First, let me thank you for using NEURON in your project.
1. with a cell from neuromorpho do I have to define the parameters such as L by hand through the cellbuilder?
When the Import3D tool reads a morphometric data file, it captures all of the length and diameter information in that file. Whatever you export from the Import3D tool contains all that information. If you export to a CellBuilder, that CellBuilder will contain all of that information.
"But the drawing of the cell in the CellBuilder looks strange--every branch is a straight line, not at all like the irregular neurites that real cells have."
That's because the CellBuilder takes a shortcut when it renders the shape of the cell on its canvas--each neurite is shown as a straight line between its endpoints. But all the morphometric data still exists inside the CellBuilder. If you click Continuous Create and then bring up a Shape plot (NEURON Main Menu / Graph / Shape plot) you'll see the real shape of the cell, with all those irregular wiggles--and you can see the diameter changes too, if you click in the Shape plot's menu box (square in upper left corner of the canvas) and select Shape Style / Show Diam. Some of the narrowest branches may not be visible unless you expand the size of the graph or zoom in on the figure.
"But if I go to the CellBuilder's Geometery page, I don't see any information about section length and diameter."
There are two ways to specify section geometry: stylized (section L and diam are specified explicitly), and 3-D (section geometry is specified by a series of x,y,z,diameter measurements). Suggest you read
https://www.neuron.yale.edu/neuron/stat ... metry.html
The CellBuilder's Geometry page only shows L and diam for sections that were specified by the stylized method. Importing a morphometric data file produces a model cell with geometry specified by the 3-D method, and the CellBuilder doesn't show you the L or diam of anything. If your CellBuilder was created by the Import3D tool, don't use its Geometry page to tinker with the L or diam of any section unless you want to cause a lot of confusion for yourself. If your model cell is based on imported morphometric data, the only part of the Geometry page's user interface that is relevant is the stuff used to specify the spatial grid.
I downloaded a cell morphology from neuromorpho and opened it with import3d and cellbuilder. I didn't modify any parameters and simply exported the model to file.
. . . once I export the cell from cellbuilder into a hoc file, how can I create a template out of it as is said in the instructions in http://www.neuron.yale.edu/phpbb/viewto ... =15&t=2306
Well, first of all, that discussion thread does not say anything about exporting hoc files and then converting them to templates.
If you exported a "top level" model cell (a model specification that is NOT in a template), and now you want to convert that to a template, you have a lot of programming to do--you'll have to add ion channels, and you'll have to encapsulate all that code in a template. Not advisable. This is tedious if you are an expert on writing templates. It is quite arduous if you are just starting to work with NEURON.
If you exported a template for a cell class, you face a task that is not much easier--you still have to write code that adds ion channels, but you have to do it in a way that doesn't break the template. Not advisable. Requires almost as much expertise as wrapping a top level model specification in a template, and involves nearly as much effort.
You'll get better results much faster and with far less effort if you use the CellBuilder to do as much development as possible, and defer exporting top level hoc code or templates until you are quite sure that your model cell(s) have the biophysical properties that you want, and are working properly. Here's a suggested workflow:
1. After you use Import3D to import morphometric data, export to a CellBuilder and save that CellBuilder to a session file, all by itself. Give that session file a meaningful name that reminds you what kind of a cell the data came from, and also that the session file is "bare"--that is, it has no ion channels. For example, if you have a CellBuilder that contains the morphology of a layer 5 pyramidal cell, save the CellBuilder to a file called something like
Put this file somewhere for safekeeping.
2. When it comes time to add channels or other biophysical mechanisms, first make a copy of L5bare.ses, then work on the copy--maybe call this L5devel.ses. Never work on the original file.
3. Defer exporting hoc code from the working copy of the session file until you are completely satisfied with the model specification that it contains. This assumes that you have tested your model cell in a toy simulation--at the very least, see how it responds to injected currents and synaptic inputs. Also, use Model View to verify that the properties of your model cell are what you expect them to be. You're going to spend a lot of time building and using your network model, so you need to make sure that all the pieces you put into it are correct.
Whatever else you do, be sure to save the final version of the working copy of your completed model cell, along with whatever other files are needed to explore and verify it. That way, you'll be able to find them 6 months or a year from now when you decide you need to revise it.
4. At the happy point where you are satisfied with the model in your CellBuilder, what should you do about exporting code from it? If your goal is to produce a model of a single cell, it's OK to use "Management / Export / Export to file" to write a hoc file. Executing the code in that hoc file will create a top level model cell. But if your goal is to build a model network, you need to create templates for cell classes. To export a template from a CellBuilder, click on Management / Cell Type, make sure to change the "class name" to what you want, and then click on the "Save hoc code in a file" button. That generates a hoc file that contains a template for a cell class.
2. Would NeuroConstruct provide any advantages for my aims?
Maybe, if you were already expert with NEURON. Also, how much time do you have to become proficient with yet another complex tool?