NETMORPH: A framework for the stochastic generation of large scale neuronal networks with realistic neuron morphologies

Neuroinformatics

Volumn 7, Issue 3, 2009, Pages 195-210

  Koene, Randal A ^a   Tijms, Betty ^a   Van Hees, Peter ^a   Postma, Frank ^a   De Ridder, Alexander ^a   Ramakers, Ger J A ^b   Van Pelt, Jaap ^a   Van Ooyen, Arjen ^a  

^a VU UNIVERSITY AMSTERDAM   (Netherlands)

^b NETHERLANDS INSTITUTE FOR NEUROSCIENCE   (Netherlands)

Author keywords

Growth cone; Growth model; Morphogenesis; Neural development; Neural networks; Neurite outgrowth; Synaptic connectivity

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGY; COMPUTER PROGRAM; COMPUTER SIMULATION; CYTOLOGY; DENDRITE; GROWTH CONE; IMAGE CYTOMETRY; MATHEMATICAL COMPUTING; METHODOLOGY; NERVE CELL; NERVE CELL NETWORK; NERVE TRACT; PHYSIOLOGY; STATISTICS; ULTRASTRUCTURE;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; DENDRITES; GROWTH CONES; IMAGE CYTOMETRY; MATHEMATICAL COMPUTING; NERVE NET; NEURAL PATHWAYS; NEURONS; SOFTWARE; STOCHASTIC PROCESSES;

EID: 70449730644     PISSN: 15392791     EISSN: None     Source Type: Journal    
DOI: 10.1007/s12021-009-9052-3     Document Type: Article

References (79)

1. Aeschlimann, M. (2000). Biophysical models of axonal pathfinding. Ph.D. thesis, University of Lausanne.
2. G Ascoli J Krichmar 2000 L-neuron: a modeling tool for the efficient generation and parsimonious description of dendritic morphology Neurocomputing 32-33 1003 1011 10.1016/S0925-2312(00)00272-1 (Pubitemid 30459823)
3. G Ascoli J Krichmar S Nasuto S Senft 2001a Generation, description and storage of dendritic morphology data Philosophical Transactions of the Royal Society of London B 356 1131 1145 10.1098/rstb.2001.0905 1:STN:280: DC%2BD3MvpvVChsw%3D%3D (Pubitemid 32876061)
4. G Ascoli J Krichmar R Scorcioni S Nasuto S Senft 2001b Computer generation and quantitative morphometric analysis of virtual neurons Anatomy and Embryology 204 283 301 10.1007/s004290100201 1:STN:280:DC%2BD3MnnsVWktg%3D%3D (Pubitemid 33022743)
5. J Bamburg 2003 Introduction to cytoskeletal dynamics and pathfinding of neuronal growth cones Journal of Histochemistry & Cytochemistry 51 4 407 409 1:CAS:528:DC%2BD3sXivVertbo%3D
6. M Belmonte T Bourgeron 2006 Fragile x syndrome and autism at the intersection of genetic and neural networks Nature Neuroscience 9 1221 1225 17001341 10.1038/nn1765 1:CAS:528:DC%2BD28XhtVSgu7bI (Pubitemid 44454259)
7. Braitenberg, V., & Schütz, A. (1998). Cortex: statistics and geometry of neuronal connectivity. Berlin: Springer.
8. M Butz K Lehmann I Dammasch G Teuchert-Noodt 2006 A theoretical network model to analyse neurogenesis and synaptogenesis in the dentate gyrus Neural Networks 19 1490 1505 17014989 10.1016/j.neunet.2006.07.007 (Pubitemid 44793173)
9. LF da Costa E Manoel J Faucereau J Chelly J Van Pelt G Ramakers 2002 A shape analysis framework for neuromorphometry Network 13 3 283 310
10. AE Dityatev NM Chmykhova L Studer OA Karamian VM Kozhanov HP Clamann 1995 Comparison of the topology and growth rules of motoneuronal dendrites J. Comp Neurol. 363 505 516 8847414 10.1002/cne.903630312 1:STN:280:DyaK283nsFWnug%3D%3D (Pubitemid 26012250)
11. R Douglas K Martin 2004 Neuronal circuits in the neocortex Annual Review of Neuroscience 27 419 451 15217339 10.1146/annurev.neuro.27.070203.144152 1:CAS:528:DC%2BD2cXmslantLw%3D (Pubitemid 39050409)
12. JP Eberhard A Wanner G Wittum 2006 NeuGen: A tool for the generation of realistic morphology of cortical neurons and neuronal networks in 3D Neurocomputing 70 1-3 327 342 10.1016/j.neucom.2006.01.028 (Pubitemid 44615787)
13. R Fields K Itoh 1996 Neural cell adhesion molecules in activity-dependent development and synaptic plasticity Trends in Neurosciences 19 473 480 8931273 10.1016/S0166-2236(96)30013-1 1:CAS:528:DyaK28XmvVyltLk%3D (Pubitemid 26359865)
14. P Gleeson V Steuber R Silver 2007 neuroConstruct: a tool for modeling networks of neurons in 3D space Neuron 54 219 235 17442244 10.1016/j.neuron. 2007.03.025 1:CAS:528:DC%2BD2sXltF2nsb8%3D (Pubitemid 46561205)
15. D Goldberg D Burmeister 1989 Looking into growth cones Trends in Neurosciences 12 12 503 506 2480665 10.1016/0166-2236(89)90110-0 1:STN:280:DyaK3c%2FosFeltg%3D%3D
16. JG Goodhill 1998 Mathematical guidance for axons Trends in Neurosciences 21 226 231 9641531 10.1016/S0166-2236(97)01203-4 1:CAS:528:DyaK1cXjs1Kgu78%3D (Pubitemid 28239976)
17. Gordon-Weeks, P. R. (2000). Neuronal Growth Cones. Cambridge, United Kingdom: Cambridge University Press.
18. B Graham A Van Ooyen 2004 Transport limited effects in a model of dendritic branching Journal of Theoretical Biology 230 421 432 15321709 10.1016/j.jtbi.2004.06.007 (Pubitemid 39092343)
19. B Hellwig 2000 A quantitative analysis of the local connectivity between pyramidal neurons in layers 2/3 of the rat visual cortex Biol. Cybern. 82 111 121 10664098 10.1007/PL00007964 1:STN:280:DC%2BD3c7ivFGhsg%3D%3D
20. T Hely B Graham A Van Ooyen 2001 A computational model of dendrite elongation and branching based on map2 phosphorylation Journal of Theoretical Biology 210 375 384 11397138 10.1006/jtbi.2001.2314 1:CAS:528: DC%2BD3MXktFKju70%3D (Pubitemid 32575215)
21. HGE Hentschel A Van Ooyen 1999 Models of axon guidance and bundling during development Proceedings of the Royal Society of London Series B 266 2231 2238 10649638 10.1098/rspb.1999.0913 1:STN:280:DC%2BD3c7htlyrtQ%3D%3D (Pubitemid 29532906)
22. Hillman, D. (1979). Neuronal shape parameters and substructures as a basis of neuronal form. In F. Schmitt (Ed.), The neurosciences, 4th study program (pp. 477-498). Cambridge: MIT.
23. Hillman, D. E. (1988). Parameters of dendritic shape and substructure: intrinsic and extrinsic determination? In R. Lasek & M. Black (Eds.), Intrinsic determinants of neuronal form and function (pp. 83-113). New York: Alan R. Liss, Inc.
24. M Hines N Carnevale 1997 The NEURON simulation environment Neural Computation 9 1179 1209 9248061 10.1162/neco.1997.9.6.1179 1:STN:280: DyaK2szptFamtg%3D%3D
25. Hines, M., & Moore, J. (1993). A NEURON simulation program. In 23 rd Annual Meeting of the Society for Neuroscience.
26. C Isbister T O'Connor 1999 Filopodial adhesion does not predict growth cone steering events in vivo Journal of Neuroscience 20 2589 2600
27. Y-N Jan L-Y Jan 2003 The control of dendrite development Neuron 40 229 242 14556706 10.1016/S0896-6273(03)00631-7 1:CAS:528:DC%2BD3sXosFCqsr4%3D (Pubitemid 37244094)
28. M Kaiser C Hilgetag 2007 Development of multi-cluster cortical networks by time windows for spatial growth Neurocomputing 70 1829 1832 10.1016/j.neucom.2006.10.060 (Pubitemid 46656970)
29. Kater, S. B. & Guthrie, P. B. (1990). Neuronal growth cone as an integrator of complex environmental information. In: Cold Spring Harbor Symposia on Quantitative Biology, vol. LV, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 35.
30. Kiddie, G., McLean, D., van Ooyen, A., & Graham, B. (2005). Biologically plausible models of neurite outgrowth. In J. van Pelt, M. Kamermans, C. Levelt, A. van Ooyen, G. Ramakers, and P. Roelfsema, (Eds.), Development, dynamics and pathology of neuronal networks: from molecules to functional circuits, Progress in Brain Research, 147, 67-80. Elsevier.
31. Koene, R., Postma, F., de Ridder, S., Hoedemaker, S., van Pelt, J., & van Ooyen A. (2009) NETMORPH Manual. http://www.neurodynamics.nl/.
32. S Konur A Ghosh 2005 Calcium signaling and the control of dendritic development Neuron 46 401 405 15882639 10.1016/j.neuron.2005.04.022 1:CAS:528:DC%2BD2MXksFKmtbs%3D (Pubitemid 40616883)
33. RJ Kowalski RJ Williams 1993 Microtubule-associated protein 2 alters the dynamic properties of microtubule assembly and disassembly Journal Biological Chemistry 268 9847 9855 1:CAS:528:DyaK3sXktVehsb0%3D
34. P Lamoureux RE Buxbaum SR Heidemann 1998 Axonal outgrowth of cultured neurons is not limited by growth cone competition Journal of Cell Science 111 3245 3252 9763518 1:CAS:528:DyaK1cXnvFOqt7g%3D
35. AU Larkman 1991 Dendritic morphology of pyramidal neurons of the visual cortex of the rat I. Branching patterns Journal of Comparative Neurology 306 307 319 1711057 10.1002/cne.903060207 1:STN:280:DyaK3M3mvVaqtg%3D%3D
36. AU Larkman G Major KJ Stratford JJB Jack 1992 Dendritic morphology of pyramidal neurones of the visual cortex of the rat. IV: Electrical geometry Journal of Comparative Neurology 323 137 152 1401253 10.1002/cne.903230202 1:STN:280:DyaK3s%2FhslSquw%3D%3D
37. J-V Le Bé G Silberberg Y Wang H Markram 2007 Morphological, electrophysiological, and synaptic properties of corticocallosal pyramidal cells in the neonatal rat neocortex Cerebral Cortex 17 2204 2213 17124287 10.1093/cercor/bhl127 (Pubitemid 47283691)
38. Letourneau, P., Kater, S., & Macagno, E. (eds). (1991). The Nerve Growth Cone. New York: Raven.
39. A Luczak 2006 Spatial embedding of neuronal trees modeled by diffusive growth Journal of Neuroscience Methods 157 132 141 16690135 10.1016/j.jneumeth. 2006.03.024 (Pubitemid 44376418)
40. SM Maskery HM Buettner T Shinbrot 2004 Growth Cone Pathfinding: a competition between deterministic and stochastic events BMC Neuroscience 5 22 15242518 10.1186/1471-2202-5-22 (Pubitemid 40177059)
41. RS Nowakowski NL Hayes MD Egger 1992 Competitive interactions during dendritic growth: a simple stochastic growth algorithm Brain Research 576 152 1381258 10.1016/0006-8993(92)90622-G 1:STN:280:DyaK38zos1anuw%3D%3D
42. A Peters 1979 Thalamic input to the cerebral cortex Trends in Neurosciences 2 1183 1185 10.1016/0166-2236(79)90074-2 (Pubitemid 10115867)
43. M Polinsky K Balzovich K Tosney 2000 Identification of an invariant response: Stable contact with schwann cells induces veil extension in sensory growth cones Journal of Neuroscience 20 1044 1055 10648710 1:CAS:528: DC%2BD3cXhtFGqtLc%3D
44. W Rall 1959 Branching dendritic trees and motoneuron membrane resistivity Experimental Neurology 1 491 527 14435979 10.1016/0014-4886(59)90046-9 1:STN:280:DyaF3c7ovVOjuw%3D%3D
45. GJA Ramakers J Winter T Hoogland MB Lequin J Van Pelt CW Pool 1998 Depolarization stimulates lamellipodia formation and axonal but not dendritic branching in cultured rat cerebral cortex neurons Development Brain Research 108 205 216 10.1016/S0165-3806(98)00050-9 1:CAS:528:DyaK1cXjs1ags7s%3D (Pubitemid 28332832)
46. Samsonovich, A., & Ascoli, G. (2007). Computational models of dendritic morphology: From parsimonious description to biological insight. In M. Laubichler & G. Müller (Eds.), Modeling Biology, Structures, Behaviors, Evolution (pp. 91-113). Cambridge, Massachusetts: MIT.
47. CJ Sánchez J Díaz-Nido J Avila 2000 Phosphorylation of microtubule-associated protein 2 (MAP2) and its relevance for the regulation of the neuronal cytoskeleton function Progress in Neurobiology 61 133 168 10704996 10.1016/S0301-0082(99)00046-5 (Pubitemid 30110476)
48. SW Scheff DA Prince FA Schmitt ST DeKosky EF Mufson 2007 Synaptic alterations in CA1 mild Alzheimer's disease and mild cognitive impairment Neurology 68 1501 1508 17470753 10.1212/01.wnl.0000260698.46517.8f 1:STN:280:DC%2BD2s3mtFersg%3D%3D (Pubitemid 46685921)
49. A Schierwagen R Grantyn 1986 Quantitative morphological analysis of deep superior colliculus neurons stained intracellularly with HRP in the cat J Hirnforsch 27 611 623 3571961 1:STN:280:DyaL2s7ps1antQ%3D%3D
50. D Schubert R Kötter HJ Luhmann JF Staiger 2006 Morphology, electrophysiology and functional input connectivity of pyramidal neurons characterizes a genuine layer Va in the primary somatosensory cortex Cereb Cortex 16 2 223 36 15872153 10.1093/cercor/bhi100 1:STN:280: DC%2BD28%2Fht12guw%3D%3D (Pubitemid 43100067)
51. R Segev E Ben-Jacob 2000 Generic modeling of chemotactic based self-wiring of neural networks Neural Networks 13 2 185 199 10935760 10.1016/S0893-6080(99)00084-2 1:STN:280:DC%2BD3cvhtFGltg%3D%3D (Pubitemid 30114355)
52. S Senft G Ascoli 1999 Reconstruction of brain networks by algorithmic amplification of morphometry data Lecture Notes in Computer Science 1606 25 33 10.1007/BFb0098157
53. GM Shepherd K Svoboda 2005 Laminar and columnar organization of ascending excitatory projections to layer 2/3 pyramidal neurons in rat barrel cortex Journal of Neuroscience 25 24 5670 5679 15958733 10.1523/JNEUROSCI.1173-05.2005 1:CAS:528:DC%2BD2MXlsFentro%3D (Pubitemid 40847879)
54. O Sporns D Chialvo M Kaiser C Hilgetag 2004 Organization, development and function of complex brain networks Trends in Cognitive Sciences 8 418 425 15350243 10.1016/j.tics.2004.07.008 (Pubitemid 39179905)
55. A Stepanyants D Chklovskii 2005 Neurogeometry and potential synaptic connectivity Trends in Neurosciences 28 7 387 394 15935485 10.1016/j.tins.2005. 05.006 1:CAS:528:DC%2BD2MXlsVequ7o%3D (Pubitemid 40853862)
56. A Stepanyants G Tamas DB Chklovskii 2004 Class-specific features of neuronal wiring Neuron 43 251 259 15260960 10.1016/j.neuron.2004.06.013 1:CAS:528:DC%2BD2cXmslKrtL8%3D (Pubitemid 38942964)
57. H Uylings G Smit 1975 Three dimensional branching structure of pyramidal cell dendrites Brain Research 87 55 60 1120255 10.1016/0006-8993(75)90778-7 1:STN:280:DyaE2M7ivVyjuw%3D%3D
58. HBM Uylings J van Pelt 2002 Measures for quantifying dendritic arborizations Network: Computation Neural System 13 397 414 10.1088/0954-898X/ 13/3/309
59. Uylings, H. B. M., Kuypers, K. & Veltman, W. A. M. (1978). Environmental influences on the neocortex in later life. In M. A. Corner (Ed.) Maturation of the nervous system. Progress in Brain Research, Vol 48, pp. 261-273. Elsevier, Amsterdam.
60. Uylings, H. B. M., Van Pelt, J., Parnavelas, J. G., & Ruiz-Marcos, A. (1994). Geometrical and topological characteristics in the dendritic development of cortical pyramidal and nonpyramidal neurons. In J. van Pelt, M. A. Corner, H. B. M. Uylings & F. H. Lopes da Silva (Eds.), Progress in Brain Research, Vol. 102, the self-organizing brain: from growth cones to functional networks (pp. 109-123). Amsterdam: Elsevier.
61. A Van Ooyen J Van Pelt 1994 Activity-dependent outgrowth of neurons and overshoot phenomena in developing neural networks Journal of Theoretical Biology 167 27 43 10.1006/jtbi.1994.1047 (Pubitemid 24212479)
62. A Van Ooyen J Van Pelt 1996 Complex periodic behavior in a neural network model with activity-dependent neurite outgrowth Journal of Theoretical Biology 179 229 242 8762335 10.1006/jtbi.1996.0063 (Pubitemid 26166866)
63. A Van Ooyen J Van Pelt M Corner 1995 Implications of activity dependent neurite outgrowth for neuronal morphology and network development Journal of Theoretical Biology 172 63 82 7891450 10.1006/jtbi.1995.0005
64. A Van Ooyen K Pakdaman A Houweling J Van Pelt J-F Vibert 1996 Networks connectivity changes through activity-dependent neurite outgrowth Neural Processing Letters 3 123 130 10.1007/BF00420281
65. A Van Ooyen B Graham G Ramakers 2001 Competition for tubulin between growing neurites during development Neurocomputing 38-40 73 78 10.1016/S0925-2312(01)00487-8 (Pubitemid 35276624)
66. J Van Pelt H Uylings 1999 Modeling the natural variability in the shape of dendritic trees: Application to basal dendrites of small rat cortical layer 5 pyramidal neurons Neurocomputing 26-27 305 311
67. J Van Pelt H Uylings 2002 Branching rates and growth functions in the outgrowth of dendritic branching patterns Network: Computational Neural Systems 13 261 281 10.1088/0954-898X/13/3/302
68. Van Pelt, J., & Uylings, H. (2003). Growth functions in dendritic outgrowth. Brain and Mind, 4:51-65. In A. van Ooyen, (Ed.), Modeling Neural Development, 75-94. Cambridge, MA: MIT Press.
69. Van Pelt, J., & Uylings, H. B. M. (2005). Natural variability in the geometry of dendritic branching patterns. In: G. N. Reeke, R. R. Poznanski, K. A. Lindsay, J. R. Rosenberg, & O. Sporns (Eds.), Modeling in the Neurosciences: From Biological Systems to Neuromimetic Robotics. CRC Press, 2005, pp. 89-115.
70. Van Pelt J. and Uylings H.B.M. (2007) Modeling neuronal growth and shape. In Modeling Biology-Structures, Behaviors, Evolution, Manfred D. Laubichler and Gerd B. Müller (Eds). The MIT Press, 2007, Cambridge, pp. 195-215.
71. J Van Pelt HBM Uylings RWH Verwer RJ Pentney MJ Woldenberg 1992 Tree asymmetry-a sensitive and practical measure for binary topological trees Bulletin of Mathematical Biology 54 759 784 1638259 10.1007/BF02459929
72. J Van Pelt AE Dityatev HBM Uylings 1997 Natural variability in the number of dendritic segments: Model-based inferences about branching during neurite outgrowth Journal of Comparative Neurology 387 325 340 9335418 10.1002/(SICI)1096-9861(19971027)387:3<325::AID-CNE1>3.0.CO;2-2 (Pubitemid 27430333)
73. Van Pelt, J., Van Ooyen, A., & Uylings, H. B. M. (2001a). Modeling dendritic geometry and the development of nerve connections. In: De Schutter E (Ed.), Cannon RC (CD-ROM) Computational Neuroscience: Realistic modeling for experimentalist, Chapter 7, CRC Press. pp 179-208.
74. J Van Pelt A Van Ooyen H Uylings 2001b The need for integrating neuronal morphology databases and computational environments in exploring neuronal structure and function Anatomy and Embryology 204 255 265 10.1007/s004290100197 (Pubitemid 33026115)
75. J Van Pelt A Schierwagen HBM Uylings 2001c Modeling dendritic morphological complexity of deep layer cat superior colliculus neurons Neurocomputing 38-40 403 408 10.1016/S0925-2312(01)00347-2 (Pubitemid 35282398)
76. Van Pelt, J., Graham, B., & Uylings, H. (2003). Formation of dendritic branching patterns. In A. van Ooyen (Ed.), Modeling neural development (pp. 75-94). Cambridge, Massachusets: The MIT.
77. MP Van Veen J Van Pelt 1993 Terminal and intermediate segment lengths in neuronal trees with finite length Bulletin of Mathematical Biology 55 277 294 8431703 10.1007/BF02460884
78. Y Wang A Gupta M Toledo-Rodriguez CZ Wu H Markram 2002 Anatomical, physiological, molecular and circuit properties of nest basket cells in the developing somatosensory cortex Cerebral Cortex 12 4 395 410 11884355 10.1093/cercor/12.4.395
79. Zubler, F., & Douglas, R. (2008) CX3D: a java package for simulation of cortical development in 3D. Frontiers in Neuroinformatics. Conference Abstract: Neuroinformatics 2008. doi: 10.3389/conf.neuro.11.2008.01.127.