., Sibarita J.-B., Salmero J. Patch-based non-local functional for denoising fluorescence microscopy image sequences. IEEE Trans. Med. Imaging 2010, 29:442-454.
4. Brox T., Kleinschmidt O., Cremers D. Efficient nonlocal means for denoising of textural patterns. IEEE Trans. Image Proc. 2008, 17:1083-1092.
5. Buades A., Coll B., Morel J.M. A review of image denoising algorithms, with a new one. Multiscale Model. Simul. 2005, 4:490-530.
6. Buades A., Coll B., Morel J.M. Nonlocal image and movie denoising. Int. J. Comput. Vis. 2008, 76:123-139.
7. Carlton, P.M., Boulanger, J., Kervrann, C., Sibarita, J., Salamero, J., Gordon-Messer, S., Bressan, D., Haber, J.E., Haase, S., Shao, L., Winoto, L., Matsuda, A., Kner, P., Uzawa, S., Gustafsson, M., Kam, Z., Agard, D.A., Sedat, J.W., in press. Fast live simultaneous multi-wavelength 4-dimensional optical microscopy. Proc. Natl. Acad. Sci. USA.
8. Chan T.F., Osher S., Shen J. The digital TV filter and nonlinear denoising. IEEE Trans. Image Proc. 2001, 10:231-241.
9. Chaux C., Blanc-Feraud L., Zerubia J. Wavelet-based restoration methods: application to 3D confocal microscopy images. Prof. SPIE 2007, 6701.
10. Frangakis A.S., Hegerl R. Noise reduction in electron tomographic reconstruction using nonlinear anisotropic diffusion. J. Struct. Biol. 2001, 135:239-250.
11. Freeman W.T., Adelson E.H. The design and use of steerable filters. IEEE Trans. Pattern Anal. Mach. Intell. 1991, 13:891-906.
12. Genovesio A., Liedl T., Emiliani V., Parak W.J., Coppey-Moisan M., Olivo-Marin J.-C. Multiple particle tracking in 3-D+t microscopy: method and application to the tracking of endocytosed quantum dots. IEEE Trans. Image Proc. 2006, 15:1062-1070.
13. Gonzalez R.C., Woods R.E. Digital Image Processing 2002, Prentice Hall. second ed.
14. Jaqaman K., Loerke D., Mettlen M., Kuwata H., Grinstein S., Schmid S.L., Danuser G. Robust single-particle tracking in live-cell time-lapse sequences. Nat. Methods 2008, 5:695-702.
15. Jiang W., Baker M.L., Wu Q., Bajaj C., Chiu W. Applications of a bilateral denoising filter in biological electron microscopy. J. Struct. Biol. 2003, 144:114-122.
16. Kervrann C., Boulanger J. Local adaptivity to variable smoothness for exemplar-based image regularization and representation. Int. J. Comput. Vis. 2008, 79:45-69.
17. Mahmoudi M., Sapiro G. Fast image and video denoising via nonlocal means of similar neighborhoods. IEEE Signal Proc. Lett. 2005, 12:839-842.
18. Meijering E., Smal I., Danuser G. Tracking in molecular bioimaging. IEEE Signal Proc. Mag. 2006, 23:46-53.
19. Pantelic R.S., Rothnagel R., Huang C.-Y., Muller D., Woodford D., Landsberg M.J., McDowall A., Pailthorpe B., Young P.R., Banks J., Hankamer B., Eriksson G. The discriminative bilateral filter: an enhanced denoising filter for electron microscopy data. J. Struct. Biol. 2006, 155:395-408.
20. Perona P., Malik J. Scale-space and edge detection using anisotropic diffusion. IEEE Trans. Pattern Anal. Mach. Intell. 1990, 12:629-639.
21. Pisano E.D., Zong S., Hemminger B.M., Deluca M., Johnston R.E., Muller K., Braeuning M.P., Pizer S.M. Contrast limited adaptive histogram equalization image processing to improve the detection of simulated spiculations in dense mammograms. J. Digit. Imaging 1998, 11:193-200.
22. Rose A. The sensitivity performance of the human eye on an absolute scale. J. Opt. Soc. Am. 1948, 38:196-208.
23. Rudin L.I., Osher S., Fatemi E. Nonlinear total variation based noise removal algorithms. Physica D 1992, 60:259-268.
24. Sbalzarini I.F., Koumoutsakos P. Feature point tracking and trajectory analysis for video imaging in cell biology. J. Struct. Biol. 2005, 151:182-195.
25. Stark J.A. Adaptive image contrast enhancement using generalization of histogram equalization. IEEE Trans. Image Proc. 2000, 9:889-896.
26. Stephens D.J., Allan V.J. Light microscopy techniques for live cell imaging. Science 2003, 300:82-86.
27. Stone M.C., Roegiers F., Rolls M.M. Microtubules have opposite orientation in axons and dendrites of Drosophila neurons. Mol. Biol. Cell 2008, 19:4122-4129.
28. Tasdizen T. Principal components for non-local means image denoising. Proc. IEEE Int. Conf. Image Proc. 2008, 1728-1731.
29. Tomasi C., Manduchi R. Bilateral filtering for gray and color images. Proc. IEEE Int. Conf. Comput. Vis. 1998, 839-846.
30. Viola P., Jones M.J. Robust real-time face detection. Int. J. Comput. Vis. 2004, 57:137-154.
31. Yang X., Clausi D.A. Structure-preserving speckle reduction of SAR images using nonlocal means filters. Proc. IEEE Int. Conf. Image Proc. 2009, 2985-2988.
32. Yu Z., Bajaj C. Detecting circular and rectangular particles based on geometric feature detection in electron micrographs. J. Struct. Biol. 2004, 145:168-180.
33. Zhu Y., Carragher B., Mouche F., Potter C.S. Automatic particle detection through efficient Hough transforms. IEEE Trans. Med. Imaging 2003, 22:1053-1062.