Use of morphological parameters

[SNNAP Board Admin]

These features was first implemented in V5.2d.

Conductance per unit area and shape (geometric) parameters

Rationale:

1. Current version of SNNAP specifies absolute value of channel
conductancesi (max.), which makes it difficult to compare the relative
density of each channel.

2. Specifying geometric parameters relieves a user the burden of calculating
the membrane area, allows re-use of the same kinetics but different size of
neuron (compartment) in the same network (neuron).

3. When a user channges the membrane area of the neuron (compartment),
there will be no need to change the maximum conductance of each ion channel.


Implementation consideration:

1. We need to replace the original "gmax" (nS) in the general formula
gmax*A*B to "S*gmax", where S is the membrane area in cm2 and the new
gmax is in S/cm2 (conductane per unit area).

original formula: g = gmax * exp(A, p) * B
new formula: g = S * gmax * exp(A, p) * B

To maintain compartibility with old version, set S=1 by default.
In fact, the original EDIT functions and the format of the parameter
files i(*.vdg) need no change. The only change in this regard
is when load/reloading the *.vdg files, mutiply the gmax (g below)
by membrane area (S).

2. For specifying the geometric parameters of a neuron (compartment),
we have three options:

a. specify membrane area directly;
b. sphere, specify diameter (d, um);
c. cylinder, specify diameter (d, um), length(l, um), and whether it
is closed at two ends (two ends open, one end open and one end
closed, two ends closed).

For b and c, the membrane area will be calculated and saved in the parameter
file (.neu) for reference (but this number will not be used directly during
runtime).


3. Details

The geometric (shape) parameters will be kept in the "neuron" (*.neu) file,
before the conductance section.

a section of the .neu file
>------------------------------->--------------------------------------->
VMINIT: -60.0 > Initial value of membrane potential. >
>------------------------------->--------------------------------------->
CM: 0.0013 > Membrane capacitance. >
>------------------------------->--------------------------------------->
>
> add shape (geometric) parameters here, e.g.:
>------------------------------->--------------------------------------->
>
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
MemArea: > Membrane Area options >
>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>>
> put calculated membrane area some where in this section for reference
>------------------------------->--------------------------------------->
0 > do not use membrane area
>------------------------------->--------------------------------------->
1 > type 1, specify membrane area directly
0.5 >S<
>------------------------------->--------------------------------------->
2 > type 2, sphere
0.8 >D< > diameter
>------------------------------->--------------------------------------->
3 > type 3, cylinder
0.8 >D< > diameter
8 >L< > length
1 >n< > number of ends closed
>------------------------------->--------------------------------------->

To maintain compatibility with previous versions, in the dialog,
it will ask whether the user want to specify the shape parameters.
If the answer is No, keep original method (S=1).
If Yes, offer three options for specifying shape parameters, and calculate
membrane area.

0: do not use membrane area (shape or geometric parameters)
1. directly specify area
2. sphere: D
3. cylinder D, L
ends: n=0 both ends open
n=1 one end open one end closed
n=2 both ends closed

4. Other changes

Capacitance (CM) will also be adjusted based on membrane area.

Cai