Citation Relationships



van Pelt J, van Ooyen A, Uylings HB (2001) The need for integrating neuronal morphology databases and computational environments in exploring neuronal structure and function. Anat Embryol (Berl) 204:255-65[PubMed]

References and models cited by this paper

References and models that cite this paper

Agmon-Snir H, Segev I (1993) Signal delay and input synchronization in passive dendritic structures. J Neurophysiol 70:2066-85 [Journal] [PubMed]

Ascoli GA (1999) Progress and perspectives in computational neuroanatomy. Anat Rec 257:195-207 [PubMed]

Ascoli GA, Krichmar JL (2000) L-Neuron: a modeling tool for the effcient generation and parsimonious description of dendritic morphology. Neurocomputing 32:1003-1011

Ascoli GA, Krichmar JL, Scorcioni R, Nasuto SJ, Senft SL (2001) Computer generation and quantitative morphometric analysis of virtual neurons. Anat Embryol (Berl) 204:283-301 [PubMed]

Barrett JN, Crill WE (1974) Specific membrane properties of cat motoneurones. J Physiol 239:301-24 [PubMed]

Barton BP, Mcgormick BH (1999) Virtual microscopy of brain tissue. Neurocomputing 26:981-987

Blackstad TW, Karagulle T, Malmierca MS, Osen KK (1993) Computer methods in neuroanatomy: determining mutual orientation of whole neuronal arbors. Comput Biol Med 23:227-50 [PubMed]

Burke RE, Marks WB, Ulfhake B (1992) A parsimonious description of motoneuron dendritic morphology using computer simulation. J Neurosci 12:2403-16 [PubMed]

Capowski JJ (1989) Computer techniques in neuroanatomy.

Capowski JJ, Sedivec MJ (1981) Accurate computer reconstruction and graphics display of complex neurons utilizing state-of-the-art interactive techniques. Comput Biomed Res 14:518-32 [PubMed]

de Brabander JM, Kramers RJ, Uylings HB (1998) Layer-specific dendritic regression of pyramidal cells with ageing in the human prefrontal cortex. Eur J Neurosci 10:1261-9 [PubMed]

de Schutter E (1994) Modelling the cerebellar Purkinje cell: experiments in computo. Prog Brain Res 102:427-41 [PubMed]

   Cerebellar purkinje cell (De Schutter and Bower 1994) [Model]

De Schutter E (2001) Computational neuroscience: more math is needed to understand the human brain. Mathematics unlimited - 2001 and beyond., Engquist B:Schmidt W, ed. pp.381

De Schutter E, Cannon RC (2001) Computational neuroscience realistic modeling for experimentalists.

Devaud JM, Quenet B, Gascuel J, Masson C (2000) Statistical analysis and parsimonious modelling of dendrograms of in vitro neurones. Bull Math Biol 62:657-74 [PubMed]

Devaul RW, Mcgormick BH (1996) Neuron developmental modeling and structural representation: an introduction to the N++ language, an open stochastic L-system. Technical Report December 4

Dima A, Scholz M, Obermayer K (1999) Semi-automatic quality determination of 3D confocal microscope scans of neuronal cells denoised by 3D-wavelet-shrinkage. PIE-Proceedings: Wavelet Applications VI, Szu HH, ed.

Glaser EM, Tagamets M, McMullen NT, Van der Loos H (1983) The image-combining computer microscope--an interactive instrument for morphometry of the nervous system. J Neurosci Methods 8:17-32 [PubMed]

GLASER EM, VANDERLOOS H (1965) A SEMI-AUTOMATIC COMPUTER-MICROSCOPE FOR THE ANALYSIS OF NEURONAL MORPHOLOGY. IEEE Trans Biomed Eng 12:22-31 [PubMed]

Glaser JR, Glaser EM (1990) Neuron imaging with Neurolucida--a PC-based system for image combining microscopy. Comput Med Imaging Graph 14:307-17 [PubMed]

Hausser M, Spruston N, Stuart GJ (2000) Diversity and dynamics of dendritic signaling. Science 290:739-44 [PubMed]

Hely TA, Graham B, Ooyen AV (2001) A computational model of dendrite elongation and branching based on MAP2 phosphorylation. J Theor Biol 210:375-84 [PubMed]

Hillman DE (1988) Parameters of dendritic shape and substructure Intrinsic and extrinsic determination? Intrinsic determinants of neuronal form and function. :83-113

Horsfield K, Woldenberg MJ, Bowes CL (1987) Sequential and synchronous growth models related to vertex analysis and branching ratios. Bull Math Biol 49:413-29 [PubMed]

Innocenti GM, Lehmann P, Houzel JC (1994) Computational structure of visual callosal axons. Eur J Neurosci 6:918-35 [PubMed]

Ireland W, Heidel J, Uemura E (1985) A mathematical model for the growth of dendritic trees. Neurosci Lett 54:243-9 [PubMed]

Jack JJ, Redman SJ (1971) An electrical description of the motoneurone, and its application to the analysis of synaptic potentials. J Physiol 215:321-52 [PubMed]

Kliemann W (1987) A stochastic dynamical model for the characterization of the geometrical structure of dendritic processes. Bull Math Biol 49:135-52 [PubMed]

Koch C, Poggio T, Torre V (1982) Retinal ganglion cells: a functional interpretation of dendritic morphology. Philos Trans R Soc Lond B Biol Sci 298:227-63 [PubMed]

Koch C, Segev I (1998) Methods In Neuronal Modeling

Koslow SH (2000) Should the neuroscience community make a paradigm shift to sharing primary data? Nat Neurosci 3:863-5 [PubMed]

Larkman AU (1991) Dendritic morphology of pyramidal neurones of the visual cortex of the rat: I. Branching patterns. J Comp Neurol 306:307-19 [PubMed]

Larkman AU, Major G, Stratford KJ, Jack JJ (1992) Dendritic morphology of pyramidal neurones of the visual cortex of the rat. IV: Electrical geometry. J Comp Neurol 323:137-52 [PubMed]

Li GH, Qin CD (1996) A model for neurite growth and neuronal morphogenesis. Math Biosci 132:97-110 [PubMed]

Mainen ZF, Sejnowski TJ (1996) Influence of dendritic structure on firing pattern in model neocortical neurons. Nature 382:363-6 [Journal] [PubMed]

   Pyramidal Neuron Deep, Superficial; Aspiny, Stellate (Mainen and Sejnowski 1996) [Model]

Maletic-Savatic M, Malinow R, Svoboda K (1999) Rapid dendritic morphogenesis in CA1 hippocampal dendrites induced by synaptic activity. Science 283:1923-7 [PubMed]

Markram H, Lubke J, Frotscher M, Sakmann B (1997) Regulation of synaptic efficacy by coincidence of postsynaptic APs and EPSPs. Science 275:213-5 [PubMed]

Mcgormick BH (1999) Design of a brain tissue scanner. Neurocomputing 26:1025-1032

Mckenna T, Davis J, Zornetzer SF (1992) Single Neuron Computation

Mel BW (1993) Synaptic integration in an excitable dendritic tree. J Neurophysiol 70:1086-101 [Journal] [PubMed]

Miller JP, Rall W, Rinzel J (1985) Synaptic amplification by active membrane in dendritic spines. Brain Res 325:325-30 [PubMed]

Mizrahi A, Ben-Ner E, Katz MJ, Kedem K, Glusman JG, Libersat F (2000) Comparative analysis of dendritic architecture of identified neurons using the Hausdorff distance metric. J Comp Neurol 422:415-28 [PubMed]

Nowakowski RS, Hayes NL, Egger MD (1992) Competitive interactions during dendritic growth: a simple stochastic growth algorithm. Brain Res 576:152-6 [PubMed]

Ooyen A van, Graham BP, Ramakers GJA (2001) Competition for tubulin between growing neurites during development. Neurocomputing 38-40:73-78

Ooyen_a VAN (1994) Activity-dependent neural network development. Network: Computation In Neural Systems 5:401-423

Overdijk J, Uylings HB, Kuypers K, Kamstra W (1978) An economical, semi-automatic system for measuring cellular tree structures in three dimensions, with special emphasis on Golgi-impregnated neurons. J Microsc 114:271-84 [PubMed]

Pelt J van, Schierwagen A, Uylings HBM (2001) Modeling dendritic morphological complexity of deep layer cat superior colliculus neurons. Neurocomputing 38-40:403-408

Pelt J van, Uylings hbm (1999) Natural variability in the geometry of dendritic branching patterns. Modeling in the neurosciences: from ionic channels to neural networks. :79-108

Pelt J van, Uylings HBM (1999) Modeling the natural variability in the shape of dendritic trees: application to basal dendrites of small rat cortical layer 5 pyramidal neurons. Neurocomputing 26:305-311

Pelt J van, Van Ooyen A, Uylings HBM (2001) Chapter 7 Modeling dendritic geometry and the development of nerve connections. Computational Neuroscience: Realistic modeling for experimentalist, De Schutter E:Cannon RC, ed. pp.179

Poznanski RR (1999) Modeling in the Neurosciences

RALL W (1959) Branching dendritic trees and motoneuron membrane resistivity. Exp Neurol 1:491-527 [PubMed]

Rall W (1977) Core conductor theory and cable properties of neurons Handbook of Physiology. The Nervous System. Cellular Biology of Neurons, Kandel ER, ed. pp.39

Rall W (1995) The Theoretical Foundation Of Dendritic Function, Segev I:Rinzel J:Shepherd GM, ed.

Rapp M, Segev I, Yarom Y (1994) Physiology, morphology and detailed passive models of guinea-pig cerebellar Purkinje cells. J Physiol 474:101-18 [PubMed]

Reinagel P, Reid RC (2000) Temporal coding of visual information in the thalamus. J Neurosci 20:5392-400 [PubMed]

Ruiz-Marcos A (1983) Mathematical models of cortical structures and their application to the study of pathological conditions. Ramon y Cajals contribution to the neurosciences., Grisolia S, Guerri C, Samson F, Norton S, Reinoso-Suarez F, ed. pp.209

Sadler M, Berry M (1983) Morphometric study of the development of Purkinje cell dendritic trees in the mouse using vertex analysis. J Microsc 131 (Pt 3):341-54 [PubMed]

Schierwagen A, Claus C (2001) Dendritic morphology and signal delay in superior colliculus neurons. Neurocomputing 38-40:343-350

Schierwagen A, Grantyn R (1986) Quantitative morphological analysis of deep superior colliculus neurons stained intracellularly with HRP in the cat. J Hirnforsch 27:611-23 [PubMed]

Segev I, Rall W, Shepherd GM (1995) The Theoretical Foundation Of Dendritic Function

Shepherd GM, Brayton RK, Miller JP, Segev I, Rinzel J, Rall W (1985) Signal enhancement in distal cortical dendrites by means of interactions between active dendritic spines. Proc Natl Acad Sci U S A 82:2192-5 [PubMed]

SHOLL DA (1953) Dendritic organization in the neurons of the visual and motor cortices of the cat. J Anat 87:387-406 [PubMed]

Smith TG, Lange GD, Marks WB (1996) Fractal methods and results in cellular morphology--dimensions, lacunarity and multifractals. J Neurosci Methods 69:123-36 [PubMed]

Stockley EW, Cole HM, Brown AD, Wheal HV (1993) A system for quantitative morphological measurement and electronic modelling of neurons: three-dimensional reconstruction. J Neurosci Methods 47:39-51

Streekstra GJ, Smeulders AW, Boomgaard R van den (1999) Tracing of curvilinear structures in 3D images with single scale diameter measurement. Proceedings of the second international conference on Scale-Space Theories in Computer Vision :501-506

Streekstra GJ, Smeulders AW, Boomgaard R van den (2000) Scale dependent differential geometry for the measurement of center line and diameter in 3D curvilinear structures. Proceedings of 6th European Conference on Computer Vision 2000. :856-870

Takeda T, Ishikawa A, Ohtomo K, Kobayashi Y, Matsuoka T (1992) Fractal dimension of dendritic tree of cerebellar Purkinje cell during onto- and phylogenetic development. Neurosci Res 13:19-31 [PubMed]

Tamori Y (1993) Theory of dendritic morphology. PHYSICAL REVIEW. E. STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 48:3124-3129

Tettoni L, Lehmann P, Houzel JC, Innocenti GM (1996) Maxsim, software for the analysis of multiple axonal arbors and their simulated activation. J Neurosci Methods 67:1-9 [PubMed]

Uemura E, Carriquiry A, Kliemann W, Goodwin J (1995) Mathematical modeling of dendritic growth in vitro. Brain Res 671:187-94 [PubMed]

Uylings HB, Ruiz-Marcos A, van Pelt J (1986) The metric analysis of three-dimensional dendritic tree patterns: a methodological review. J Neurosci Methods 18:127-51 [PubMed]

Uylings HBM, Pelt J van, Verwer RW, McConnell P (1989) Statistical analysis of neuronal populations. Computer techniques in neuroanatomy., Capowski J, ed. pp.241

Uylings HBM, West MJ, Coleman PD, de Brabander JM, Flood DG (2000) Neuronal and cellular changes in aging brain. Neurodegenerative dementias. Clinical features and pathological mechanisms., Clark C:Trojanowski J, ed.

Van Ooyen A, Van Pelt J, Corner MA (1995) Implications of activity dependent neurite outgrowth for neuronal morphology and network development. J Theor Biol 172:63-82 [PubMed]

van Pelt J, Dityatev AE, Uylings HB (1997) Natural variability in the number of dendritic segments: model-based inferences about branching during neurite outgrowth. J Comp Neurol 387:325-40 [PubMed]

Van Pelt J, Uylings HB, Verwer RW, Pentney RJ, Woldenberg MJ (1992) Tree asymmetry--a sensitive and practical measure for binary topological trees. Bull Math Biol 54:759-84 [PubMed]

Van Pelt J, Verwer RW (1983) The exact probabilities of branching patterns under terminal and segmental growth hypotheses. Bull Math Biol 45:269-85 [PubMed]

Van Veen MP, Van Pelt J (1994) Neuritic growth rate described by modeling microtubule dynamics. Bull Math Biol 56:249-73 [PubMed]

Zhang LI, Tao HW, Holt CE, Harris WA, Poo M (1998) A critical window for cooperation and competition among developing retinotectal synapses. Nature 395:37-44 [PubMed]

Koene RA, Tijms B, van Hees P, Postma F, de Ridder A, Ramakers GJ, van Pelt J, van Ooyen A (2009) NETMORPH: a framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies. Neuroinformatics 7:195-210 [Journal] [PubMed]

   NETMORPH: creates NNs with realistic neuron morphologies (Koene et al. 2009, van Ooyen et al. 2014) [Model]

van Elburg R (2011) Stochastic Continuous Time Neurite Branching Models with Tree and Segment Dependent Rates Journal of Theoretical Biology 276(1):159-173 [Journal]

   Continuous time stochastic model for neurite branching (van Elburg 2011) [Model]

van Ooyen A, Carnell A, de Ridder S, Tarigan B, Mansvelder HD, Bijma F, de Gunst M, van Pelt (2014) Independently outgrowing neurons and geometry-based synapse formation produce networks with realistic synaptic connectivity. PLoS One 9:e85858 [Journal] [PubMed]

   NETMORPH: creates NNs with realistic neuron morphologies (Koene et al. 2009, van Ooyen et al. 2014) [Model]

(83 refs)