Using Import3D

These tutorials are about NEURON's Import3D tool, which can translate common varieties of cellular morphometric data into a CellBuilder that specifies the anatomical properties of a model neuron. The capabilities of this tool are still evolving, and so are these tutorials.

Currently the Import3D tool can read these data formats: Eutectic, Neurolucida (v1 and v3 text files), and swc. It can also detect and localize errors in these files, and repair many of the more common errors automatically or with user guidance.

Overview of the Import3D tool

Before launching into procedural details, it will be helpful to set up a conceptual framework by asking ourselves what features we'd expect in a tool that translates morphometric data into a model specification. Broadly speaking, these fall into two categories:
  • data input and model output
  • analysis and repair

Data input and model output are pretty straightforward. We'd expect there to be a file browser for choosing the morphometric data file to be read. We'd also expect a button that lets us send the tool's output to a CellBuilder (which we can then save to a session file for future use), or straight to the hoc interpreter (immediately creating sections that have the proper dimensions and connectivity).

But what about analysis and repair?

It would be nice for the tool to automatically handle common trivial errors. It might also offer to fix somewhat more complex problems at the click of a button, and notify us of serious problems that may require the exercise of judgment.

One of the goals of analysis is to gather the information that such judgment might require. But the primary reason to analyze morphometric data is simply to understand the structure of the cell, which has important functional consequences.

We'll definitely want to see a graphical rendering of the shape of the cell or cells whose measurements are in the file. It would be very helpful if this figure is "browsable," so that we can click on any point to display its measured x,y,z coordinates and diameter, as well as the corresponding line in the data file. It should also be possible to use a mouse click to highlight items such as a single neurite (section) or subtree. We would also like to be able to see the root of the data (the section that has no parent), and those sections whose data points are flagged as belonging to special subsets or "types" (these generally correspond to significant anatomical subdivisions of a cell, e.g. soma, axon, or a particular dendritic field).

The Import3D tool can do all these things and more--as you will see in the following tutorials.