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Bingham CS, Mergenthal A, Bouteiller JC, Song D, Lazzi G, Berger TW (2020) ROOTS: An Algorithm to Generate Biologically Realistic Cortical Axons and an Application to Electroceutical Modeling Frontiers in Computational Neuroscience 14:13

   ROOTS: An Algorithm to Generate Biologically Realistic Cortical Axons (Bingham et al 2020)

References and models cited by this paper

References and models that cite this paper

Al-Humaidi A (2011) Resistor Networks and Finite Element Models [Journal]
Alpert C,Hu T,Huang J,Kahng A,Karger D (1995) Prim-Dijkstra tradeoffs for improved performance-driven routing tree design IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems 14:890-896 [Journal]
Anastassiou CA, Koch C (2015) Ephaptic coupling to endogenous electric field activity: why bother? Curr Opin Neurobiol 31:95-103 [Journal] [PubMed]
Anderson RW, Farokhniaee A, Gunalan K, Howell B, McIntyre CC (2018) Action potential initiation, propagation, and cortical invasion in the hyperdirect pathway during subthalamic deep brain stimulation. Brain Stimul 11:1140-1150 [Journal] [PubMed]
Ascoli GA, Krichmar JL (2000) L-Neuron: a modeling tool for the efficient generation and parsimonious description of dendritic morphology. Neurocomputing 32:1003-1011
Bindocci E, Savtchouk I, Liaudet N, Becker D, Carriero G, Volterra A (2017) Three-dimensional Ca2+ imaging advances understanding of astrocyte biology. Science [Journal] [PubMed]
Bingham CS, Loizos K, Gene Yu , Gilbert A, Bouteiller JM, Dong Song , Lazzi G, Berger TW (2016) A large-scale detailed neuronal model of electrical stimulation of the dentate gyrus and perforant path as a platform for electrode design and optimization. Conf Proc IEEE Eng Med Biol Soc 2016:2794-2797 [Journal] [PubMed]
Bingham CS, Loizos K, Yu GJ, Gilbert A, Bouteiller JC, Song D, Lazzi G, Berger TW (2018) Model-Based Analysis of Electrode Placement and Pulse Amplitude for Hippocampal Stimulation. IEEE Trans Biomed Eng 65:2278-2289 [Journal] [PubMed]
Bossetti CA, Birdno MJ, Grill WM (2008) Analysis of the quasi-static approximation for calculating potentials generated by neural stimulation. J Neural Eng 5:44-53 [Journal] [PubMed]
Bouteiller JM,Berger TW (2017) The role of simulations in neuropharmacology Computational Neurology and Psychiatry,  P.Érdi, B.Sen Bhattacharya, A.Cochran, ed. pp.429 [Journal]
Budd JM, Kisvárday ZF (2012) Communication and wiring in the cortical connectome. Front Neuroanat 6:42 [Journal] [PubMed]
Budd JM, Kovács K, Ferecskó AS, Buzás P, Eysel UT, Kisvárday ZF (2010) Neocortical axon arbors trade-off material and conduction delay conservation. PLoS Comput Biol 6:e1000711 [Journal] [PubMed]
Cayley A (1889) A theorem on Trees The Quarterly Journal of Pure and Applied Mathematics, N.M. Ferrers, A Cayley, GWL Glaisher, AR Forsyth, ed. pp.376 [Journal]
Chen J (2003) Dijkstra's shortest path algorithm Journal of Formalized Mathematics 15:237-47 [Journal]
Chew L (1989) Constrained delaunay triangulations Algoritmica 4:97-108 [Journal]
Claiborne BJ, Amaral DG, Cowan WM (1990) Quantitative, three-dimensional analysis of granule cell dendrites in the rat dentate gyrus. J Comp Neurol 302:206-19 [Journal] [PubMed]
Clark JW, Plonsey R (1970) A mathematical study of nerve fiber interaction. Biophys J 10:937-57 [Journal] [PubMed]
Cuntz H, Borst A, Segev I (2007) Optimization principles of dendritic structure. Theor Biol Med Model 4:21 [Journal] [PubMed]
Cuntz H, Forstner F, Borst A, Häusser M (2010) One rule to grow them all: a general theory of neuronal branching and its practical application. PLoS Comput Biol [Journal] [PubMed]
Desmond NL, Levy WB (1985) Granule cell dendritic spine density in the rat hippocampus varies with spine shape and location. Neurosci Lett 54:219-24 [PubMed]
Foutz TJ, Arlow RL, McIntyre CC (2012) Theoretical principles underlying optical stimulation of a channelrhodopsin-2 positive pyramidal neuron. J Neurophysiol 107:3235-45 [Journal] [PubMed]
   Optical stimulation of a channelrhodopsin-2 positive pyramidal neuron model (Foutz et al 2012) [Model]
Fries P (2005) A mechanism for cognitive dynamics: neuronal communication through neuronal coherence. Trends Cogn Sci 9:474-80 [Journal] [PubMed]
Gaarskjaer FB (1978) Organization of the mossy fiber system of the rat studied in extended hippocampi. I. Terminal area related to number of granule and pyramidal cells. J Comp Neurol 178:49-72 [Journal] [PubMed]
Gastner MT,Newman MEJ (2006) Shape and efficiency in spatial distribution networks Journal of Statistical Mechanics [Journal]
Grill WM (1999) Modeling the effects of electric fields on nerve fibers: influence of tissue electrical properties. IEEE Trans Biomed Eng 46:918-28 [Journal] [PubMed]
Hagberg A,Schult D,Swart P (2005) Networkx: Python Software for the Analysis of Networks.
Hama K, Arii T, Kosaka T (1989) Three-dimensional morphometrical study of dendritic spines of the granule cell in the rat dentate gyrus with HVEM stereo images. J Electron Microsc Tech 12:80-7 [Journal] [PubMed]
Hampson R,Song D,Robinson B,Fetterhoff D,Dakos A,Roeder B (2018) Developing a hippocampal neural prosthetic to facilitate human memory encoding and recall J. Neural Eng [Journal]
Hartigan J,Wong M (1979) Algorithm AS 136: a k-means clustering algorithm Journal of the Royal Statistical Society 28:100-108 [Journal]
Hendrickson PJ, Yu GJ, Song D, Berger TW (2016) A Million-Plus Neuron Model of the Hippocampal Dentate Gyrus: Critical Role for Topography in Determining Spatiotemporal Network Dynamics. IEEE Trans Biomed Eng 63:199-209 [Journal] [PubMed]
Hines ML, Carnevale NT (2003) NEURON simulation environment The Handbook of Brain Theory and Neural Networks (2nd Ed)
Hjorth-Simonsen A, Jeune B (1972) Origin and termination of the hippocampal perforant path in the rat studied by silver impregnation. J Comp Neurol 144:215-32 [Journal] [PubMed]
Holt GR, Koch C (1999) Electrical interactions via the extracellular potential near cell bodies. J Comput Neurosci 6:169-84 [Journal] [PubMed]
   Extracellular Action Potential Simulations (Gold et al 2007) [Model]
Howell B, McIntyre CC (2017) Role of Soft-Tissue Heterogeneity in Computational Models of Deep Brain Stimulation. Brain Stimul 10:46-50 [Journal] [PubMed]
Hu T (1974) Optimum communication spanning trees Siam Journal on Computing 3:188-195 [Journal]
Johnson MD, McIntyre CC (2008) Quantifying the neural elements activated and inhibited by globus pallidus deep brain stimulation. J Neurophysiol 100:2549-63 [Journal] [PubMed]
   GPi/GPe neuron models (Johnson and McIntyre 2008) [Model]
Joucla S, Yvert B (2009) The "mirror" estimate: an intuitive predictor of membrane polarization during extracellular stimulation. Biophys J 96:3495-508 [Journal] [PubMed]
Khuller S,Raghavachari B,Young NFront. Neuroinform (1995) Balancing minimum spanning trees and shortest-path trees Algorithmica 14:305-321 [Journal]
Kim JH, Lee HJ, Choi W, Lee KJ (2019) Encoding information into autonomously bursting neural network with pairs of time-delayed pulses. Sci Rep 9:1394 [Journal] [PubMed]
Kjonigsen L,Leergaard T,Kjode J,Witter M,Bjaalie J (2008) Interactive histological atlas system for anatomical parcellation of the rat hippocampus proper, fasciola and associated parahippocampal cortex Frontiers in Neuroinformatics [Journal]
López-Aguado L, Ibarz JM, Herreras O (2001) Activity-dependent changes of tissue resistivity in the CA1 region in vivo are layer-specific: modulation of evoked potentials. Neuroscience 108:249-62 [PubMed]
Lujan JL, Chaturvedi A, Choi KS, Holtzheimer PE, Gross RE, Mayberg HS, McIntyre CC (2013) Tractography-activation models applied to subcallosal cingulate deep brain stimulation. Brain Stimul 6:737-9 [Journal] [PubMed]
McIntyre C (2009) Computational modeling of deep brain stimulation. Neuromodulation, Elliot S. Krames, P. Hunter Peckham and Ali R. Rezai, ed. pp.171 [Journal]
McIntyre CC, Grill WM (1999) Excitation of central nervous system neurons by nonuniform electric fields. Biophys J 76:878-88 [Journal] [PubMed]
McKinney W (2010) Data structures for statistical computing in python Proceedings of the 9th Python in Science Conference [Journal]
Michailidou I, Willems JG, Kooi EJ, van Eden C, Gold SM, Geurts JJ, Baas F, Huitinga I, Ramaglia V (2015) Complement C1q-C3-associated synaptic changes in multiple sclerosis hippocampus. Ann Neurol 77:1007-26 [Journal] [PubMed]
Nowak LG, Bullier J (1996) Spread of stimulating current in the cortical grey matter of rat visual cortex studied on a new in vitro slice preparation. J Neurosci Methods 67:237-48 [PubMed]
Nowak LG, Bullier J (1998) Axons, but not cell bodies, are activated by electrical stimulation in cortical gray matter. I. Evidence from chronaxie measurements. Exp Brain Res 118:477-88 [PubMed]
Patton PE, McNaughton B (1995) Connection matrix of the hippocampal formation: I. The dentate gyrus. Hippocampus 5:245-86 [Journal] [PubMed]
Quilichini P, Sirota A, Buzsáki G (2010) Intrinsic circuit organization and theta-gamma oscillation dynamics in the entorhinal cortex of the rat. J Neurosci 30:11128-42 [Journal] [PubMed]
Ramachandran P (2001) MayaVi: a free tool for CFD data visualization Proceedings Of The 4Th Annual CFD Symposium, Aeronautical Society Of India
Ranck JB (1975) Which elements are excited in electrical stimulation of mammalian central nervous system: a review. Brain Res 98:417-40 [PubMed]
Rattay F, Paredes LP, Leao RN (2012) Strength-duration relationship for intra- versus extracellular stimulation with microelectrodes. Neuroscience 214:1-13 [Journal] [PubMed]
Rozenberg G,Salomaa A (1980) The Mathematical Theory of L Systems
Saalfeld A (1999) Topologically consistent line simplification with the DouglasPeucker algorithm Cartography and Geographic Information Science 26:7-18 [Journal]
Schwartz SP, Coleman PD (1981) Neurons of origin of the perforant path. Exp Neurol 74:305-12 [Journal] [PubMed]
Scorcioni R, Polavaram S, Ascoli GA (2008) L-Measure: a web-accessible tool for the analysis, comparison and search of digital reconstructions of neuronal morphologies. Nat Protoc 3:866-76 [Journal] [PubMed]
Scorcioni R,Ascoli G (2005) Algorithmic reconstruction of complete axonal arborizations in rat hippocampal neurons. Neurocomputing 65:15-22 [Journal]
Tamamaki N, Nojyo Y (1993) Projection of the entorhinal layer II neurons in the rat as revealed by intracellular pressure-injection of neurobiotin. Hippocampus 3:471-80 [Journal] [PubMed]
Türetken E, González G, Blum C, Fua P (2011) Automated reconstruction of dendritic and axonal trees by global optimization with geometric priors. Neuroinformatics 9:279-302 [Journal] [PubMed]
Whittington MA, Stanford IM, Colling SB, Jefferys JG, Traub RD (1997) Spatiotemporal patterns of gamma frequency oscillations tetanically induced in the rat hippocampal slice. J Physiol 502 ( Pt 3):591-607 [PubMed]
Witter MP (2007) The perforant path: projections from the entorhinal cortex to the dentate gyrus. Prog Brain Res 163:43-61 [Journal] [PubMed]
Wu B,Chao K-M,Tang C (2000) Approximation algorithms for some optimum communication spanning tree problems. Discrete Appl. Math 102:245-266 [Journal]
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