Bayesian decoding using unsorted spikes in the rat hippocampus

Journal of Neurophysiology

Volumn 111, Issue 1, 2014, Pages 217-227

  Kloosterman, Fabian ^a,b,c,d   Layton, Stuart P ^a   Chen, Zhe ^a,e   Wilson, Matthew A ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

^b Belgium   (Belgium)

^c IMEC   (Belgium)

^d UNIVERSITY OF LEUVEN   (Belgium)

^e MASSACHUSETTS GENERAL HOSPITAL   (United States)

Author keywords

Kernel density estimation; Neural decoding; Population codes; Spatial temporal Poisson process; Spike sorting

Indexed keywords

ALGORITHM; ANIMAL TISSUE; ARTICLE; BAYES THEOREM; COMPARATIVE STUDY; HIPPOCAMPUS; NONHUMAN; PERFORMANCE; PRIORITY JOURNAL; RAT; SPIKE; SPIKE WAVE;

KERNEL DENSITY ESTIMATION; NEURAL DECODING; POPULATION CODES; SPATIAL-TEMPORAL POISSON PROCESS; SPIKE SORTING;

ACTION POTENTIALS; ALGORITHMS; ANIMALS; BAYES THEOREM; HIPPOCAMPUS; MODELS, NEUROLOGICAL; RATS;

EID: 84890012712     PISSN: 00223077     EISSN: 15221598     Source Type: Journal    
DOI: 10.1152/jn.01046.2012     Document Type: Article

References (40)

1. Bartlett MS. The spectral analysis of two-dimensional point processes. Biometrika 51: 299-311, 1964.
2. Boloori AR, Jenks RA, Desbordes G, Stanley GB. Encoding and decoding cortical representations of tactile features in the vibrissa system. J Neurosci 30: 9990-10005, 2010.
3. Botev ZI, Grotowski JF, Kroese DP. Kernel density estimation via diffusion. Ann Stat 38: 2916-2957, 2010.
4. Brown EN, Frank LM, Tang D, Quirk MC, Wilson MA. A statistical paradigm for neural spike train decoding applied to position prediction from ensemble firing patterns of rat hippocampal place cells. J Neurosci 18: 7411-7425, 1998.
5. Chapin JK. Using multi-neuron population recordings for neural prosthetics. Nat Neurosci 7: 452-455, 2004.
6. Davidson TJ, Kloosterman F, Wilson MA. Hippocampal replay of extended experience. Neuron 63: 497-507, 2009.
7. Diggle PJ. Statistical Analysis of Spatial Point Patterns (2nd ed.). Oxford, UK: Oxford Univ. Press, 2003.
8. Fraser GW, Chase SM, Whitford A, Schwartz AB. Control of a braincomputer interface without spike sorting. J Neural Eng 6: 055004, 2009.
9. Georgopoulos AP, Schwartz AB, Kettner RE. Neuronal population coding of movement direction. Science 233: 1416-1419, 1986.
10. Girolami M. Probability density estimation from optimally condensed data samples. IEEE Trans Pattern Anal Mach Intell 25: 1253-1264, 2003.
11. Goodman IN, Johnson DH. Information theoretic bounds on neural prosthesis effectiveness: the importance of spike sorting. In: Proc IEEE Int Conf Acoust Speech Signal Process 2008: 5204-5207, 2008.
12. Gupta AS, Van der Meer MA, Touretzky DS, Redish AD. Hippocampal replay is not a simple function of experience. Neuron 65: 695-705, 2010.
13. Harris KD, Henze DA, Csicsvari J, Hirase H, Buzsáki G. Accuracy of tetrode spike separation as determined by simultaneous intracellular and extracellular measurements. J Neurophysiol 84: 401-414, 2000.
14. Hochberg LR, Bacher D, Jarosiewicz B, Masse NY, Simeral JD, Vogel J, Haddadin S, Liu J, Cash SS, Van der Smagt P, Donoghue JP. Reach and grasp by people with tetraplegia using a neurally controlled robotic arm. Nature 485: 372-375, 2012.
15. Huang D, Chow TW. Enhancing density-based data reduction using entropy. Neural Comput 18: 470-495, 2006.
16. Huys QJ, Zemel RS, Natarajan R, Dayan P. Fast population coding. Neural Comput 19: 404-441, 2007.
17. Jacobs AL, Fridman G, Douglas RM, Alam NM, Latham PE, Prusky GT, Nirenberg S. Ruling out and ruling in neural codes. Proc Natl Acad Sci USA 106: 5936-5941, 2009.
18. Kloosterman F. Analysis of hippocampal memory replay using neural population decoding. Neuromethods 67: 259-282, 2012.
19. Kloosterman F, Davidson TJ, Gomperts SN, Layton SP, Hale G, Nguyen DP, Wilson MA. Micro-drive array for chronic in vivo recording: drive fabrication. J Vis Exp 26: 1094, 2009.
20. Luczak A, Narayanan NS. Spectral representation-analyzing single-unit activity in extracellularly recorded neuronal data without spike sorting. J Neurosci Methods 144: 53-61, 2005.
21. Mitra P, Murthy C, Pal S. Density-based multiscale data condensation. Pattern Anal Mach 24: 734-747, 2002.
22. Nguyen DP, Layton SP, Hale G, Gomperts SN, Davidson TJ, Kloosterman F, Wilson MA. Micro-drive array for chronic in vivo recording: tetrode assembly. J Vis Exp 26: 1098, 2009.
23. Paninski L, Pillow J, Lewi J. Statistical models for neural encoding, decoding, and optimal stimulus design. Prog Brain Res 165: 493-507, 2007.
24. Quian Quiroga R, Panzeri S. Extracting information from neuronal populations: information theory and decoding approaches. Nat Rev Neurosci 10: 173-185, 2009.
25. Sanger T. Neural population codes. Curr Opin Neurobiol 13: 238-249, 2003.
26. Schmitzer-Torbert N, Jackson J, Henze D, Harris K, Redish AD. Quantitative measures of cluster quality for use in extracellular recordings. Neuroscience 131: 1-11, 2005.
27. Schwartz AB, Cui XT, Weber DJ, Moran DW. Brain-controlled interfaces: movement restoration with neural prosthetics. Neuron 52: 205-220, 2006.
28. Scott DW. Multivariate Density Estimation: Theory, Practice, and Visualization. New York: Wiley, 1992.
29. Stark E, Abeles M. Predicting movement from multiunit activity. J Neurosci 27: 8387-8394, 2007.
30. Truccolo W, Eden UT, Fellows MR, Donoghue JP, Brown EN. A point process framework for relating neural spiking activity to spiking history, neural ensemble, and extrinsic covariate effects. J Neurophysiol 93: 1074-1089, 2005.
31. Ventura V. Spike train decoding without spike sorting. Neural Comput 20: 923-963, 2008.
32. Ventura V. Automatic spike sorting using tuning information. Neural Comput 21: 2466-2501, 2009a.
33. Ventura V. Traditional waveform based spike sorting yields biased rate code estimates. Proc Natl Acad Sci USA 106: 6921-6926, 2009b.
34. Wand MP, Jones MC. Kernel Smoothing. London: Chapman and Hall, 1995.
35. Wolpert R, Ickstadt K. Poisson/gamma random field models for spatial statistics. Biometrika 85: 251-267, 1998.
36. Wood F, Black MJ. A nonparametric Bayesian alternative to spike sorting. J Neurosci Methods 173: 1-12, 2008.
37. Zhang K, Ginzburg I, McNaughton BL, Sejnowski TJ. Interpreting neuronal population activity by reconstruction: unified framework with application to hippocampal place cells. J Neurophysiol 79: 1017-1044, 1998.
38. Zhang X, King ML, Hyndman RJ. A Bayesian approach to bandwidth selection for multivariate density estimation. J Comput Stat Data Anal 50: 3009-3031, 2006.
39. Zhou A, Cai Z, Wei L, Qian W. M-kernel merging: towards density estimation over data streams. Proc IEEE Int Conf Database Syst Adv Appl 2003: 285-292, 2003.
40. Zhuang J, Truccolo W, Vargas-Irwin C, Donoghue JP. Decoding 3-D reach and grasp kinematics from high-frequency local field potentials in primate primary motor cortex. IEEE Trans Biomed Eng 57: 1774-1784, 2010.