Neuron Registry Template

Name (V1 layer 5 pyramidal cell)
Short or historical name, and other synonyms (if applicable)
Source (this has been added as a result of RDTF and SLTF work)
- the original reference or person contributing the initial information/definition
- need a way of deciding when this entity has changed enough that it is no longer what was created by the source
Creator (date)
- need the ability to have multiple creators-it may be an attribute for each attribute
Version (curation status)
Species (and developmental stage, genetic or other manipulations, etc.)
- Species equivalents; interspecies mapping
Somatodendritic location (specify parcellation scheme)
Link to publication: PMID, DOI + specific text, figure(s)
Definition
Defining criteria (morphological, physiological, molecular,…)
Profile (expression, binding, physiology, etc…)
Instances (reference to specific studies or source data files)(later discussions suggest we may wish to tie this to each entity)
Super- and sub-classes, exclusive classes, and partially overlaps
Connectivity (links)
The system should be designed for extension to other attributes desirable in the future, e.g., ‘functions’ (behavioral, physiological, etc.), ‘public data sets that involve the cell type’, ‘models that include the cell type’, etc.

Suggestions from Gordon:

February 3/2010 Hi reason for this template can be found here, Common Features of Neurons

Species:
Specific cell type:
Brain region:
Histological layer: (canonical types: single layer cortex, single layer nucleus, scattered layer cortex, scattered nucleus)
Cell body shape: (canonical types: spherical, pyramidal, mitral, fusiform)
Dendritic fields (canonical types: bipolar, stellate, apical/basal, apical/basal/oblique - smooth or spiny)
Axon (canonical types: Local terminal: single layer; multilayer). Local collateral: single layer; multiple layer. Distant branching: single region; multiregion. En passant or terminal boutons)

Olfactory bulb (main) mitral cell

Cell template: histology
Species: mouse
Specific cell type: Mitral cell
Brain region: Olfactory bulb (main)
Histological layer: (canonical type: single cell layer)
- Mitral cell body layer (between external and internal plexiform layers)
Cell body shape: (canonical type: mitral)
- Bishop's mitre (cone shaped with convex sides), with point toward axon, away from dendrites
Dendritic fields (canonical type: apical and basal)
- Apical: single, smooth, usually unbranched, oriented radially across the external plexiform layer, ending in a tuft of branches in a single olfactory glomerulus
- Basal: several, smooth, sparingly branched, oriented laterally and externally within the external plexiform layer, extending up to 1 mm, terminating toward the outer border of the external plexiform layer.
Axon (canonical type: local (multilayer) and distant (multiregional))
- Single usually arising from the inner point of the cell body, courses deep then turns posteriorly to enter the lateral olfactory tract.
- Local: gives off local axon collaterals - short ones deep, long ones superficial - which branch and terminate in the external plexiform layer
- Distant: gives off branches from the lateral olfactory tract which end in the superficial layer of the olfactory cortex

Afferent input connectivity: from olfactory sensory neuron axon terminals onto the apical dendritic tuft (type I, excitatory, glutamatergic, AMPA, NMDA)
Intrinsic input connectivity: from PG cell dendrites in glomerulus onto glomerular tuft dendritic branches (type I, inhibitory, GABAergic); from PG cell axon terminals onto the initial part of the apical dendrite arising from the glomerulus (type I, inhibitory, GABAergic); from granule cell apical dendritic spines onto basal dendrites (type I, inhibitory, GABAergic)
Efferent output connectivity: from distal axon terminals to the superficial layer of olfactory cortical regions (type I, excitatory, glutamatergic, AMPA, NMDA)
Intrinsic output connectivity: from glomerular dendritic branches onto PG cell glomerular dendritic branches (type I, excitatory, glutamatergic, AMPA, NMDA); from basal (lateral) dendrites onto granule cell dendritic spines (type I, excitatory, glutamatergic, AMPA, NMDA); from axon collaterals ending in the granule cell and external plexiform layer.

Neocortex layer 3 pyramidal neuron

Species: mouse
Specific cell type: Neocortex layer 3 pyramidal neuron
Brain region: Neocortex
Histological layer: (canonical type: scattered layer cortex): layer 3
Cell body shape: (canonical type: pyramidal): pyramidal
Dendritic fields (canonical type: apical/basal)
- Apical: single, initially unbranched trunk, spiny, oriented across superficial layer 3 and 2 to branch and terminate in layer 1.
Axon (canonical type: local collaterals multilayer and distant multiple regions)
- Single, usually arising from base of pyramidal soma, descends to leave the cortex and enter the white matter
- Local: axon gives off rich arborization of axon collaterals that branch and terminate in layers 2-4.
- Distant: axon courses through the white matter to terminate in deep layers of other cortical regions

Afferent input connectivity: terminal branches of thalamocortical fibers end on spines of basal dendrites in layer 4
Efferent output connectivity: deep layers of other cortical regions
Intrinsic input connectivity: cortical intrinsic neuron axons: basket cells ending on the soma: chandelier cells ending on the initial axonal segment; fusiform cells ending on apical dendritic branches
Intrinsic output connectivity: from apical dendrite onto axon terminals of inhibitory interneurons; from axon collaterals ending in layers 2-4.