The Community for Technology Leaders
RSS Icon
Issue No.11 - Nov. (2013 vol.35)
pp: 2736-3750
N. Chenouard , Quantitative Image Anal. Unit, Inst. Pasteur, Paris, France
I. Bloch , LTCI, Telecom ParisTech, Paris, France
J. Olivo-Marin , Quantitative Image Anal. Unit, Inst. Pasteur, Paris, France
In this paper, we present a method for simultaneously tracking thousands of targets in biological image sequences, which is of major importance in modern biology. The complexity and inherent randomness of the problem lead us to propose a unified probabilistic framework for tracking biological particles in microscope images. The framework includes realistic models of particle motion and existence and of fluorescence image features. For the track extraction process per se, the very cluttered conditions motivate the adoption of a multiframe approach that enforces tracking decision robustness to poor imaging conditions and to random target movements. We tackle the large-scale nature of the problem by adapting the multiple hypothesis tracking algorithm to the proposed framework, resulting in a method with a favorable tradeoff between the model complexity and the computational cost of the tracking procedure. When compared to the state-of-the-art tracking techniques for bioimaging, the proposed algorithm is shown to be the only method providing high-quality results despite the critically poor imaging conditions and the dense target presence. We thus demonstrate the benefits of advanced Bayesian tracking techniques for the accurate computational modeling of dynamical biological processes, which is promising for further developments in this domain.
Target tracking, Radar tracking, Bayes methods, Computational modeling, Biological system modeling,cluttered images, Particle tracking, biological imaging, multiple hypothesis tracking, target perceivability
N. Chenouard, I. Bloch, J. Olivo-Marin, "Multiple Hypothesis Tracking for Cluttered Biological Image Sequences", IEEE Transactions on Pattern Analysis & Machine Intelligence, vol.35, no. 11, pp. 2736-3750, Nov. 2013, doi:10.1109/TPAMI.2013.97
[1] N. Arhel, A. Genovesio, K.A. Kim, S. Miko, E. Perret, J.-C. Olivo-Marin, S. Shorte, and P. Charneau, "Quantitative Four-Dimensional Tracking of Cytoplasmic and Nuclear HIV-1 Complexes," Nature Methods, vol. 3, pp. 817-824, Oct. 2006.
[2] Y. Bar-Shalom and W.D. Blair, Multitarget-Multisensor Tracking Applications and Advances, vol. 3. Artech House, Oct. 2000.
[3] Y. Bar-Shalom, R.X. Li, and T. Kirubarajan, Estimation with Applications to Tracking and Navigation: Theory Algorithms and Software. Wiley-Blackwell, July 2001.
[4] M. Berkelaar, K. Eikland, and P. Notebaert, lp_solve version 5.5, 2010.
[5] S.S. Blackman, "Multiple Hypothesis Tracking for Multiple Target Tracking," IEEE Trans. Aerospace Electronic Systems, vol. 19, no. 1, pp. 5-18, Jan. 2004.
[6] S.S. Blackman, R.J. Dempster, and R.W. Reed, "Demonstration of Multiple-Hypothesis Tracking (MHT) Practical Real-Time Implementation Feasibility," Proc. SPIE, vol. 4473, pp. 470-475, 2001.
[7] S.S. Blackman and R. Popoli, Design and Analysis of Modern Tracking Systems. Artech House, 1999.
[8] H.A.P. Blom and Y. Bar-Shalom, "The Interacting Multiple Model Algorithm for Systems with Markovian Switching Coefficients," IEEE Trans. Automatic Control, vol. 33, no. 8, pp. 780-783, Aug. 1988.
[9] S. Bonneau, M. Dahan, and L.D. Cohen, "Single Quantum Dot Tracking Based on Perceptual Grouping Using Minimal Paths in a Spatiotemporal Volume," IEEE Trans. Image Processing, vol. 14, no. 9, pp. 1384-1395, Sept. 2005.
[10] B. Brandenburg and X. Zhuang, "Virus Trafficking—Learning from Single-Virus Tracking," Nature Rev. Microbiology, vol. 5, no. 3, pp. 197-208, Mar. 2007.
[11] M.K. Cheezum, W.F. Walker, and W.H. Guilford, "Quantitative Comparison of Algorithms for Tracking Single Fluorescent Particles," Biophysical J., vol. 81, pp. 2378-2388, Oct. 2001.
[12] D.-S. Chen, R.G. Batson, and Y. Dang, Applied Integer Programming: Modeling and Solution. Wiley & Sons, Jan. 2010.
[13] N. Chenouard, "Advances in Probabilistic Particle Tracking for Biological Imaging," PhD thesis, Télécom ParisTech, Jan. 2010.
[14] D. Chetverikov and J. Verestoi, "Feature Point Tracking for Incomplete Trajectories," Computing, vol. 62, pp. 321-338, 1999.
[15] I.J. Cox and S.L. Hingorani, "An Efficient Implementation of Reid's Multiple Hypothesis Tracking Algorithm and Its Evaluation for the Purpose of Visual Tracking," IEEE Trans. Pattern Analysis and Machine Intelligence, vol. 18, no. 2, pp. 138-150, Feb. 1996.
[16] F. de Chaumont, S. Dallongeville, N. Chenouard, N. Herve, S. Pop, T. Provoost, V. Meas-Yedid, P. Pankajakshan, T. Lecomte, Y.L. Montagner, T. Lagache, A. Dufour, and J.-C. Olivo-Marin, "Icy: An Open Bioimage Informatics Platform for Extended Reproducible Research," Nature Methods, vol. 9, no. 7, pp. 690-696, 2012.
[17] Sequential Monte Carlo Methods in Practice, A. Doucet, N. De Freitas, and N.J. Gordon, eds. Springer-Verlag, 2001.
[18] A. Genovesio, T. Liedl, V. Emiliani, W.J. Parak, M. Coppey-Moisan, and J.-C. Olivo-Marin, "Multiple Particle Tracking in 3-D+t Microscopy: Methods and Application to the Tracking of Endocytosed Quantum Dots," IEEE Trans. Image Processing, vol. 15, no. 5, pp. 1062-1070, May 2006.
[19] M. Guerriero, L. Svensson, D. Svensson, and P. Willett, "Shooting Two Birds with Two Bullets: How to Find Minimum Mean OSPA Estimates," Proc. Int'l Conf. Information Fusion, pp. 1-8, July 2010.
[20] K. Jaqaman, D. Loerke, M. Mettlen, H. Kuwata, S. Grinstein, S.L.L. Schmid, and G. Danuser, "Robust Single-Particle Tracking in Live-Cell Time-Lapse Sequences," Nature Methods, vol. 5, no. 8, pp. 695-702, July 2008.
[21] T. Kurien, "Issues in the Design of Practical Multitarget Tracking Algorithms," Multitarget-Multisensor Tracking: Advanced Applications, Y. Bar-Shalom, ed., Artech House, 1990.
[22] N. Li and X.R. Li, "Target Perceivability and Its Applications," IEEE Trans. Signal Processing, vol. 49, no. 11, pp. 2588-2604, Nov. 2001.
[23] N. Li and X.R. Li, "Tracker Design Based on Target Perceivability," IEEE Trans. Aerospace Electronic Systems, vol. 37, no. 1, pp. 214-225, Jan. 2001.
[24] R.P.S. Mahler, "Multitarget Bayes Filtering via First-Order Multitarget Moments," IEEE Trans. Aerospace Electronic Systems, vol. 39, no. 4, pp. 1152-1178, Oct. 2003.
[25] R.P.S. Mahler, "PHD Filters of Higher Order in Target Number," IEEE Trans. Aerospace Electronic Systems, vol. 43, no. 4, pp. 1523-1543, Oct. 2007.
[26] R.P.S. Mahler, Statistical Multisource-Multitarget Information Fusion. Artech House, 2007.
[27] C. Morefield, "Application of 0-1 Integer Programming to Multitarget Tracking Problems," IEEE Trans. Automatic Control, vol. 22, no. 3, pp. 302-312, June 1977.
[28] D. Musicki and R.J. Evans, "Target Existence Based MHT," Proc. IEEE Conf. Decision and Control, pp. 1228-1233, Dec. 2005.
[29] E. Nicolas, N. Chenouard, J.-C. Olivo-Marin, and A. Guichet, "A Dual Role for Actin and Microtubule Cytoskeleton in the Transport of Golgi Units from the Nurse Cells to the Oocyte across Ring Canals," Molecular Biology Cell, vol. 20, no. 1, pp. 556-568, Jan. 2009.
[30] J.-C. Olivo-Marin, "Extraction of Spots in Biological Images Using Multiscale Products," Pattern Recognition, vol. 35, no. 9, pp. 1989-1996, 2002.
[31] A.B. Poore and A.J. Robertson, "A New Lagrangian Relaxation Based Algorithm for a Class of Multidimensional Assignment Problems," Computational Optimization Applications, vol. 8, no. 2, pp. 129-150, Sept. 1997.
[32] V. Racine, M. Sachse, J. Salermo, V. Fraisier, A. Trubuil, and J.-B. Sibarita, "Visualization and Quantification of Vesicle Trafficking on a Three-Dimensional Cytoskeleton Network in Living Cells," J. Microscopy, vol. 225, no. 3, pp. 214-228, Mar. 2006.
[33] D. Reid, "An Algorithm for Tracking Multiple Targets," IEEE Trans. Automatic Control, vol. 24, no. 6, pp. 843-854, Dec. 1979.
[34] B. Ristic, S. Arulampalam, and N. Gordon, Beyond the Kalman Filter. Artech House, 2004.
[35] B. Ristic, B.-N. Vo, D. Clark, and B.-T. Vo, "A Metric for Performance Evaluation of Multi-Target Tracking Algorithms," IEEE Trans. Signal Processing, vol. 59, no. 7, pp. 3452-3457, July 2011.
[36] D. Sage, F.R. Neumann, F. Hediger, S.M. Gasser, and M. Unser, "Automatic Tracking of Individual Fluorescence Particles: Application to the Study of Chromosome Dynamics," IEEE Trans. Image Processing, vol. 14, no. 9, pp. 1372-1383, Sept. 2005.
[37] M.J. Saxton and K. Jacobson, "Single-Particle Tracking: Applications to Membrane Dynamics," Ann. Rev. Biophysics Biomolecular Structure, vol. 26, pp. 373-399, June 1997.
[38] I.F. Sbalzarini and P. Koumoutsakos, "Feature Point Tracking and Trajectory Analysis for Video Imaging in Cell Biology," J. Structural Biology, vol. 151, pp. 182-195, Aug. 2005.
[39] D. Schuhmacher, B.-T. Vo, and B.-N. Vo, "A Consistent Metric for Performance Evaluation of Multi-Object Filters," IEEE Trans. Signal Processing, vol. 56, no. 8, pp. 3447-3457, Aug. 2008.
[40] I. Smal, K. Draegestein, N. Galjart, W. Niessen, and E. Meijering, "Particle Filtering for Multiple Object Tracking in Dynamic Fluorescence Microscopy Images: Application to Microtubule Growth Analysis," IEEE Trans. Medical Imaging, vol. 27, no. 6, pp. 789-804, June 2008.
[41] I. Smal, M. Loog, W.J. Niessen, and E. Meijering, "Quantitative Comparison of Spot Detection Methods in Fluorescence Microscopy," IEEE Trans. Medical Imaging, vol. 29, no. 2, pp. 282-301, Feb. 2010.
[42] I. Smal, E. Meijering, K. Draegestein, N. Galjart, I. Grigoriev, A. Akhmanova, M.E. van Royen, A.B. Houtsmuller, and W.J. Niessen, "Multiple Object Tracking in Molecular Bioimaging by Rao-Blackwellized Marginal Particle Filtering," Medical Image Analysis, vol. 12, no. 6, pp. 764-777, Dec. 2008.
[43] L. Svensson, D. Svensson, M. Guerriero, and P. Willett, "Set JPDA Filter for Multitarget Tracking," IEEE Trans. Signal Processing, vol. 59, no. 10, pp. 4677-4691, Oct. 2011.
[44] D. Thomann, D.R. Rines, P.K. Sorger, and G. Danuser, "Automatic Fluorescent Tag Detection in 3D with Super-Resolution: Application to the Analysis of Chromosome Movement," J. Microscopy, vol. 208, no. 1, pp. 49-64, Oct. 2002.
[45] J. Vermaak, S. Maskell, and M. Briers, "A Unifying Framework for Multi-Target Tracking and Existence," Proc. Int'l Conf. Information Fusion, vol. 1, July 2005.
[46] B.-T. Vo, B.-N. Vo, and A. Cantoni, "Analytic Implementations of the Cardinalized Probability Hypothesis Density Filter," IEEE Trans. Signal Processing, vol. 55, no. 7, pp. 3553-3567, July 2007.
[47] C. Vonesch, F. Aguet, J.-L. Vonesch, and M. Unser, "The Colored Revolution of Bioimaging," IEEE Signal Processing Magazine, vol. 23, no. 3, pp. 20-31, May 2006.
120 ms
(Ver 2.0)

Marketing Automation Platform Marketing Automation Tool