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:

49KB

SAChocLea.hoc.zip

archive

SAC morphology

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:

Using Import3D | NEURON

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:

• Referencing a Python function, which traverses the morphology sections and iteratively adjusting them

• Providing an SBML-specified function to correct the sections, e.g., the sections' diameter.

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.

<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.

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:

149KB

cell_12_trace.hoc