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feat: document external morphologies
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sanjayankur31 committed Jun 19, 2024
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(userdocs:importing_morphology_files:formats)=
## Formats

(userdocs:importing_morphology_files:formats:neuroml)=
### NeuroML2

In NeuroML, morphologies are encapsulated in the {ref}`morphology <schema:morphology>` modelling element.
A morphology includes {ref}`segments <schema:segment>` and {ref}`segments groups <schema:segmentgroup>`, and these can be used to refer to parts of the cell's morphology, for example, when placing ionic conductances.
A number of conventions for use in morphologies are listed {ref}`here <userdocs:conventions:segments>`.

(userdocs:importing_morphology_files:formats:neuroml:external)=
#### Morphologies can be stored in external files

```{admonition} Requires jNeuroML v0.13.2, pyNeuroML v1.3.2
:class: note
The functionality to store morphology information in external files was implemented in jNeuroML v0.13.2, and pyNeuroML v1.3.2. Please ensure you are using these or newer versions to use this feature.
```

Usually, morphologies are embedded in NeuroML cell definition files, {ref}`for example <userdocs:getting_started:multi_compartment_example>`:

```{code-block} xml
<cell id="pyr_soma_m_in_b_in">
<!-- ... -->
<morphology id="morph0">
<segment >
<!-- more segments and segment groups -->
</morphology>
<biophysicalProperties id="biophys1">
<!-- biophysical properties contents -->
</biophysicalProperties>
</cell>
```

However, morphologies (and {ref}`biophysical properties <schema:biophysicalproperties>`) can also be stored as "standalone" entities outside the cell definition and referred to.
Further, they can also be stored in external files that may be "included" in the cell definition file (using the [IncludeType](https://libneuroml.readthedocs.io/en/latest/userdocs/coreclasses.html#includetype) model element).
This allows the re-use of morphology and biophysical properties in multiple cell models:

```{code-block} xml
<cell id="pyr_soma_m_out_b_out" morphology="morph0" biophysicalProperties="biophys1">
<!-- cell contents without morphology and biophysical properties -->
</cell>
<!-- Potentially in other files... -->
<morphology id="morph0">
<segment >
<!-- more segments and segment groups -->
</morphology>
<biophysicalProperties id="biophys1">
<!-- biophysical properties contents -->
</biophysicalProperties>
```

(userdocs:importing_morphology_files:formats:neuron)=
### NEURON

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