Investigating neuronal activity by SPYCODE multi-channel data analyzer

Neural Networks

Volumn 23, Issue 6, 2010, Pages 685-697

  Bologna, Luca Leonardo ^a,c   Pasquale, Valentina ^a   Garofalo, Matteo ^a   Gandolfo, Mauro ^b   Baljon, Pieter Laurens ^b,d   Maccione, Alessandro ^a   Martinoia, Sergio ^a,b   Chiappalone, Michela ^a  

^a ISTITUTO ITALIANO DI TECNOLOGIA   (Italy)

^b UNIVERSITY OF GENOA   (Italy)

^c SORBONNE UNIVERSITÉ   (France)

^d CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Batch processing; Cell culture; Connectivity; Micro electrode array

Indexed keywords

BATCH PROCESSING; CELL ASSEMBLY; COMPUTATIONAL OPERATIONS; EXTRACTING INFORMATION; IN-VITRO; IN-VIVO; MANUAL INTERVENTION; MICROELECTRODE ARRAY; MULTI-CHANNEL ACQUISITION; MULTI-CHANNEL RECORDING; MULTICHANNEL DATA; NETWORK LEVEL; NEURONAL ACTIVITIES; NEURONAL NETWORKS; OPEN-SOURCE; SCIENTIFIC COMMUNITY; SINGLE CHANNELS;

CELL CULTURE; DATA PROCESSING; NEURAL NETWORKS;

BATCH CELL CULTURE;

ALGORITHM; ANALYZER; ARTICLE; ARTIFICIAL NEURAL NETWORK; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER PROGRAM; INFORMATION PROCESSING; MULTICHANNEL RECORDER; NEUROPHARMACOLOGY; PRIORITY JOURNAL; SPIKE WAVE;

ACTION POTENTIALS; ANIMALS; CELLS, CULTURED; ELECTROPHYSIOLOGY; HUMANS; NERVE NET; NEURONS; NEUROPHYSIOLOGY; RATS; RATS, SPRAGUE-DAWLEY; SIGNAL PROCESSING, COMPUTER-ASSISTED; SOFTWARE;

EID: 77953812856     PISSN: 08936080     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neunet.2010.05.002     Document Type: Article

References (70)

1. Adrian, E. D. (1928). The basis of sensation: the action of sense organs. New York, NJ.
2. Arnold F.J.L., Hofmann F., Bengtson C.P., Witmtmann M., Vanhoutte P., Bading H. Microelectrode array recordings of cultured hippocampal networks reveal a simple model for transcription and protein synthesis-dependent plasticity. The Journal of Physiology 2005, 564:3-19.
3. Baker R.E., Corner M.A., van Pelt J. Spontaneous neuronal discharge patterns in developing organotypic mega-co-cultures of neonatal rat cerebral cortex. Brain Research 2006, 1101(1):29-35.
4. Bakkum D.J., Chao Z.C., Potter S.M. Long-term activity-dependent plasticity of action potential propagation delay and amplitude in cortical networks. PLoS One 2008, 3(5):e2088.
5. Baljon P.L., Chiappalone M., Martinoia S. Interaction of electrically evoked responses in networks of dissociated cortical neurons. Physical Review E 2009, 80(3):031906.
6. Baruchi I., Volman V., Raichman N., Shein M., Ben-Jacob E. The emergence and properties of mutual synchronization in in vitro coupled cortical networks. European Journal of Neuroscience 2008, 28:1825-1835.
7. Beggs J.M., Plenz D. Neuronal avalanches in neocortical circuits. The Journal of Neuroscience 2003, 23(35):11167-11177.
8. Beggs J.M., Plenz D. Neuronal avalanches are diverse and precise activity patterns that are stable for many hours in cortical slice cultures. The Journal of Neuroscience 2004, 24:5216-5229.
9. Ben-Ari Y. Developing networks play a similar melody. Trends in Neurosciences 2001, 24(6):353-360.
10. Blanche T.J., Spacek M.A., Hetke J.F., Swindale N.V. Polytrodes: high-density silicon electrode arrays for large-scale multiunit recording. Journal of Neurophysiology 2005, 93(5):2987-3000.
11. Bologna L.L., Nieus T., Tedesco M., Chiappalone M., Benfenati F., Martinoia S. Low-frequency stimulation enhances burst activity in cortical cultures during development. Neuroscience 2010, 165(3):692-704.
12. Bonzano L., Bove M., Martinoia S. Effects of NMDA and non-NMDA receptors antagonists on the dynamic behavior of cultured cortical networks. Neurocomputing 2006, 69(16-18):1897-1903.
13. Borst A., Theunissen F. Information theory and neural code [review]. Nature 1999, 11.
14. Borst A., Theunissen F.E. Information theory and neural coding. Nature Neuroscience 1999, 2(11):947-957.
15. Bove M., Grattarola M., Verreschi G. In vitro 2D networks of neurons characterized by processing the signals recorded with a planar microtransducer array. IEEE Transactions on Biomedical Engineering 1997, 44(10):964-977.
16. Buzsaki G. Large-scale recording of neuronal ensembles. Nature Neuroscience 2004, 7(5):446-451.
17. Chavez M., Martinerie J., Le Van Quyen M. Statistical assessment of nonlinear causality: application to epileptic EEG signals. Journal of Neuroscience Methods 2003, 124:113-128.
18. Chiappalone M., Bove M., Vato A., Tedesco M., Martinoia S. Dissociated cortical networks show spontaneously correlated activity patterns during in vitro development. Brain Research 2006, 1093(1):41-53.
19. Chiappalone M., Massobrio P., Martinoia S. Network plasticity in cortical assemblies. European Journal of Neuroscience 2008, 28:221-237.
20. Chiappalone M., Novellino A., Vajda I., Vato A., Martinoia S., van Pelt J. Burst detection algorithms for the analysis of spatio-temporal patterns in cortical networks of neurons. Neurocomputing 2005, 65-66:653-662.
21. Chiappalone M., Vato A., Berdondini L., Koudelka-Hep M., Martinoia S. Network dynamics and synchronous activity in cultured cortical neurons. International Journal of Neural Systems 2007, 17(2):87-103.
22. Cocater-Zilgien J.H., Delcomyn F. Identification of bursts in spike trains. Journal of Neuroscience Methods 1992, 41:19-30.
23. Corner M.A. Spontaneous neuronal burst discharges as dependent and independent variables in the maturation of cerebral cortex tissue cultured in vitro: a review of activity-dependent studies in live 'model' systems for the development of intrinsically generated bioelectric slow-wave sleep patterns. Brain Research Reviews 2008, 59(1):221-244.
24. Cozzi L., D'Angelo P., Sanguineti V. Encoding of time-varying stimuli in population of cultured neurons. Biological Cybernetics 2006, 94(5):335-349.
25. Cui J., Xu L., Bressler S.L., Ding M., Liang H. BSMART: a MATLAB/C toolbox for analysis of multichannel neural time series. Neural Networks 2008, 21:1094-1104.
26. Dayan P., Abbott L.F. Theoretical neuroscience: computational and mathematical modeling of neural systems 2001, MIT Press, Cambridge.
27. Egert U., Heck D., Aertsen A. Two-dimensional monitoring of spiking networks in acute brain slices. Experimental Brain Research 2002, 142:268-274.
28. Egert U., Knott T., Schwarz C., Nawrot M., Brandt A., Rotter S., et al. MEA-Tools: an open source toolbox for the analysis of multi-electrode data with MATLAB. Journal of Neuroscience Methods 2002, 117:33-42.
29. Eytan D., Marom S. Dynamics and effective topology underlying synchronization in networks of cortical neurons. The Journal of Neuroscience 2006, 26(33):8465-8476.
30. Garofalo M., Nieus T., Massobrio P., Martinoia S. Evaluation of the performance of information theory-based methods and cross-correlation to estimate the functional connectivity in cortical networks. PLoS One 2009, 4(8):e6482.
31. Gourévitch B., Eggermont J.J. Evaluating information transfer between auditory cortical neurons. Journal of Neurophysiology 2007, 97:2533-2543.
32. Gramowski A., Jügelt K., Stüwe S., Schulze R., McGregor G.P., Wartenberg-Demand A., et al. Functional screening of traditional antidepressants with primary cortical neuronal networks grown on multielectrode neurochips. European Journal of Neuroscience 2006, 24(2):455-465.
33. Gramowski A., Jugelt K., Weiss D.G., Gross G.W. Substance identification by quantitative characterization of oscillatoryactivity in murine spinal cord networks on microelectrode arrays. European Journal of Neuroscience 2004, 19(10):2815-2825.
34. Gross G.W., Azzazy H.M.E., Wu M.C., Rhodes B.K. The use of neuronal networks on multielectrode arrays as biosensors. Biosensors & Bioelectronics 1995, 10:553-567.
35. Gross G.W., Rhoades B.K., Jordan R.J. Neuronal networks for biochemical sensing. Sensors and Actuators 1992, 6:1-8.
36. Gross G.W., Rieske E., Kreutzberg G.W., Meyer A. A new fixed-array multi-microelectrode system designed for long-term monitoring of extracellular single unit neuronal activity in vitro. Neuroscience Letters 1977, 6:101-105.
37. Hebb D.O. Organization of behavior 1949, John Wiley & Sons, New York.
38. Jimbo Y., Tateno Y., Robinson H.P.C. Simultaneous induction of pathway-specific potentiation and depression in networks of cortical neurons. Biophysical Journal 1999, 76(February):670-678.
39. Kass R.E., Ventura V., Brown E.N. Statistical issues in the analysis of neuronal data. Journal of Neurophysiology 2005, 94:8-25.
40. Knox C.K. Detection of neuronal interactions using correlation analysis. Trends in Neurosciences 1981, 4:222-225.
41. Lungarella M., Pitti A., Kuniyoshi Y. Information transfer at multiple scales. Physical Review E 2007, 76:561171-5611710.
42. Maccione A., Gandolfo M., Massobrio P., Novellino A., Martinoia S., Chiappalone M. A novel algorithm for precise identification of spikes in extracellularly recorded neuronal signals. Journal of Neuroscience Methods 2009, 177(1):241-249.
43. Maeda E., Robinson H.P.C., Kawana A. The mechanism of generation and propagation of synchronized bursting in developing networks of cortical neurons. The Journal of Neuroscience 1995, 15:6834-6845.
44. Marom S., Shahaf G. Development, learning and memory in large random networks of cortical neurons: lessons beyond anatomy. Quarterly Reviews of Biophysics 2002, 35(1):63-87.
45. Meier R., Egert U., Aertsen A., Nawrot M.P. FIND-a unified framework for neuronal data analysis. Neural Networks 2008, 21:1085-1093.
46. Miller E.K., Wilson M.A. All my circuits: using multiple electrodes to understand functioning neural networks. Neuron 2008, 60:483-488.
47. Minerbi A., Kahana R., Goldfeld L., Kaufman M., Marom S., Ziv N.E. Long-term relationship between synaptic tenacity, synaptic remodeling, and network activity. PLoS Biology 2009, 7(6).
48. Nicolelis M.A.L. Advances in population coding. Progress in Brain Research 2001, 130:49-62.
49. Nicolelis M.A.L. Brain-machine interfaces to restore motor function and probe neural circuits. Nature Reviews Neuroscience 2003, 4:417-422.
50. Pasquale V., Martinoia S., Chiappalone M. A self-adapting approach for the detection of bursts and network bursts in neuronal cultures. Journal of Computational Neuroscience 2009.
51. Pasquale V., Massobrio P., Bologna L.L., Chiappalone M., Martinoia S. Self-organization and neuronal avalanches in networks of dissociated cortical neurons. Neuroscience 2008, 153(4):1354-1369.
52. Perkel D.H., Gerstein G.L., Moore G.P. Neuronal spike train and stochastic point processes I. The single spike train. Biophysical Journal 1967, 7:391-418.
53. Plenz D., Thiagarajan T.C. The organizing principles of neuronal avalanches: cell assemblies in the cortex?. Trends in Neurosciences 2007, 30(3).
54. Potter S.M. Distributed processing in cultured neural networks. Progress in Brain Research 2001, 130:49-62.
55. Quiroga R.Q., Panzeri S. Extracting information from neuronal populations: information theory and decoding approaches. Nature Reviews Neuroscience 2009, 10:173-185.
56. Raichman N., Ben-Jacob E. Identifying repeating motifs in the activation of synchronized bursts in cultured neuronal networks. Journal of Neuroscience Methods 2008, 170(1):96-110.
57. Raichman N., Volman V., Ben-Jacob E. Collective plasticity and individual stability in cultured neuronal networks. Neurocomputing 2006, 69:1150-1154.
58. Rieke F., Warland D., de Ruyter van Steveninck R., Bialek W. Spikes: exploring the neural code 1997, The MIT Press, Cambridge, MA.
59. Salinas E., Sejnowski T.J. Correlated neuronal activity and the flow of neural information. Nature Reviews Neuroscience 2001, 2(August):539-550.
60. Schneidman E., Berry M.J., Segev R., Bialek W. Weak pairwise correlations imply strongly correlated network states in a neural population. Nature 2006, 440:1007-1012.
61. Selinger J.V., Kulagina N.V., O'Shaughnessy T.J., Ma W., Pancrazio J.J. Methods for characterizing interspike intervals and identifying bursts in neuronal activity. Journal of Neuroscience Methods 2007, 162:64-71.
62. Shannon B.E. The mathematical theory of communication. The Bell System Technical Journal 1948, 27:379-423.
63. Tam D.C. An alternate burst analysis for detecting intra-burst firings based on inter-burst periods. Neurocomputing 2002, 44-46:1155-1159.
64. Tam D.C., Gross G.W. Extraction of dynamical changes in neuronal network circuitries using multiunit spike train analysis. Enabling technologies for cultured neural networks 1994, Academic Press, New York. D.A. Stenger, T.M. McKenna (Eds.).
65. Tateno T., Kawana A., Jimbo Y. Analytical characterization of spontaneous firing in networks of developing rat cultured cortical neurons. Physical Review Letters E 2002, 65(5 Pt 1):051924.
66. Van Pelt J., Wolters P.S., Corner M.A., Rutten W.L.C., Ramakers G.J.A. Long-term characterization of firing dynamics of spontaneous bursts in cultured neural networks. IEEE Transactions on Biomedical Engineering 2004, 51(11):2051-2062.
67. Vato A., Bonzano L., Chiappalone M., Cicero S., Morabito F., Novellino A., et al. Spike manager: a new tool for spontaneous and evoked neuronal networks activity characterization. Neurocomputing 2004, 58-60:1153-1161.
68. Wagenaar, D. A., DeMarse, T. B., & Potter, S. M. (2005). MeaBench: a toolset for multi-electrode data acquisition and on-line analysis. Paper presented in The 2nd Intl. IEEE EMBS conference on neural engineering.
69. Wagenaar D.A., Pine J., Potter S.M. An extremely rich repertoire of bursting patterns during the development of cortical cultures. BMC Neuroscience 2006, 7(11).
70. Xu J., Liu Z.-r., Liu R., Yang Q.-f. Information transmission in human cerebral cortex. Physica D 1997, 106:363-374.