root/NeuroML2/examples/NML2_SimpleMorphology.nml

<?xml version="1.0" encoding="UTF-8"?>

<neuroml xmlns="http://www.neuroml.org/schema/neuroml2"
    xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
    xsi:schemaLocation="http://www.neuroml.org/schema/neuroml2  ../Schemas/NeuroML2/NeuroML_v2alpha.xsd"
    id="NML2_SimpleMorphology">

<!-- Example of a cell morphology in NeuroML 2 -->

<!-- This is a "pure" NeuroML 2 file. It cannot yet be used a simulation by the LEMS 
     Interpreter as this does not yet support multicompartment cells -->   

    <!-- Note: no <cells> element -->

    <cell id="SimpleCell">

        <morphology id="SimpleCell_Morphology">

            <!-- Note: no <segments> -->

            <segment id ="0" name="Soma">    <!-- name is optional-->
                <!-- no parent => root segment -->
                <proximal x="0" y="0" z="0" diameter="10"/>
                <distal x="10" y="0" z="0" diameter="10"/>
            </segment>

            <segment id ="1" name="MainDendrite1" >
                <parent segment="0"/>
                <!-- Same proximal 3D point as parent but different diameter -->
                <proximal x="10" y="0" z="0" diameter="3"/> 
                <distal x="20" y="0" z="0" diameter="3"/>
            </segment>

            <segment id ="2" name="MainDendrite2">
                <parent segment="1"/>
                <!-- no proximal => use distal (including diameter) of parent -->
                <distal x="30" y="0" z="0" diameter="1"/>
            </segment>

            <segment id ="3" name="Spine" >
                <!-- Electrically connected to point 0.5 along parent -->
                <parent segment="2" fractionAlong="0.5"/>
                <proximal x="25" y="0" z="0" diameter="0.2"/>
                <distal x="25" y="1" z="0" diameter="0.2"/>
            </segment>

            <!-- segmentGroups follow -->

            <segmentGroup id="soma_group" neuroLexId="sao1044911821">    <!-- Reserved/special name of a group -->
                <member segment="0"/>
            </segmentGroup>

            <segmentGroup id="thick_dendrites">
                <member segment="1"/>
                <member segment="2"/>
            </segmentGroup>


            <!-- The NeuroLex reference points to the concept of a spine -->
            <segmentGroup id="spines" neuroLexId="sao1145756102"> 
                <member segment="3"/>
            </segmentGroup>


            <segmentGroup id="dendrite_group" neuroLexId="sao1211023249">     <!-- Reserved/special name of a group -->
                <include segmentGroup="thick_dendrites"/>
                <include segmentGroup="spines"/>
                <!-- <exclude ...> could be present here -->
            </segmentGroup>


            <segmentGroup id="middle">            <!-- group defined between 2 segs -->
                <path>
                    <from segment="1"/>
                    <to segment="2"/>
                </path>
            </segmentGroup>

            <segmentGroup id="tip">              <!-- group defined between 2 segs -->
                <subTree>
                    <from segment="1"/>
                </subTree>
            </segmentGroup>

            <!-- TODO: Allow wildcard on names?-->

        </morphology>

    </cell>

</neuroml>