Reconstruction and Simulation of Neocortical Microcircuitry

@article{Markram2015ReconstructionAS,
  title={Reconstruction and Simulation of Neocortical Microcircuitry},
  author={Henry Markram and Eilif B. 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 {\'A}ngel 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 Howard 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 Juan Luis Riquelme and Christian A. R{\"o}ssert and Konstantinos Sfyrakis and Ying Shi and Julian C. Shillcock and Gilad Silberberg and Ricardo A.C. 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}
}

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex

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.

Rich cell-type-specific network topology in neocortical microcircuitry

A systematic approach enables interpretation of microconnectomics 'big data' and provides several experimentally testable predictions about cell-type-specific network properties when synaptic strength and sign were considered in generating a functional topology.

Controlling Complexity of Cerebral Cortex Simulations—II: Streamlined Microcircuits

It is shown that having a slow inhibitory synaptic conductance (GABAB) allows replication of oscillatory behavior in the high-calcium state and that qualitatively similar dynamics are seen even with a reduced number of cell types, suggesting that qualitative dynamics of cortical microcircuits can be studied using limited neuroinformatics and computing resources supporting parameter exploration and simulation of cortical systems.

Modeling and Simulation of Rat Non-Barrel Somatosensory Cortex. Part I: Modeling Anatomy

A data-driven computational model of the anatomy of non-barrel primary somatosensory cortex of juvenile rat is presented, which integrates whole-brain scale data while providing cellular and subcellular specificity and supports the notion that local and interregional connectivity exist on a spectrum of scales, rather than as separate and distinct networks as is commonly assumed.

Reconstruction and simulation of thalamoreticular microcircuitry

The first detailed microcircuit model of mouse thalamus and thalamic reticular nucleus is developed that captures morphological and biophysical properties of ~14,000 neurons connected via ~6M synapses, and recreates biological synaptic and gap junction connectivity.

A realistic morpho-anatomical connection strategy for modelling full-scale point-neuron microcircuits

A method to implement a neuronal network at single cell resolution by using the geometrical probability volumes associated with pre- and postsynaptic neurites to build a network with plausible connectivity properties without the explicit use of computationally intensive touch detection algorithms using full 3D neuron reconstructions.

Anatomically Detailed and Large-Scale Simulations Studying Synapse Loss and Synchrony Using NeuroBox

NeuroBox is used to study the electrical and biochemical effects of synapse loss vs. synchrony in neurons, to investigate large morphology data sets within detailed biophysical simulations, and to demonstrate the capability of utilizing high-performance computing infrastructure for large scale network simulations.

Large-scale biophysically detailed model of somatosensory thalamocortical circuits in NetPyNE

This work provides a widely accessible, data-driven and biophysically-detailed model of the somatosensory thalamocortical circuits that can be employed as a community tool for researchers to study neural dynamics, function and disease.

An algorithm to predict the connectome of neural microcircuits

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.

Visual physiology of the layer 4 cortical circuit in silico

A biophysically detailed circuit model of layer 4 in the mouse primary visual cortex, receiving thalamo-cortical visual inputs is reported, highlighting the importance of functional rules of cortical wiring and enabling a next generation of data-driven models of in vivo neural activity and computations.
...

References

SHOWING 1-10 OF 304 REFERENCES

The neocortical microcircuit collaboration portal: a resource for rat somatosensory cortex

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.

An algorithm to predict the connectome of neural microcircuits

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.

Saturated Reconstruction of a Volume of Neocortex

Statistical connectivity provides a sufficient foundation for specific functional connectivity in neocortical neural microcircuits

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.

Identifying, tabulating, and analyzing contacts between branched neuron morphologies

This paper describes how anatomical structure is model by identfying, tabulating, and analyzing contacts between 104 neurons in a morphologically precise model of a column in the Blue Brain Project.

Models of Neocortical Layer 5b Pyramidal Cells Capturing a Wide Range of Dendritic and Perisomatic Active Properties

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.

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 in

Computer generation and quantitative morphometric analysis of virtual neurons

An extensive, quantitative anatomical characterization of simulated motoneurons and Purkinje cells is reported, showing virtual neurons systematically displayed greater anatomical variability than real cells, suggesting the need for additional constraints in the models.

Physiology and anatomy of synaptic connections between thick tufted pyramidal neurones in the developing rat neocortex.

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.
...