File extension





Arbor offers limited support for models described in NeuroML version 2. Arbor is able to parse and check the validity of morphologies described in NeuroML files, and present the encoded data to the user. This is more than a simple segment tree.

NeuroML can encode in the same file multiple top-level morphologies, as well as cells:


<neuroml xmlns="">
<morphology id="m1">
    <segment id="seg-0">
        <proximal x="1" y="1" z="1" diameter="1"/>
        <distal x="2" y="2" z="2" diameter="2"/>
    <segmentGroup id="group-0">
        <member segment="1"/>
<morphology id="m2"/>
<cell id="c1" morphology="m1"/>
<cell id="c2">
    <morphology id="m3"/>

The above NeuroML description defines two top-level morphologies m1 and m2 (empty); a cell c1 that uses morphology m1; and a cell c2 that uses an internally defined (empty) morphology m3.

Arbor can query the cells and morphologies using their ids and return all the associated morphological data for each. The morphological data includes the actual morphology as well as the named segments and groups of the morphology. For example, the above m1 morphology has one named segment seg-0 and one named group group-0 that are both represented using Arbor’s region expressions.