Frequently asked questions (FAQ)

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This page lists some commonly asked questions related to NeuroML. Please feel free to open issues to add more entries to this FAQ.

Are length 0 segments allowed in NeuroML?

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There are a lot of SWC reconstructions which have adjacent points, which would get converted to zero length segments. This shouldn’t be an issue for most visualisation applications, so no need for them to say that they can’t visualise the cell if they see it’s invalid.

The jnml -validate option could throw a warning when it sees these segments, but currently doesn’t (it could be added here).

For individual simulators, they could have an issue with this, if they map each segment to a compartment (as Moose might), but for Neuron using cables/sections with multiple segments, it shouldn’t matter as long as the section doesn’t just have one segment.

So ideally it should be the application which loads the NeuroML in (or the conversion/export code) which decides whether this is an issue.