Innovations in Electrophysiology

Methods, spike detection and sorting

Pastore VP (2020) Estimating functional connectivity and topology in large-scale neuronal assemblies. Department of Informatics, Bioengineering, Robotics and System Engineering (DIBRIS).

Yeganegi H, Salami P, Daliri MR (2020) A Template-Based Sequential Algorithm for Online Clustering of Spikes in Extracellular Recordings. Cognitive Computation.

Zhao Y, Jiang R, Xu Z, Guzman E, Hansma PK, Petzold L (2020) Scalable Bayesian Functional Connectivity Inference for Multi-Electrode Array Recordings. ArXiv.

Buccino AP, Hurwitz CL, Magland J, Garcia S, Siegle JH, Hurwitz R, Hennig MH (2019) SpikeInterface, a unified framework for spike sorting. bioRxiv:796599.

Dastgheyb RM, Yoo SW, Haughey NJ (2019) MEAnalyzer - a Spike Train Analysis Tool for Multi Electrode Arrays. Neuroinformatics.

Drebitz E, Schledde B, Kreiter AK, Wegener D (2019) Optimizing the Yield of Multi-Unit Activity by Including the Entire Spiking Activity. Front Neurosci 13:83.

Moca VV, Nagy-Dăbâcan A, Bârzan H, Mureşan RC (2019) Superlets: time-frequency super-resolution using wavelet sets. bioRxiv:583732.

Klempíř O, Krupička R, Petráková V, Krůšek J, Dittert I, Taylor A (2018) Automated Neurons Recognition and Sorting for Diamond Based Microelectrode Arrays Recording: A Feasibility Study. In: World Congress on Medical Physics and Biomedical Engineering 2018. IFMBE Proceedings (Lhotska L, Sukupova L, Lacković I, G I, eds): Springer Singapore

Yger P, Spampinato GL, Esposito E, Lefebvre B, Deny S, Gardella C, Stimberg M, Jetter F, Zeck G, Picaud S, Duebel J, Marre O (2018) A spike sorting toolbox for up to thousands of electrodes validated with ground truth recordings in vitro and in vivo. Elife 7.

Ferrari U, Gardella C, Marre O, Mora T (2017) Closed-loop estimation of retinal network sensitivity reveals signature of efficient coding. bioRxiv.

Henningson M, Illes S (2017) Analysis and Modeling of Subthreshold Neural Multi-Electrode Array Data by Statistical Field Theory. Front Comput Neurosci 11.

Maheswaranathan N, Baccus SA, Ganguli S (2017) Inferring hidden structure in multilayered neural circuits. bioRxiv.

Mayer M, Arrizabalaga O, Lieb F, Ciba M, Ritter S, Thielemann C (2017) Electrophysiological investigation of human embryonic stem cell derived neurospheres using a novel spike detection algorithm. Biosens Bioelectron 100:462-468.

Mottaghi S, Joseph K, Christ O, Feuerstein TJ, Hofmann UG (2017) When the ostrich-algorithm fails: Blanking method affects spike train statistics. bioRxiv.

Pastore VP, Godjoski A, Martinoia S, Massobrio P (2017) SPICODYN: A Toolbox for the Analysis of Neuronal Network Dynamics and Connectivity from Multi-Site Spike Signal Recordings. Neuroinformatics.

Valkki IA, Lenk K, Mikkonen JE, Kapucu FE, Hyttinen JAK (2017) Network-Wide Adaptive Burst Detection Depicts Neuronal Activity with Improved Accuracy. Front Comput Neurosci 11:40.

Wibral M, Finn C, Wollstadt P, Lizier J, Priesemann V (2017) Quantifying Information Modification in Developing Neural Networks via Partial Information Decomposition. Entropy 19:494.

Alegre-Cortes J, Soto-Sanchez C, Piza AG, Albarracin AL, Farfan FD, Felice CJ, Fernandez E (2016) Time-frequency analysis of neuronal populations with instantaneous resolution based on noise-assisted multivariate empirical mode decomposition. J Neurosci Methods 267:35-44.

Cotterill E, Charlesworth P, Thomas CW, Paulsen O, Eglen SJ (2016) A comparison of computational methods for detecting bursts in neuronal spike trains and their application to human stem cell-derived neuronal networks. J Neurophysiol 116:306-321.

Kapucu FE, Makinen ME, Tanskanen JM, Yla-Outinen L, Narkilahti S, Hyttinen JA (2016) Joint analysis of extracellular spike waveforms and neuronal network bursts. J Neurosci Methods 259:143-155.

Lefebvre B, Yger P, Marre O (2016) Recent progress in multi-electrode spike sorting methods. bioRxiv.

Leibig C, Wachtler T, Zeck G (2016) Unsupervised neural spike sorting for high-density microelectrode arrays with convolutive independent component analysis. Journal of Neuroscience Methods 271:1-13.

Mahmud M, Vassanelli S (2016) Processing and Analysis of Multichannel Extracellular Neuronal Signals: State-of-the-Art and Challenges. Front Neurosci 10:248.

Regalia G, Coelli S, Biffi E, Ferrigno G, Pedrocchi A (2016) A Framework for the Comparative Assessment of Neuronal Spike Sorting Algorithms towards More Accurate Off-Line and On-Line Microelectrode Arrays Data Analysis. Comput Intell Neurosci 2016:8416237.

Timme NM, Marshall NJ, Bennett N, Ripp M, Lautzenhiser E, Beggs JM (2016) Criticality Maximizes Complexity in Neural Tissue. Front Physiol 7:425.

Yger P, Spampinato GLB, Esposito E, Lefebvre B, Deny S, Gardella C, Stimberg M, Jetter F, Zeck G, Picaud S, Duebel J, Marre O (2016) Fast and accurate spike sorting in vitro and in vivo for up to thousands of electrodes. bioRxiv.

Eisenman LN, Emnett CM, Mohan J, Zorumski CF, Mennerick S (2015) Quantification of bursting and synchrony in cultured hippocampal neurons. J Neurophysiol 114:1059-1071.

Ness TV, Chintaluri C, Potworowski J, Leski S, Glabska H, Wojcik DK, Einevoll GT (2015) Modelling and Analysis of Electrical Potentials Recorded in Microelectrode Arrays (MEAs). Neuroinformatics 13:403-426.

le Feber J, Stoyanova, II, Chiappalone M (2014) Connectivity, excitability and activity patterns in neuronal networks. Phys Biol 11:036005.

Mahmud M, Pulizzi R, Vasilaki E, Giugliano M (2014) QSpike tools: a generic framework for parallel batch preprocessing of extracellular neuronal signals recorded by substrate microelectrode arrays. Front Neuroinform 8:26.

Martens MB, Chiappalone M, Schubert D, Tiesinga PH (2014) Separating burst from background spikes in multichannel neuronal recordings using return map analysis. Int J Neural Syst 24:1450012.

Petit LF, Jalabert M, Buhler E, Malvache A, Peret A, Chauvin Y, Watrin F, Represa A, Manent JB (2014) Normotopic cortex is the major contributor to epilepsy in experimental double cortex. Ann Neurol 76:428-442.

Stone T, Khawaja U, Perko N, Kiehl TR, Bergeron C (2014) Best practices for avoiding dominant experimental bias in analysis of multielectrode array signals. The Twenty Third Annual Computational Neuroscience Meeting.

Vardi R, Marmari H, Kanter I (2014) Error correction and fast detectors implemented by ultrafast neuronal plasticity. Phys Rev E 89.

Weir K, Blanquie O, Kilb W, Luhmann HJ, Sinning A (2014) Comparison of spike parameters from optically identified GABAergic and glutamatergic neurons in sparse cortical cultures. Front Cell Neurosci 8:460.

Mack CM, Lin B, Turner JD, Johnstone AF, Burgoon LD, Shafer TJ (2013) Burst and principal components analyses of mea data for 16 chemicals describe at least three effects classes. Neurotoxicology.

Nick C, Goldhammer M, Bestel R, Steger F, Daus AW, Thielemann C (2013) DrCell – A Software Tool for the Analysis of Cell Signals Recorded with Extracellular Microelectrodes Signal Processing: An International Journal (SPIJ) 7.

Vardi R, Goldental A, Guberman S, Kalmanovich A, Marmari H, Kanter I (2013) Sudden synchrony leaps accompanied by frequency multiplications in neuronal activity. Front Neural Circuits 7:176.

Becchetti A, Gullo F, Bruno G, Dossi E, Lecchi M, Wanke E (2012) Exact distinction of excitatory and inhibitory neurons in neural networks: a study with GFP-GAD67 neurons optically and electrophysiologically recognized on multielectrode arrays. Front Neural Circuits 6:63.

Bestel R, Daus AW, Thielemann C (2012) A novel automated spike sorting algorithm with adaptable feature extraction. J Neurosci Methods 211:168-178.

Gullo F, Maffezzoli A, Dossi E, Lecchi M, Wanke E (2012) Classifying heterogeneity of spontaneous up-states: a method for revealing variations in firing probability, engaged neurons and Fano factor. J Neurosci Methods 203:407-417.

Kapucu FE, Tanskanen JM, Mikkonen JE, Yla-Outinen L, Narkilahti S, Hyttinen JA (2012) Burst analysis tool for developing neuronal networks exhibiting highly varying action potential dynamics. Front Comput Neurosci 6:38.

Martiniuc AV, Knoll A (2012) Interspike interval based filtering of directional selective retinal ganglion cells spike trains. Comput Intell Neurosci 2012:918030.

Quotb A, Bornat Y, Raoux M, Lang J, Renaud S (2012) NeuroBetaMed: A re-configurable wavelet-based event detection circuit for in vitro biological signals. In: Circuits and Systems (ISCAS), 2012 IEEE International Symposium.

Wuchter J, Beuter S, Treindl F, Herrmann T, Zeck G, Templin MF, Volkmer H (2012) A comprehensive small interfering RNA screen identifies signaling pathways required for gephyrin clustering. J Neurosci 32:14821-14834.

Zullo L, Chiappalone M, Martinoia S, Benfenati F (2012) A "spike-based" grammar underlies directional modification in network connectivity: effect on bursting activity and implications for bio-hybrids systems. PLoS ONE 7:e49299.

Blenkinsop TA, Lang EJ (2011) Synaptic action of the olivocerebellar system on cerebellar nuclear spike activity. J Neurosci 31:14708-14720.

Fendyur A, Mazurski N, Shappir J, Spira ME (2011) Formation of Essential Ultrastructural Interface between Cultured Hippocampal Cells and Gold Mushroom-Shaped MEA- Toward "IN-CELL" Recordings from Vertebrate Neurons. Front Neuroeng 4:14.

Feng W, Cao Y, Patnaik D, Ramakrishnan N (2011) Temporal Data Mining for Neuroscience. In: GPU Computing Gems.

Langhammer CG, Kutzing MK, Luo V, Zahn JD, Firestein BL (2011) Skeletal myotube integration with planar microelectrode arrays in vitro for spatially selective recording and stimulation: a comparison of neuronal and myotube extracellular action potentials. Biotechnol Prog 27:891-895.

Mahn M (2011) Dynamical modes in coupled large scale networks.

Makarova J, Ibarz JM, Makarov VA, Benito N, Herreras O (2011) Parallel readout of pathway-specific inputs to laminated brain structures. Front Syst Neurosci 5:77.

Nam Y, Wheeler BC (2011) In vitro microelectrode array technology and neural recordings. Crit Rev Biomed Eng 39:45-61.

Prentice JS, Homann J, Simmons KD, Tkacik G, Balasubramanian V, Nelson PC (2011) Fast, scalable, bayesian spike identification for multi-electrode arrays. PLoS ONE 6:e19884.

Xydas D, Downes JH, Spencer MC, Hammond MW, Nasuto SJ, Whalley BJ, Becerra VM, Warwick K (2011) Revealing ensemble state transition patterns in multi-electrode neuronal recordings using hidden Markov models. IEEE Trans Neural Syst Rehabil Eng 19:345-355.

Biffi E, Ghezzi D, Pedrocchi A, Ferrigno G (2010) Development and validation of a spike detection and classification algorithm aimed at implementation on hardware devices. Comput Intell Neurosci:659050.

Krumin M, Reutsky I, Shoham S (2010) Correlation-based analysis and generation of multiple spike trains using hawkes models with an exogenous input. Front Comput Neurosci 4:147.

Passaro PA (2010) Multi-electrode Array Recording and Data Analysis Methods for Molluscan Central Nervous Systems.

Sun JJ, Kilb W, Luhmann HJ (2010) Self-organization of repetitive spike patterns in developing neuronal networks in vitro. Eur J Neurosci 32:1289-1299.

Zebinden CF (2010) Leader neurons in living neural networks and in leaky integrate and fire neuron models. Département de physique théorique.

Gullo F, Maffezzoli A, Dossi E, Wanke E (2009) Short-latency cross- and autocorrelation identify clusters of interacting cortical neurons recorded from multi-electrode array. J Neurosci Methods 181:186-198.

Maccione A, Gandolfo M, Massobrio P, Novellino A, Martinoia S, Chiappalone M (2009) A novel algorithm for precise identification of spikes in extracellularly recorded neuronal signals. J Neurosci Methods 177:241-249.

Pasquale V, Martinoia S, Chiappalone M (2009) A self-adapting approach for the detection of bursts and network bursts in neuronal cultures. J Comput Neurosci.

Moulin C, Gliere A, Barbier D, Joucla S, Yvert B, Mailley P, Guillemaud R (2008) A new 3-D finite-element model based on thin-film approximation for microelectrode array recording of extracellular action potential. IEEE Trans Biomed Eng 55:683-692.

Park I, Paiva AR, Demarse TB, Principe JC (2008) An efficient algorithm for continuous time cross correlogram of spike trains. J Neurosci Methods 168:514-523.

Raichman N, Ben-Jacob E (2008) Identifying repeating motifs in the activation of synchronized bursts in cultured neuronal networks. J Neurosci Methods 170:96-110.

Chao ZC, Bakkum DJ, Potter SM (2007) Region-specific network plasticity in simulated and living cortical networks: comparison of the center of activity trajectory (CAT) with other statistics. J Neural Eng 4:294-308.

Maffezzoli A, Signorini MG, Gullo F, Wanke E (2007) Non linear methods estimating neural network behavior on Micro-Electrode Array technology. Conf Proc IEEE Eng Med Biol Soc 1:449-452.

Rolston JD, Wagenaar DA, Potter SM (2007) Precisely timed spatiotemporal patterns of neural activity in dissociated cortical cultures. Neuroscience.

Zeck GM, Masland RH (2007) Spike train signatures of retinal ganglion cell types. Eur J Neurosci 26:367-380.

Blanche TJ, Swindale NV (2006) Nyquist interpolation improves neuron yield in multiunit recordings. J Neurosci Methods 155:81-91.

Liang PJ (2006) A New Method for Multiple Spike Train Analysis Based on Information Discrepancy. LNCS 4232, pp. 30–38, 2006.

Moulin C, Gliere A (2006) A new 3D finite element model of extracellular action potentials recording with a microelectrode in a tissue slice. Conf Proc IEEE Eng Med Biol Soc 1:603-606.

Raichman N, Volman V, Ben-Jacob E (2006) Collective plasticity and individual stability in cultured neuronal networks. Neurocomputing 69:1150-1154.

Wang GL, Liu X, Zhang PM, Liang PJ (2006) A New Method for Multiple Spike Train Analysis Based on Information Discrepancy. In: ICONIP 2006, Part I, (King I, ed).

Lin Y, Chen C, Chen L, Zeng S, Luo Q (2005) The analysis of electrode-recording-horizon in multi-electrode array(MEA). Conf Proc IEEE Eng Med Biol Soc 7:7345-7348.

Chiappalone M, Novellino A, Vajda I, Vato A, Martinoia S, van Pelt J (2004) Burst detection algorithms for the analysis of spatio-temporal patterns in cortical networks of neurons. Neurocomputing 65-66:653-662.

Segev R, Baruchi I, Hulata E, Ben-Jacob E (2004) Hidden neuronal correlations in cultured networks. Phys Rev Lett 92:118102.

Vato A, Bonzano L, Chiappalone M, Cicero S, Morabito F, Novellina A, Stillo G (2004) Spike manager: a new tool for spontaneous and evoked neuronal networks activity characterization. Neurocomputing:9.

Halbach M, Egert U, Hescheler J, Banach K (2003) Estimation of action potential changes from field potential recordings in multicellular mouse cardiac myocyte cultures. Cell Physiol Biochem 13:271-284.

Zhang P, Wu J, Zhou Y, Liang PJ, Yuan J (2003) Spike sorting based on automatic template reconstructing with a partial solution to the overlapping problem. Journal of Neuroscience Methods:11.

Egert U, Heck D, Aertsen A (2002) Two-dimensional monitoring of spiking networks in acute brain slices. Exp Brain Res 142:268-274.

Egert U, Knott T, Schwarz C, Nawrot M, Brandt A, Rotter S, Diesmann M (2002) MEA-Tools: an open source toolbox for the analysis of multi-electrode data with MATLAB. J Neurosci Methods 117:33-42.

Hulata E, Segev R, Shapira Y, Benveniste M, Ben-Jacob E (2000) Detection and sorting of neural spikes using wavelet packets. Phys Rev Lett 85:4637-4640.