Specify geometry

Step 4. Specify geometry

The Geometry page lets us specify the physical dimensions of the sections in our model, and how NEURON will compartmentalize the model (nseg).

A. Set up a strategy

The first thing we need to do is to set up an efficient strategy for assigning L, diam, and nseg. The aim is to figure out how to specify these parameters in a way that requires the least effort. So we start with the Specify Strategy checkbox ON (checked). After we have built our strategy, we will toggle the Specify Strategy checkbox OFF, and then we can enter numeric values for these parameters.

An important aside: when planning a strategy, keep the sequence of subsets and sections in mind. If the order isn't right, or if you need more subsets, then go back to the Subsets page and make the necessary changes.

We begin by dealing with the spatial grid (i.e. discretization or compartmentalization). This is really just a computational issue, not a biological one--we should be focussing on anatomically- and physiologically-relevant subdivisions of the cell, not "how small should the pieces be to get numerical accuracy and stability."

The CellBuilder offers three different ways to make this as painless as possible.

The "nseg" button lets us set nseg manually.
The "d_X" button lets us specify a maximum physical length, in microns, for each segment.
The "d_lambda" button is probably the best all-round choice. This lets us specify a maximum length for each segment, expressed as a fraction ("d_lambda") of the AC length constant at 100 Hz for a cylindrical cable with the same diameter, Ra, and cm. We'll return to this topic later.

If we choose d_X or d_lambda, the CellBuilder will always set nseg to an odd number. This ensures that each section will have a node exactly halfway down its length, which makes a lot of sense (see "Why should I use an odd value for nseg?" in the FAQ list). If we enter nseg manually, we can specify an even or odd number as we like.

Let's apply the d_lambda strategy to every section in the model. Click on the "all" subset to make sure it is selected, and glance at the shape plot just to check--every section should be red. Then click on the d_lambda checkbox.

Each section of our model is a different size, so we need to specify L and diam individually for every one of them. With versions of NEURON prior to 5.7, this would have required us to select each section individually, and click on its L and diam buttons. That's a lot of clicks.

However, starting with NEURON 5.7 we can save a few clicks by using the "Distinct values over subset" buttons. These tell the CellBuilder that each member of a subset has its own value of L (and/or diam).

So let's stick with the "all" set, and click on the "Distinct values over subset" L and diam buttons.

And if we had a set whose members should have identical lengths, we'd click on the "Constant value over subset" L button, etc..

This is what the strategy should look like now.

Having set up the strategy, we're ready to implement it. But first, save a session file!

B. Execute the strategy

Click on the Specify Strategy box to turn it OFF.

The right panel of the Geometry page now contains a set of buttons with numeric fields and spinners which we can use to enter the values of d_lambda, L, and diam. The sequence of these controls parallels their sequence in the middle panel of the CellBuilder.

The first parameter is d_lambda, which controls the spatial grid. Its default value is 0.1, i.e. one tenth of a length constant at 100 Hz, This is short enough for most models, so we can leave it alone. We can always come back later and try a different value if we like.

All of the lengths need to be changed.

But where are the diameters?

The drag bar at the right edge is our clue--we only have to pull it down . . .

. . . to see that some diameters also need changing.

Here they are with the desired values.

Time once again to save a session file!

The Biophysics page is next.

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