Fractal dimension analysis for spike detection in low SNR extracellular signals

Journal of Neural Engineering

Volumn 13, Issue 3, 2016, Pages

  Salmasi, Mehrdad ^a   Büttner, Ulrich ^a   Glasauer, Stefan ^a,b  

^a UNIVERSITY OF MUNICH   (Germany)

^b Bernstein Center for Computational Neuroscience   (Germany)

Author keywords

box counting; extracellular signal; fractal dimension; low SNR; semi intact spikes; spike detection

Indexed keywords

ALGORITHMS; ELECTRODES; FRACTAL DIMENSION; FRACTALS; NEURONS; SIGNAL ANALYSIS; SIGNAL DETECTION;

BOX-COUNTING; EXTRACELLULAR SIGNALS; LOW SNR; SEMI-INTACT; SPIKE DETECTION;

SIGNAL TO NOISE RATIO;

ALGORITHM; ARTICLE; FRACTAL ANALYSIS; NOISE; PRIORITY JOURNAL; PROBABILITY; SIGNAL NOISE RATIO; SIMULATION; ANIMAL; BIOLOGICAL MODEL; COMPUTER SIMULATION; EVOKED RESPONSE; EXTRACELLULAR SPACE; MACACA; PHYSIOLOGY; SIGNAL PROCESSING; WAVELET ANALYSIS;

ALGORITHMS; ANIMALS; COMPUTER SIMULATION; EVOKED POTENTIALS; EXTRACELLULAR SPACE; FRACTALS; MACACA; MODELS, NEUROLOGICAL; SIGNAL PROCESSING, COMPUTER-ASSISTED; SIGNAL-TO-NOISE RATIO; WAVELET ANALYSIS;

EID: 84969944950     PISSN: 17412560     EISSN: 17412552     Source Type: Journal    
DOI: 10.1088/1741-2560/13/3/036004     Document Type: Article

References (65)

1. Lewicki M S 1998 A review of methods for spike sorting: the detection and classification of neural action potentials Netw., Comput. Neural Syst. 9 R53-78
2. Guillory K and Normann R 1999 A 100-channel system for real time detection and storage of extracellular spike waveforms J. Neurosci. Methods 91 21-9
3. Takahashi S, Anzai Y and Sakurai Y 2003 Automatic sorting for multi-neuronal activity recorded with tetrodes in the presence of overlapping spikes J. Neurophysiol. 89 2245-58
4. Lewicki M S 1994 Bayesian modeling and classification of neural signals Neural Comput. 6 1005-30
5. Nicolelis M A 2007 Methods for Neural Ensemble Recordings (Boca Raton, FL: CRC Press)
6. Kim S and McNames J 2007 Automatic spike detection based on adaptive template matching for extracellular neural recordings J. Neurosci. Methods 165 165-74
7. Obeid I and Wolf P D 2004 Evaluation of spike-detection algorithms for a brain-machine interface application IEEE Trans. Biomed. Eng. 51 905-11
8. Adamos D A, Kosmidis E K and Theophilidis G 2008 Performance evaluation of PCA-based spike sorting algorithms Comput. Methods Programs Biomed. 91 232-44
9. Abeles M and Goldstein M H Jr 1977 Multispike train analysis Proc. IEEE 65 762-73
10. Chitaliya N G and Trivedi A 2010 Feature extraction using wavelet-PCA and neural network for application of object classification and face recognition 2nd Int. Conf. on Computer Engineering and Applications (ICCEA) vol 1 (Piscataway, NJ: IEEE) pp 510-4
11. Gupta M R and Jacobson N P 2006 Wavelet principal component analysis and its application to hyperspectral images IEEE Int. Conf. on Image Processing (Piscataway, NJ: IEEE) pp 1585-8
12. Mandelbrot B B 1983 The Fractal Geometry of Nature (London: Macmillan)
13. Falconer K 2013 Fractal Geometry Mathematical Foundations and Applications (New York: Wiley)
14. Lo T, Leung H, Litva J and Haykin S 1993 Fractal characterisation of sea-scattered signals and detection of sea-surface targets IEE Proc. Radar and Signal Processing (IET) vol 140 pp 243-50
15. Baish J W and Jain R K 2000 Fractals and cancer Cancer Res. 60 3683-8
16. Wardlaw G, Wong R and Noseworthy M D 2008 Identification of intratumour low frequency microvascular components via bold signal fractal dimension mapping Phys. Medica 24 87-91
17. Esteller R, Vachtsevanos G, Echauz J, Henry T, Pennell P, Epstein C, Bakay R, Bowen C and Litt B 1999 Fractal dimension characterizes seizure onset in epileptic patients IEEE Int. Conf. on Acoustics, Speech, and Signal Processing vol 4 (Piscataway, NJ: IEEE) pp 2343-6
18. Acharya R U, Faust O, Kannathal N, Chua T and Laxminarayan S 2005 Nonlinear analysis of EEG signals at various sleep stages Comput. Methods Programs Biomed. 80 37-45
19. Klonowski W, Olejarczyk E, Stepien R, Jalowiecki P and Rudner R 2006 Monitoring the depth of anaesthesia using fractal complexity method Emergent Patterns in Nature Complexus Mundi pp 333-42
20. Liu Y, Sourina O and Nguyen M K 2010 Real-time EEG-based human emotion recognition and visualization Int. Conf. on Cyberworlds (CW) (Piscataway, NJ: IEEE) pp 262-9
21. Zhang L, Liu J Z, Dean D, Sahgal V and Yue G H 2006 A three-dimensional fractal analysis method for quantifying white matter structure in human brain J. Neurosci. Methods 150 242-53
22. Pradhan N and Narayana Dutt D 1993 Use of running fractal dimension for the analysis of changing patterns in electroencephalograms Comput. Biol. Med. 23 381-8
23. Arle J E and Simon R H 1990 An application of fractal dimension to the detection of transients in the electroencephalogram Electroencephalogr. Clin. Neurophysiol. 75 296-305
24. Holt G R and Koch C 1999 Electrical interactions via the extracellular potential near cell bodies J. Comput. Neurosci. 6 169-84
25. Pettersen K H, Hagen E and Einevoll G T 2008 Estimation of population firing rates and current source densities from laminar electrode recordings J. Comput. Neurosci. 24 291-313
26. Smith L S and Mtetwa N 2007 A tool for synthesizing spike trains with realistic interference J. Neurosci. Methods 159 170-80
27. Thorbergsson P T, Garwicz M, Schouenborg J and Johansson A J 2012 Computationally efficient simulation of extracellular recordings with multielectrode arrays J. Neurosci. Methods 211 133-44
28. Camuñas-Mesa L A and Quiroga R Q 2013 A detailed and fast model of extracellular recordings Neural Comput. 25 1191-212
29. Nakatani H et al 2001 Detection of nerve action potentials under low signal-to-noise ratio condition IEEE Trans. Biomed. Eng. 48 845-9
30. Nenadic Z and Burdick J W 2005 Spike detection using the continuous wavelet transform IEEE Trans. Biomed. Eng. 52 74-87
31. Rutishauser U, Schuman E M and Mamelak A N 2006 Online detection and sorting of extracellularly recorded action potentials in human medial temporal lobe recordings, in vivo J. Neurosci. Methods 154 204-24
32. Borghi T, Gusmeroli R, Spinelli A and Baranauskas G 2007 A simple method for efficient spike detection in multiunit recordings J. Neurosci. Methods 163 176-80
33. Deng S, Srinivasan R, Lappas T and D'Zmura M 2010 EEG classification of imagined syllable rhythm using hilbert spectrum methods J. Neural Eng. 7 046006
34. Fatourechi M, Ward R and Birch G 2008 A self-paced brain-computer interface system with a low false positive rate J. Neural Eng. 5 9
35. Jolliffe I 2005 Principal Component Analysis (New York: Wiley)
36. Bashashati A, Fatourechi M, Ward R K and Birch G E 2007 A survey of signal processing algorithms in brain-computer interfaces based on electrical brain signals J. Neural Eng. 4 R32
37. Harris K D, Henze D A, Csicsvari J, Hirase H and Buzsáki G 2000 Accuracy of tetrode spike separation as determined by simultaneous intracellular and extracellular measurements J. Neurophysiol. 84 401-14
38. Quotb A, Bornat Y and Renaud S 2011 Wavelet transform for real-time detection of action potentials in neural signals Frontiers Neuroeng. 4 1-0
39. Quiroga R Q, Nadasdy Z and Ben-Shaul Y 2004 Unsupervised spike detection and sorting with wavelets and superparamagnetic clustering Neural Comput. 16 1661-87
40. Letelier J C and Weber P P 2000 Spike sorting based on discrete wavelet transform coefficients J. Neurosci. Methods 101 93-106
41. Hulata E, Segev R, Shapira Y, Benveniste M and Ben-Jacob E 2000 Detection and sorting of neural spikes using wavelet packets Phys. Rev. Lett. 85 4637-40
42. Pavlov A, Makarov V A, Makarova I and Panetsos F 2007 Sorting of neural spikes: when wavelet based methods outperform principal component analysis Nat. Comput. 6 269-81
43. Feng G-C, Yuen P C and Dai D-Q 2000 Human face recognition using PCA on wavelet subband J. Electron. Imaging 9 226-33
44. Falconer K and Howroyd J 1997 Packing dimensions of projections and dimension profiles Mathematical Proc. Cambridge Philosophical Society vol 121 (Cambridge: Cambridge University Press) pp 269-86
45. Su H and Wenxia L 1996 Packing dimension of generalized moran sets Prog. Nat. Sci. 6 148-52
46. Talagrand M and Xiao Y 1996 Fractional brownian motion and packing dimension J. Theor. Probab. 9 579-93
47. Ding M, Grebogi C, Ott E, Sauer T and Yorke J A 1993 Estimating correlation dimension from a chaotic time series: when does plateau onset occur? Physica D 69 404-24
48. Carvajal R, Wessel N, Vallverdú M, Caminal P and Voss A 2005 Correlation dimension analysis of heart rate variability in patients with dilated cardiomyopathy Comput. Methods Programs Biomed. 78 133-40
49. Wang W, Wu Z and Chen J 2001 Fault identification in rotating machinery using the correlation dimension and bispectra Nonlinear Dyn. 25 383-93
50. Camastra F and Vinciarelli A 2002 Estimating the intrinsic dimension of data with a fractal-based method IEEE Trans. Pattern Anal. Mach. Intell. 24 1404-7
51. Lam L 2003 Introduction to Nonlinear Physics (Berlin: Springer)
52. Li X, Jiang J, Zhu W, Yu C, Sui M, Wang Y and Jiang T 2007 Asymmetry of prefrontal cortical convolution complexity in males with attention-deficit/hyperactivity disorder using fractal information dimension Brain Dev. 29 649-55
53. Yu L, Zhang D, Wang K and Yang W 2005 Coarse iris classification using box-counting to estimate fractal dimensions Pattern Recognit. 38 1791-8
54. Salmasi M and Modarres-Hashemi M 2009 Design and analysis of fractal detector for high resolution radars Chaos Solitons Fractals 40 2133-45
55. Ercolini E, Valle F, Adamcik J, Witz G, Metzler R, De Los Rios P, Roca J and Dietler G 2007 Fractal dimension and localization of DNA knots Phys. Rev. Lett. 98 058102
56. Bruno O M, de Oliveira Plotze R, Falvo M and de Castro M 2008 Fractal dimension applied to plant identification Inf. Sci. 178 2722-33
57. Dubuc B, Quiniou J, Roques-Carmes C, Tricot C and Zucker S 1989 Evaluating the fractal dimension of profiles Phys. Rev. A 39 1500
58. Glidden D V, Shiboski S C and McCulloch C E 2011 Regression Methods in Biostatistics: Linear, Logistic, Survival, and Repeated Measures Models (Berlin: Springer)
59. Gnitecki J and Moussavi Z 2005 The fractality of lung sounds: a comparison of three waveform fractal dimension algorithms Chaos Solitons Fractals 26 1065-72
60. Henze D, Harris K, Borhegyi Z, Csicsvari J, Mamiya A, Hirase H, Sirota A and Buzsáki G Simultaneous intracellular and extracellular recordings from hippocampus region CA1 of anesthetized rats CRCNS.org DOI: http://dx.doi.org/10.6080/K02Z13FP
61. Zviagintsev A, Perelman Y and Ginosar R 2006 Algorithms and architectures for low power spike detection and alignment J. Neural Eng. 3 35
62. Yang C, Olson B and Si J 2011 A multiscale correlation of wavelet coefficients approach to spike detection Neural Comput. 23 215-50
63. Shahid S and Smith L S 2008 A novel technique for spike detection in extracellular neurophysiological recordings using cepstrum of bispectrum Proc. European Signal Processing Conf.
64. Grassberger P 1993 On efficient box counting algorithms Int. J. Mod. Phys. C 4 515-23
65. Hou X-J, Gilmore R, Mindlin G B and Solari H G 1990 An efficient algorithm for fast O(N∗ln(N)) box counting Phys. Lett. A 151 43-6