Reading the Book of Memory: Sparse Sampling versus Dense Mapping of Connectomes

Neuron

Volumn 62, Issue 1, 2009, Pages 17-29

  Seung, H Sebastian ^a  

^a MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BRAIN FUNCTION; CELL FUNCTION; COGNITION; NERVE CELL NETWORK; PRIORITY JOURNAL; PROCEDURAL MEMORY; READING; REVIEW;

ANIMALS; BRAIN; BRAIN MAPPING; CAENORHABDITIS ELEGANS; HUMANS; MEMORY; MODELS, NEUROLOGICAL; NERVE NET; NEURAL NETWORKS (COMPUTER); NEURAL PATHWAYS; NEURONS; RETINA; SYNAPTIC TRANSMISSION;

EID: 64149093014     PISSN: 08966273     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.neuron.2009.03.020     Document Type: Review

References (83)

1. Abeles M. Corticonics: Neural Circuits of the Cerebral Cortex (1991), Cambridge University Press, Cambridge
2. Amari S. Learning patterns and pattern sequences by self-organizing nets of threshold elements. IEEE Trans. Comput. 21 (1972) 1197-1206
3. Andres B., Köthe U., Helmstaedter M., Denk W., and Hamprecht F.A. Segmentation of SBFSEM volume data of neural tissue by hierarchical classification. In: Rigoll G. (Ed). Pattern Recognition: 30th DAGM Symposium (2008), Springer, New York 142-152
4. Avery L., and Horvitz H.R. Pharyngeal pumping continues after laser killing of the pharyngeal nervous system of C. elegans. Neuron 3 (1989) 473-485
5. Badea T.C., and Nathans J. Quantitative analysis of neuronal morphologies in the mouse retina visualized by using a genetically directed reporter. J. Comp. Neurol 480 (2004) 331-351
6. Barlow R. Inhibitory fields in the Limulus lateral eye. J. Gen. Physiol. 54 (1969) 383-396
7. Battaglia F.P., and Treves A. Attractor neural networks storing multiple space representations: A model for hippocampal place fields. Phys. Rev. E Stat. Phys. Plasmas Fluids Relat. Interdiscip. Topics 58 (1998) 7738-7753
8. Ben-Yishai R., Bar-Or R.L., and Sompolinsky H. Theory of orientation tuning in visual cortex. Proc. Natl. Acad. Sci. USA 92 (1995) 3844-3848
9. Bota M., and Swanson L.W. The neuron classification problem. Brain Res. Rev. 56 (2007) 79-88
10. Bota M., Dong H.W., and Swanson L.W. From gene networks to neural networks. Nat. Neurosci. 6 (2003) 795-799
11. Briggman K.L., and Denk W. Towards neural circuit reconstruction with volume electron microscopy techniques. Curr. Opin. Neurobiol. 16 (2006) 562-570
12. Burgess N., and Hitch G.J. Memory for serial order: A network model of the phonological loop and its timing. Psychol. Rev. 106 (1999) 551-581
13. Carmel L., Harel D., and Koren Y. Combining hierarchy and energy for drawing directed graphs. IEEE Trans. Vis. Comput. Graph. 10 (2004) 46-57
14. Catani M., and ffytche D.H. The rises and falls of disconnection syndromes. Brain 128 (2005) 2224-2239
15. Chalfie M., and Sulston J. Developmental genetics of the mechanosensory neurons of Caenorhabditis elegans. Dev. Biol. 82 (1981) 358-370
16. Chalfie M., Sulston J.E., White J.G., Southgate E., Thomson J.N., and Brenner S. The neural circuit for touch sensitivity in Caenorhabditis elegans. J. Neurosci. 5 (1985) 956-964
17. Chen B.L., Hall D.H., and Chklovskii D.B. Wiring optimization can relate neuronal structure and function. Proc. Natl. Acad. Sci. USA 103 (2006) 4723-4728
18. Denk W., and Horstmann H. Serial block-face scanning electron microscopy to reconstruct three-dimensional tissue nanostructure. PLoS Biol. 2 (2004) e329
19. Díaz J., Petit J., and Serna M. A survey of graph layout problems. ACM Comput. Surv. 34 (2002) 313-356
20. Douglas R.J., Koch C., Mahowald M., Martin K.A., and Suarez H.H. Recurrent excitation in neocortical circuits. Science 269 (1995) 981-985
21. Drew P.J., and Abbott L.F. Model of song selectivity and sequence generation in area HVc of the songbird. J. Neurophysiol. 89 (2003) 2697-2706
22. Dutar P., Vu H.M., and Perkel D.J. Multiple cell types distinguished by physiological, pharmacological, and anatomic properties in nucleus HVc of the adult zebra finch. J. Neurophysiol. 80 (1998) 1828-1838
23. Eichenbaum H. Hippocampus cognitive processes and neural representations that underlie declarative memory. Neuron 44 (2004) 109-120
24. Estes W.K. An Associative Basis for Coding and Organization in Memory. In: Melton A.W., and Martin E. (Eds). Coding Processes in Human Memory, Chapter 7 (1972), Winston, Washington, DC 161-190
25. Fee M.S., Kozhevnikov A.A., and Hahnloser R.H.R. Neural mechanisms of vocal sequence generation in the songbird. Ann. N Y Acad. Sci. 1016 (2004) 153-170
26. Fiala J.C., and Harris K.M. Dendrite structure. In: Stuart G., Spruston N., and Häusser M. (Eds). Dendrites (1999), Oxford University Press, New York 1-34
27. Girman S.V., Sauve Y., and Lund R.D. Receptive field properties of single neurons in rat primary visual cortex. J. Neurophysiol. 82 (1999) 301-311
28. Gray J.M., Hill J.J., and Bargmann C.I. A circuit for navigation in Caenorhabditis elegans. Proc. Natl. Acad. Sci. USA 102 (2005) 3184-3191
29. Hahnloser R.H.R., Kozhevnikov A.A., and Fee M.S. An ultra-sparse code underlies the generation of neural sequences in a songbird. Nature 419 (2002) 65-70
30. Harris K.M., and Stevens J.K. Dendritic spines of CA1 pyramidal cells in the rat hippocampus: serial electron microscopy with reference to their biophysical characteristics. J. Neurosci. 9 (1989) 2982-2997
31. Harris K.M., Perry E., Bourne J., Feinberg M., Ostroff L., and Hurlburt J. Uniform serial sectioning for transmission electron microscopy. J. Neurosci. 26 (2006) 12101-12103
32. Hartline H.K., and Ratliff F. Inhibitory interaction in the retina of Limulus. In: Fuortes M.G.F. (Ed). Handbook of Sensory Physiology. Physiology of Photoreceptor Organs, Volume VII/2 (1972), Springer-Verlag, Berlin 381-447
33. Hell S.W. Far-field optical nanoscopy. Science 316 (2007) 1153-1158
34. Hobert O., and Hall D.H. Neuroanatomy: A second look with GFP reporters and some comments. Worm Breed. Gaz. 16 (1999) 24
35. Jain, V., Murray, J.F., Roth, F., Turaga, S., Zhigulin, V., Briggman, K.L., Helmstaedter, M.N., Denk, W., and Seung, H.S. (2007). Supervised learning of image restoration with convolutional networks. IEEE 11th International Conference on Computer Vision (ICCV), pp. 1-8.
36. Jin D.Z., Ramazanoglu F.M., and Seung H.S. Intrinsic bursting enhances the robustness of a neural network model of sequence generation by avian brain area hvc. J. Comput. Neurosci. 23 (2007) 283-299
37. Kasthuri N., Hayworth K., Lichtman J., Erdman N., and Ackerley C.A. New technique for ultra-thin serial brain section imaging using scanning electron microscopy. Microsc. Microanal. 13 (2007) 26-27
38. Katz L.C., and Gurney M.E. Auditory responses in the zebra finch's motor system for song. Brain Res. 221 (1981) 192-197
39. Kim I.J., Zhang Y., Yamagata M., Meister M., and Sanes J.R. Molecular identification of a retinal cell type that responds to upward motion. Nature 452 (2008) 478-482
40. Kong J., Fish D.R., Rockhill R.L., and Masland R.H. Diversity of ganglion cells in the mouse retina: Unsupervised morphological classification and its limits. J. Comp. Neurol. 489 (2005) 293-310
41. Lashley K.S. The problem of serial order in behaviour. Cerebral Mechanisms in Behaviour (1951), Wiley, New York 112-136
42. Leonardo A., and Fee M.S. Ensemble coding of vocal control in birdsong. J. Neurosci. 25 (2005) 652-661
43. Li M.R., and Greenside H. Stable propagation of a burst through a one-dimensional homogeneous excitatory chain model of songbird nucleus HVC. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 74 (2006) 011918
44. Lichtman J.W., and Sanes J.R. Ome sweet ome: what can the genome tell us about the connectome?. Curr. Opin. Neurobiol. 18 (2008) 346-353
45. Luo L., Callaway E.M., and Svoboda K. Genetic dissection of neural circuits. Neuron 57 (2008) 634-660
46. Mackenzie P.J., Kenner G.S., Prange O., Shayan H., Umemiya M., and Murphy T.H. Ultrastructural Correlates of Quantal Synaptic Function at Single CNS Synapses. J. Neurosci. 19 (1999) RC13
47. Mahowald M.A., and Mead C.A. A silicon model of early visual processing. Neural Netw. 1 (1988) 91-97
48. Markram H., Toledo-Rodriguez M., Wang Y., Gupta A., Silberberg G., and Wu C. Interneurons of the neocortical inhibitory system. Nat. Rev. Neurosci. 5 (2004) 793-807
49. Marr D. Simple memory: a theory for archicortex. Philos. Trans. R. Soc. Lond. B Biol. Sci. 262 (1971) 23-81
50. Masland R. Neuronal diversity in the retina. Curr. Opin. Neurobiol. 11 (2001) 431-436
51. Masland R.H. The fundamental plan of the retina. Nat. Neurosci. 4 (2001) 877-886
52. Masland R.H. Neuronal cell types. Curr. Biol. 14 (2004) R497-R500
53. Matsuzaki M., Ellis-Davies G., Nemoto T., Miyashita Y., Iino M., and Kasai H. Dendritic spine geometry is critical for AMPA receptor expression in hippocampal CA1 pyramidal neurons. Nat. Neurosci. 4 (2001) 1086-1092
54. Mooney R. Different subthreshold mechanisms underlie song selectivity in identified hvc neurons of the zebra finch. J. Neurosci. 20 (2000) 5420-5436
55. Mooney R., and Prather J.F. The HVC microcircuit: The synaptic basis for interactions between song motor and vocal plasticity pathways. J. Neurosci. 25 (2005) 1952-1964
56. Murthy V.N., Schikorski T., Stevens C.F., and Zhu Y. Inactivity produces increases in neurotransmitter release and synapse size. Neuron 32 (2001) 673-682
57. Naka K.I., and Rushton W.A. The generation and spread of S-potentials in fish (Cyprinidae). J. Physiol. 192 (1967) 437-461
58. Nelson S.B., Hempel C., and Sugino K. Probing the transcriptome of neuronal cell types. Curr. Opin. Neurobiol. 16 (2006) 571-576
59. Nottebohm F., Stokes T.M., and Leonard C.M. Central control of song in the canary, serinus canarius. J. Comp. Neurol. 165 (1976) 457-486
60. Ohki K., Chung S., Ch'ng Y.H., Kara P., and Reid R.C. Functional imaging with cellular resolution reveals precise micro-architecture in visual cortex. Nature 433 (2005) 597-603
61. O'Keefe J., and Nadel L. The Hippocampus as a Cognitive Map (1978), Oxford University Press, New York
62. Orban G. Neuronal Operations in the Visual Cortex (1984), Springer, Berlin
63. Oyster C.W., Amthor F.R., and Takahashi E.S. Dendritic architecture of ON-OFF direction-selective ganglion cells in the rabbit retina. Vision Res. 33 (1993) 579-608
64. Pierce J.P., and Lewin G.R. An ultrastructural size principle. J. Neurosci. 58 (1994) 441-446
65. Ratliff F. Mach Bands: Quantitative Studies on Neural Networks in the Retina (1965), Holden-Day, San Francisco
66. Redish A.D., Battaglia F.P., Chawla M.K., Ekstrom A.D., Gerrard J.L., Lipa P., Rosenzweig E.S., Worley P.F., Guzowski J.F., McNaughton B.L., et al. Independence of firing correlates of anatomically proximate hippocampal pyramidal cells. J. Neurosci. 21 (2001) RC134
67. Reigl M., Alon U., and Chklovskii D.B. Search for computational modules in the C. elegans brain. BMC Biol. 2 (2004) 25
68. Rumelhart D.E., and Norman D.A. Simulating a skilled typist: a study of skilled cognitive-motor performance. Cogn. Sci. 6 (1982) 1-36
69. Samsonovich A., and McNaughton B.L. Path integration and cognitive mapping in a continuous attractor neural network model. J. Neurosci. 17 (1997) 5900-5920
70. Schikorski T., and Stevens C.F. Quantitative ultrastructural analysis of hippocampal excitatory synapses. J. Neurosci. 17 (1997) 5858-5867
71. Shendure J., Mitra R.D., Varma C., and Church G.M. Advanced sequencing technologies: methods and goals. Nat. Rev. Genet. 5 (2004) 335-344
72. Shepherd G.M.G., and Harris K.M. Three-dimensional structure and composition of CA3→ CA1 axons in rat hippocampal slices: implications for presynaptic connectivity and compartmentalization. J. Neurosci. 18 (1998) 8300-8310
73. Smith S.J. Circuit reconstruction tools today. Curr. Opin. Neurobiol. 17 (2007) 601-608
74. Somers D.C., Nelson S.B., and Sur M. An emergent model of orientation selectivity in cat visual cortical simple cells. J. Neurosci. 15 (1995) 5448-5465
75. Song S., Sjostrom P.J., Reigl M., Nelson S., and Chklovskii D.B. Highly nonrandom features of synaptic connectivity in local cortical circuits. PLoS Biol. 3 (2005) e68
76. Sporns O., Tononi G., and Kotter R. The human connectome: a structural description of the human brain. PLoS Comput. Biol. 1 (2005) e42
77. Striedter G.F. Prècis of principles of brain evolution. Behav. Brain Sci. 29 (2006) 1-12
78. Tsodyks M., and Sejnowski T. Associative memory and hippocampal place cells. Int. J. Neural Syst. 6 (1995) 81-86
79. Vapnik V.N. The Nature of Statistical Learning Theory (2000), Springer, New York
80. White J.G., Southgate E., Thomson J.N., and Brenner S. The structure of the nervous system of the nematode Caenorhabditis elegans. Philos. Trans. R. Soc. Lond. B Biol. Sci. 314 (1986) 1-340
81. Wickersham I.R., Lyon D.C., Barnard R.J.O., Mori T., Finke S., Conzelmann K.K., Young J.A.T., and Callaway E.M. Monosynaptic restriction of transsynaptic tracing from single, genetically targeted neurons. Neuron 53 (2007) 639-647
82. Worgotter F., and Koch C. A detailed model of the primary visual pathway in the cat: comparison of afferent excitatory and intracortical inhibitory connection schemes for orientation selectivity. J. Neurosci. 11 (1991) 1959-1979
83. Yoshimura Y., Dantzker J.L., and Callaway E.M. Excitatory cortical neurons form fine-scale functional networks. Nature 433 (2005) 868-873