> For the complete documentation index, see [llms.txt](https://elishai.gitbook.io/retinal-stimulation-modeling-environment/llms.txt). Markdown versions of documentation pages are available by appending `.md` to page URLs; this page is available as [Markdown](https://elishai.gitbook.io/retinal-stimulation-modeling-environment/model-specification/morphology-description.md).

# Morphology Description

While morphologies in NEURON could be explicitly defined used sections and connections, RSME assumes that your cell morphology is given as a 'HOC' file. 

In this example, we will use a traced morphology of a SAC. The morphology file can be downloaded here:

{% file src="/files/-MlOiWnptnlfFIWipXsz" %}
SAC morphology
{% endfile %}

Conversion between morphological data types is provided by NEURON. See the 'Reading a morphometric data file and converting it to a NEURON model' tutorial at: 

{% embed url="<https://neuron.yale.edu/neuron/docs/import3d>" %}

In RSME morphology specification XML we will need to specify the path to your morphology file. You can further modify your morphology by two means:&#x20;

* Referencing a Python function, which traverses the morphology sections and iteratively adjusting them&#x20;
* Providing an SBML-specified function to correct the sections, e.g., the sections' diameter.&#x20;

In the following XML file, we define one morphology, describe by the SAC morphology file attached above. Each morphology is given an ID, which is later used to define a network and the cell's biophysical characteristics. We refer the model to the morphology\_adhoc\_fix function in which section corrections are defined and specify an SBML-defined function, which we use to set the morphological sections' diameter.&#x20;

```
<morphology xmlns = "RSME.simulation_parameters">

  <morphology_description> TEST </morphology_description>
  
  <morphologies>
    
      <morphology_id id = "0" fix_function = "morphology_adhoc_fix">

        <morphology_hoc_file> SAChocLea.hoc </morphology_hoc_file>

        <section_diameter>
            <math>
                <apply> 
                    <plus/> 
                    <apply>
                        <times/>
                        <cn> 0.2 </cn>
                        <apply> 
                            <ci> exp </ci> 
                            <apply>
                                <divide/>
                                <ci> -x  </ci>
                                <cn> 40 </cn>
                            </apply>
                        </apply>
                    </apply>
                    <cn> 0.15 </cn>
                </apply>
            </math>
        </section_diameter>

      </morphology_id>
      
    </morphologies>
    
</morphology>

```

Note:

* The morphology\_adhoc\_fix function is explicitly defined in SimParameters.py file.
* The section diameter function specifies the diameter of each section as a function of its distance from the soma.&#x20;

In the following example, we define a second cell - a DSGC:

```
<morphology_id id = "1" fix_function = "None">
    <morphology_hoc_file> cell_12_trace.hoc</morphology_hoc_file>
</morphology_id>
```

You can download the DSGC morphology here:

{% file src="/files/58tsfmV9tqoxLbnAow7t" %}


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