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Notes on LFPy

Morphology files

Cell morphologies can be specified manually in a .hoc file. For a simple example, see examples/morphologies/example_morphology.hoc. Note the following conventions:

  • Sections should be named according to the following scheme:
    • soma*[] for somatic sections, * is optional
    • dend*[] for dendritic sections
    • apic*[] for apical dendrite sections
    • axon*[] for axonal sections
  • Sections must be defined as types Section or SectionList (as soma[1] or soma)

Also the morphologies exported from the NEURON simulator (for example using Cell Builder -> Export) should work with LFPy, but some times create soma may have to be corrected to create soma[1] directly in the files. Multi-sectioned somas may occurr e.g., due to faulty conversion from NeuroLucida or SWC format, however, we recommend that these files are corrected. It may not affect the predictions of intracellular voltages, but have implications for predictions of extracellular potentials. We usually assume that the soma is a single compartment and that it is the root section for all other sections.

NEURON convention for creating morphology files in hoc:

/* ----------------------------------------------------
example_morphology.hoc

This hoc file creates a neuron of the following shape:

            \
             \
              \   /
               \ /
                V
                |
                |
                |
                O

Note the conventions:
 - use soma for the soma compartment,
 - use a name starting with dend or apic for the dendrites.
-----------------------------------------------------*/


create soma[1]
create dend[3]

soma[0] {
    pt3dadd(0, 0, 0, 25)
    pt3dadd(0, 0, 35, 25)
}

dend[0] {
    pt3dadd(0, 0, 35, 5)
    pt3dadd(0, 0, 150, 5)
}

dend[1] {
    pt3dadd(0, 0, 150, 2)
    pt3dadd(-50, 20, 200, 1)
}

dend[2] {
    pt3dadd(0, 0, 150, 2)
    pt3dadd(30, 0, 160, 2)
}

connect dend[0](0), soma[0](1)
connect dend[1](0), dend[0](1)
connect dend[2](0), dend[0](1)

Other file formats

Support for SWC, NeuroLucida3 and NeuroML morphology file formats is added in LFPy, but consider this an experimental feature as the functionality is not properly tested. If there is something wrong with the files, strange behaviour may occur or LFPy may even fail to load the desired morphology.

Using NEURON NMODL mechanisms

Custom NEURON mechanisms can be loaded from external .hoc- or .py-files - see example2.py and example3.py. Python function definitions with arguments can also be given as input to the Cell-class, specifying model specific conductances etc. Remeber to compile any mod files (if needed) using nrnivmodl (or mknrdll on Windows).

These model specific declarations is typically run after the Cell-class try to read the morphology file, and before running the _set_nsegs() and _collect_geometry() procedures. Hence, code that modifies the segmentation of the morphology will affect the properties of the instantiated LFPy.Cell object.

Units

Units follow the NEURON conventions found here. The units in LFPy for given quantities are:

Quantity Unit
Potential [mV]
Current [nA]
Conductance [S/cm2]
Extracellular conductivity [S/m]
Capacitance [μF/cm2]
Dimension [μm]
Synaptic weight [µS]
Current dipole moment [nA µm]
Magnetic field (H) [nA/µm]
Permeability (µ) [T m/A]

Note: resistance, conductance and capacitance are usually specific values, i.e per membrane area (lowercase r_m, g, c_m) Depending on the mechanism files, some may use different units altogether, but this should be taken care of internally by NEURON.

Contributors

LFPy was developed by (as per commit):

Contact

If you want to contact us with questions, bugs and comments, please create an issue on GitHub.com/LFPy/LFPy/issues. We are of course happy to receive feedback of any kind.