Reconstruction and Simulation of Neocortical Microcircuitry

@article{Markram2015ReconstructionAS,
  title={Reconstruction and Simulation of Neocortical Microcircuitry},
  author={Henry Markram and Eilif Muller and Srikanth Ramaswamy and Michael W. Reimann and Marwan Abdellah and Carlos Aguado Sanchez and Anastasia Ailamaki and Lidia Alonso-Nanclares and Nicolas Antille and Selim Arsever and Guy Antoine Atenekeng Kahou and Thomas K. Berger and Ahmet Mert Bilgili and Nenad Buncic and Athanassia Chalimourda and Giuseppe Chindemi and Jean-Denis Courcol and Fabien Delalondre and Vincent Delattre and Shaul Druckmann and Raphael Dumusc and J. A. Dynes and Stefan Eilemann and Eyal Gal and Michael Gevaert and Jean-Pierre Ghobril and Albert Gidon and Joe Graham and Anirudh Gupta and Valentin Haenel and Etay Hay and Thomas Heinis and Juan B. Hernando and Michael Hines and Lida Kanari and Daniel X. Keller and John Kenyon and Georges Khazen and Yihwa Kim and James G. King and Zolt{\'a}n F. Kisv{\'a}rday and Pramod S. Kumbhar and Sebastien Lasserre and Jean-Vincent Le B{\'e} and Bruno R. C. Magalh{\~a}es and Angel Merch{\'a}n-P{\'e}rez and Julie Meystre and Benjamin Roy Morrice and Jeffrey Muller and Alberto Mu{\~n}oz-C{\'e}spedes and Shruti Muralidhar and Keerthan Muthurasa and Daniel Nachbaur and Taylor H Newton and Max Nolte and Aleksandr Ovcharenko and Juan Palacios and Luis Pastor and Rodrigo Perin and Rajnish Ranjan and Imad Riachi and Jose R. Rodriguez and J L Riquelme and Christian A. R{\"o}ssert and Konstantinos Sfyrakis and Ying Shi and Julian C. Shillcock and Gilad Silberberg and Ricardo Silva and Farhan Tauheed and Martin Telefont and Maria Toledo-Rodriguez and Thomas Tr{\"a}nkler and Werner Van Geit and Jafet Villafranca D{\'i}az and Richard Walker and Yun Wang and Stefano M. Zaninetta and Javier DeFelipe and Sean L. Hill and Idan Segev and Felix Sch{\"u}rmann},
  journal={Cell},
  year={2015},
  volume={163},
  pages={456-492}
}
UNLABELLED We present a first-draft digital reconstruction of the microcircuitry of somatosensory cortex of juvenile rat. The reconstruction uses cellular and synaptic organizing principles to algorithmically reconstruct detailed anatomy and physiology from sparse experimental data. An objective anatomical method defines a neocortical volume of 0.29 ± 0.01 mm(3) containing ~31,000 neurons, and patch-clamp studies identify 55 layer-specific morphological and 207 morpho-electrical neuron subtypes… Expand
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References

SHOWING 1-10 OF 265 REFERENCES
The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex
TLDR
A multi-constraint, data-driven process to digitally reconstruct, and simulate prototypical neocortical microcircuitry, using sparse experimental data is established and considered a major step in the development of in silica neuroscience. Expand
An algorithm to predict the connectome of neural microcircuits
TLDR
It is concluded that an algorithmic approach to the connectome can serve as a tool to accelerate experimental mapping, indicating the minimal dataset required to make useful predictions, identifying the datasets required to improve their accuracy, testing the feasibility of experimental measurements, and making it possible to test hypotheses of synaptic connectivity. Expand
Saturated Reconstruction of a Volume of Neocortex
We describe automated technologies to probe the structure of neural tissue at nanometer resolution and use them to generate a saturated reconstruction of a sub-volume of mouse neocortex in which allExpand
Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits
TLDR
It is found that random alignment of axonal and dendritic arbors provides a sufficient foundation for specific functional connectivity to emerge in local neural microcircuits, suggesting that chemospecific steering and aligning of the arbors may occur for some types of connections. Expand
Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties
TLDR
Key features of the somatic and dendritic firing of L5b pyramidal cells in adult rats are characterized and a useful way to analyze model parameters with their sets of models is shown, which enabled them to identify some of the mechanisms responsible for the dynamic properties of L 5b pyramsidal cells as well as mechanisms that are sensitive to morphological changes. Expand
Functional Maps of Neocortical Local Circuitry
This review aims to summarize data obtained with different techniques to provide a functional map of the local circuit connections made by neocortical neurones, a reference for those interested inExpand
Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex.
TLDR
Dual voltage recordings were made from pairs of adjacent, synaptically connected thick tufted layer 5 pyramidal neurones in brain slices of young rat (14‐16 days) somatosensory cortex to examine the physiological properties of unitary EPSPs and the axonal and dendritic anatomy of both projecting and target neurones was uniform. Expand
Dynamics of Spontaneous Activity in Neocortical Slices
TLDR
It is concluded that the isolated neocortical microcircuit generates spontaneous activity, mediated by a combination of intrinsic and circuit mechanisms, and that this activity can be temporally precise. Expand
Monosynaptic connections between pairs of L5A pyramidal neurons in columns of juvenile rat somatosensory cortex.
TLDR
Paired recordings probed the anatomy and physiology of monosynaptic connections between L5A pyramidal neurons within the barrel columns of somatosensory cortex in acute slices of approximately 3-week-old rats to suggest a mechanism of feed-forward excitation by which synchronized single action potentials are efficiently transmitted. Expand
Dense, Unspecific Connectivity of Neocortical Parvalbumin-Positive Interneurons: A Canonical Microcircuit for Inhibition?
TLDR
It is concluded that the microcircuit architecture for PV+ interneurons, and probably neocortical inhibition in general, is an unspecific, densely homogenous matrix covering all nearby pyramidal cells. Expand
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