Overview of the task
- Specify the
- subset
- distance metric
p
- parameter
param
that depends on distance
- function
f
that governs the relationship between the parameter and the distance metric
param = f(p)
- Verify the implementation.
Details
This involves a lot of steps--remember to save intermediate results to session files!
Act 1: Specify the subset
On the CellBuilder's Subsets page, create the subset.
Act 2: Specify the distance metric
Do this with a SubsetDomainIterator.
- Create a SubsetDomainIterator.
- Click on the subset, then click on "Parameterized Domain Page"
- Click on "Create a SubsetDomainIterator".
The name of the SubsetDomainIterator will appear in the middle panel of the CellBuilder. It will be called name_x, where name is the name of the subset.
- Use the SubsetDomainIterator to specify the distance metric.
- Click on name_x.
The right panel of the CellBuider will show the controls for specifying the distance metric. Default is path length in um from the root of the cell (0 end of soma).
Drag the slider back and forth to see the corresponding location(s) in the shape plot (boundary between red and black). Distance from the root to the red-black boundary is shown on the canvas as "p=nnn.nnn". You can also click on the canvas near the shape and drag the cursor back and forth; the canvas will now show the "range" of the boundary in the nearest section, and the name of that section.
- metric offers three choices: path length from root, radial (euclidian) distance from root, and "projection onto line" (distance from a plane that passes through the root and is orthogonal to the principal axis of the root section).
- proximal allows specifying an "offset" for the proximal end(s) of the subset. This lets you assign a distance of 0 to the origin of the apical tree.
- distal allows specifying whether or not to normalize the distance metric, and if normalized, whether the metric is to become 1 only at the most distal end, or at all distal ends.
Act 3: Specify the parameters that depend on distance
Do this on the CellBuilder's Biophysics page.
- Select Strategy (make a check mark appear in the box).
name_x (the name of the SubsetDomainIterator) will appear in the middle panel.
- Click on name_x.
- In the right panel of the CellBuider, select the parameters that the SubsetDomainIterator will control.
Intermezzo
Time to step back and see where we are.
At this point, name_x "knows" these things:
- the sections that are in its subset
- the distance metric for each spatial location in these sections
- the parameters in these sections that will be governed by this distance metric
But it doesn't know the functional relationships between the parameters and the distance metric--and each parameter can have its own function.
Defining these functions is the next item to take care of.
Act 4: Specify the functional relationship between each parameter and the distance metric
Finale trionfale
Turn on Continuous Create, and use Model View to verify the channel distributions.
NEURON hands-on course
Copyright © 2010 by N.T. Carnevale and M.L. Hines,
all rights reserved.