The neocortex is a major part of the mammalian brain and is made up of a continuous microcircuit sheet of neurons
with stereotypical types of neurons that are also intricately interconnected in a stereotypical manner
(Ramon y Cajal, 1911; Peters and Jones,
1984; White, 1989; Gupta et al., 2000; Toledo-Rodriguez et al., 2002; Thomson and Bannister, 2003)
.
During sensory input, assemblies of neurons spontaneously form to parcellate the neocortex into functionally
specialized modules (Hubel and Wiesel, 1977;
Shmuel and Grinvald, 1996; Mountcastle, 1998) allowing sensory processing. The microcircuitry of these modules lies at the heart of the information
processing capability of the neocortex enabling perception, attention, memory, and higher cognitive functions.
The Neocortical Microcircuit Database (NMDB) is dedicated to organizing
the anatomical, physiological and molecular properties of this microcircuit.
The microcircuit is formed of different types
of neurons and synaptic connections (for review, see: (Toledo-Rodriguez et al., 2002)). The data is based on a
principle of numerical breakdown of key properties to produce “profiles” which form the foundation of the database.
Neurons are characterized in terms of their morphological, physiological and gene expression profiles. Synaptic
connections are characterized in terms of their physiological and anatomical profiles. Neuron morphology profiles
are obtained from detailed morphometric breakdown of 3D reconstructed neurons (m-Profiles), neuron physiology
profiles are obtained from detailed measurement of the electrophysiological responses to a series of stimulus
protocols (e-Profiles), and neuron gene expression profiles are obtained from single cell RT-PCR data (g-Profiles)
and in the near future from gene-chips. Synaptic connections are characterized by the identity of the pre and
postsynaptic neurons (sn-Profile), the anatomy of synaptic connections as characterized by the axonal and
dendritic location of light microscopically identified putative synapses (sm-Profile), and the physiology of
synaptic connections as characterized by a profile of electrophysiological parameters obtained from a series of
stimulation protocols applied to the presynaptic neuron (se-Profile).
The development of the database will follow a series
of phases. In the first phase, the database will focus on indexing neuronal and synaptic profiles. In the second
phase, canonical neuron types and synaptic connections will be defined. In the third phase, the distribution and
relative numbers of neurons will be defined for the different layers of the neocortex, and in the final phase, the
microcircuit will be fully reconstructed for visual guided exploration of the microcircuit structure and physiology.
In parallel to the NMDB a database of mathematical models of the different neurons, synaptic connections and
various size microcircuits is being constructed to eventually allow visualization of the activated neocortical
microcircuit. In later phases, various long range input and output pathways into neocortical neurons will be
incorporated into the database. The NMDB is populated with microcircuit data primarily from rat, but data from any
species can be entered.
