Sample Network Definition File

*
* External nuclei are LIGHT and OPTIC_RADIATION
* Note we now have an LGN in addition to our retina.
*

NETWORK EYE
CENTER (0, 0, 0)
EXTENT (12000,12000,12000)

NUCLEUS EXTERNAL_LIGHT
CENTER (0,0,1000)
EXTENT (10000,10000,5)

CELL LIGHT
CENTER (0,0,1000)
EXTENT (10000,10000,1)
NEURON_TYPE EXTERNAL
N_NEURONS 400
ARRANGEMENT GRID_2D

NUCLEUS EXTERNAL_OPTIC_RADIATION
CENTER (0,0,11000)
EXTENT (1000,1000,5)
* to V1
CELL OPTIC_RADIATION
CENTER (0,0,11000)
EXTENT (1000,1000,1)
NEURON_TYPE EXTERNAL
ARRANGEMENT GRID_2D
N_NEURONS 400

NUCLEUS LGN
CENTER (0,0,9000)
EXTENT (10000,10000,5)

CELL THALAMOCORTICAL_RELAY_NEURONS

CENTER (0,0,9000)
EXTENT (10000,10000,5)
NEURON_SIZE (10,10,5)
N_NEURONS 400
ARRANGEMENT GRID_2D
NEURON_TYPE IAF
RESTING_POTENTIAL -70
THRESHOLD -50
TAU 0.2

NUCLEUS RETINA
CENTER (0,0,6000)
EXTENT (10000,10000,2000)

CELL RODS

CENTER (0,0,6300)
EXTENT (10000,10000,5)
NEURON_SHAPE CYLINDER LENGTH 5 DIAMETER 2
N_NEURONS 400
ARRANGEMENT GRID_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -50
TAU 0.05

CELL RED_CONES

CENTER (0,0,6200)
EXTENT (10000,10000,5)
NEURON_SHAPE CYLINDER LENGTH 5 DIAMETER 3
N_NEURONS 400
ARRANGEMENT HEX_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -50
TAU 0.05

CELL GREEN_CONES

CENTER (10,10,6100)
EXTENT (10000,10000,5)
NEURON_SHAPE CYLINDER LENGTH 5 DIAMETER 3
N_NEURONS 400
ARRANGEMENT HEX_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -50
TAU 0.05

CELL BLUE_CONES

CENTER (20,20,6000)
EXTENT (10000,10000,5)
NEURON_SHAPE CYLINDER LENGTH 5 DIAMETER 3
NEURONS 400
ARRANGEMENT HEX_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -50
TAU 0.05

CELL H1_HORIZONTAL_CELLS

CENTER (0,0,5600)
EXTENT (10000,10000,5)
NEURON_SIZE (5,5,2)
NEURONS 100
ARRANGEMENT GRID_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -60
AXON VELOCITY 1.0 DIRECTIONAL (0,-40,0)
TAU 0.1

CELL H2_HORIZONTAL_CELLS

CENTER (0,0,5500)
EXTENT (10000,10000,5)
NEURON_SIZE (5,5,2)
NEURONS 100
ARRANGEMENT GRID_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -60
TAU 0.1

LAYER INNER_NUCLEAR_LAYER

INCLUDES RODS
INCLUDES RED_CONES
INCLUDES GREEN_CONES
INCLUDES BLUE_CONES
INCLUDES H1_HORIZONTAL_CELLS
INCLUDES H2_HORIZONTAL_CELLS

CELL ON_BIPOLAR_CELLS

CENTER (0,0,5000)
EXTENT (10000,10000,5)
NEURON_SIZE (5,5,2) VARIANCE (2,2,1)
N_NEURONS 400
ARRANGEMENT TRIANGLE_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -60
TAU 0.1

CELL OFF_BIPOLAR_CELLS

CENTER (0,0,4900)
EXTENT (10000,10000,5)
NEURON_SIZE (5,5,2) VARIANCE (2,2,1)
N_NEURONS 400
ARRANGEMENT TRIANGLE_2D
NEURON_TYPE LINEAR
RESTING_POTENTIAL -60
TAU 0.1

CELL AMACRINE_CELLS

CENTER (0,0,4500)
EXTENT (10000,10000,5)
NEURON_SIZE (5,5,2) VARIANCE (2,2,1)
N_NEURONS 400
ARRANGEMENT GRID_2D
NEURON_TYPE RATE
RESTING_POTENTIAL -70
THRESHOLD -65
REFRACTORY_PERIOD 1.0
* directions are in degrees off axis
AXON DIRECTIONAL (0,10,0) VELOCITY 1.0
TAU 0.05

CELL ON_GANGLION_CELLS

CENTER (0,0,4000)
EXTENT (10000,10000,5)
NEURON_SIZE (5,5,2) VARIANCE (2,2,1)
N_NEURONS 400
ARRANGEMENT HEX_2D
NEURON_TYPE HH-2
RESTING_POTENTIAL -70
THRESHOLD -50
TAU 0.1
REFRACTORY_PERIOD 0.1
INITIAL_ACTIVITY 0.1
SPONTANEOUS_ACTIVITY 0.1
MAXIMUM_LEVEL 0.1

CELL OFF_GANGLION_CELLS

CENTER (10,10,4000)
EXTENT (10000,10000,5)
NEURON_SIZE (5,5,2) VARIANCE (2,2,1)
N_NEURONS 400
ARRANGEMENT HEX_2D
NEURON_TYPE HH-2
RESTING_POTENTIAL -70
THRESHOLD -50
TAU 0.1
REFRACTORY_PERIOD 0.1
INITIAL_ACTIVITY 0.1
SPONTANEOUS_ACTIVITY 0.1
MAXIMUM_LEVEL 0.1

LAYER OUTER_NUCLEAR_LAYER

INCLUDES AMACRINE_CELLS
INCLUDES ON_GANGLION_CELLS
INCLUDES OFF_GANGLION_CELLS

*
* define two neuropils for the retina
*

NEUROPIL OUTER_PLEXIFORM_LAYER
CENTER (0,0,5800)
EXTENT (10000,10000,5)
USED_BY RODS
USED_BY RED_CONES
USED_BY GREEN_CONES
USED_BY BLUE_CONES
USED_BY H1_HORIZONTAL_CELLS
USED_BY H2_HORIZONTAL_CELLS
USED_BY ON_BIPOLAR_CELLS DENDRITES
USED_BY OFF_BIPOLAR_CELLS DENDRITES

NEUROPIL INNER_PLEXIFORM_LAYER
CENTER (0,0,4700)
EXTENT (10000,10000,5)
USED_BY ON_BIPOLAR_CELLS AXONS
USED_BY OFF_BIPOLAR_CELLS AXONS
USED_BY AMACRINE_CELLS AXONS DENDRITES
USED_BY ON_GANGLION_CELLS DENDRITES
USED_BY OFF_GANGLION_CELLS DENDRITES

*
* Specification of connections between cell types
*
* Note that divergence can be given in number of nearest neighbors,
* or in coordinate extent.
*

CONNECTION FROM RODS TO H1_HORIZONTAL_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT
TAU 0.05
DELAY 0.01

CONNECTION FROM RED_CONES TO H1_HORIZONTAL_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM GREEN_CONES TO H1_HORIZONTAL_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM RODS TO H2_HORIZONTAL_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM BLUE_CONES TO H2_HORIZONTAL_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM H1_HORIZONTAL_CELLS TO H1_HORIZONTAL_CELLS

TYPE LATERAL
TYPE DENDRODENDRITIC
TYPE BIDIRECTIONAL
TYPE INHIBITORY
DIVERGENCE 5
WEIGHT 0.05
TOPOGRAPHY POINT

CONNECTION FROM H2_HORIZONTAL_CELLS TO H2_HORIZONTAL_CELLS

TYPE LATERAL
TYPE DENDRODENDRITIC
TYPE BIDIRECTIONAL
TYPE INHIBITORY
DIVERGENCE 5
WEIGHT 0.05
TOPOGRAPHY POINT

CONNECTION FROM RODS TO ON_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM RODS TO OFF_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM RED_CONES TO ON_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM GREEN_CONES TO ON_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM BLUE_CONES TO ON_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM RED_CONES TO OFF_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM GREEN_CONES TO OFF_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM BLUE_CONES TO OFF_BIPOLAR_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.5
TOPOGRAPHY POINT

CONNECTION FROM H1_HORIZONTAL_CELLS TO ON_BIPOLAR_CELLS

TYPE DIRECT
TYPE DENDRODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM H1_HORIZONTAL_CELLS TO OFF_BIPOLAR_CELLS

TYPE DIRECT
TYPE DENDRODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM H2_HORIZONTAL_CELLS TO ON_BIPOLAR_CELLS

TYPE DIRECT
TYPE DENDRODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.1 VARIANCE 0.01
TOPOGRAPHY POINT

CONNECTION FROM H2_HORIZONTAL_CELLS TO OFF_BIPOLAR_CELLS

TYPE DIRECT
TYPE DENDRODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM ON_BIPOLAR_CELLS TO AMACRINE_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT .3
TOPOGRAPHY POINT

CONNECTION FROM OFF_BIPOLAR_CELLS TO AMACRINE_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT .1
TOPOGRAPHY POINT

CONNECTION FROM AMACRINE_CELLS TO AMACRINE_CELLS

TYPE LATERAL
TYPE DENDRODENDRITIC
TYPE BIDIRECTIONAL
TYPE INHIBITORY
DIVERGENCE (2500,2500,5)
WEIGHT 0.05
TOPOGRAPHY POINT

CONNECTION FROM ON_BIPOLAR_CELLS TO ON_GANGLION_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 1
TOPOGRAPHY POINT

CONNECTION FROM OFF_BIPOLAR_CELLS TO OFF_GANGLION_CELLS

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 1
TOPOGRAPHY POINT

CONNECTION FROM AMACRINE_CELLS TO ON_GANGLION_CELLS

TYPE DIRECT
TYPE INHIBITORY
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM AMACRINE_CELLS TO OFF_GANGLION_CELLS

TYPE DIRECT
TYPE INHIBITORY
TYPE AXODENDRITIC
DIVERGENCE 1
WEIGHT 0.1
TOPOGRAPHY POINT

CONNECTION FROM LIGHT TO RODS

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 1.0
TOPOGRAPHY POINT

CONNECTION FROM LIGHT TO RED_CONES

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 1.0
TOPOGRAPHY POINT

CONNECTION FROM LIGHT TO GREEN_CONES

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 1.0
TOPOGRAPHY POINT

CONNECTION FROM LIGHT TO BLUE_CONES

TYPE DIRECT
TYPE AXODENDRITIC
TYPE INHIBITORY
DIVERGENCE 1
WEIGHT 1.0
TOPOGRAPHY POINT

CONNECTION FROM ON_GANGLION_CELLS TO THALAMOCORTICAL_RELAY_NEURONS

TYPE DIRECT
TYPE AXODENDRITIC
WEIGHT 1.0
MAP on_ganglion.map

CONNECTION FROM OFF_GANGLION_CELLS TO THALAMOCORTICAL_RELAY_NEURONS

TYPE DIRECT
TYPE AXODENDRITIC
WEIGHT 0.5
MAP off_ganglion.map

CONNECTION FROM THALAMOCORTICAL_RELAY_NEURONS TO OPTIC_RADIATION

TYPE DIRECT
TYPE AXODENDRITIC
WEIGHT 0.5
TOPOGRAPHY POINT
DIVERGENCE 1

MODULE WIDE_FIELD_MODULE

INCLUDES 100 RODS
INCLUDES 10 H1_HORIZONTAL_CELLS
INCLUDES 1 ON_BIPOLAR_CELLS
INCLUDES 1 OFF_BIPOLAR_CELLS

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