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*[1] 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 must be corrected to create soma[1] directly in the files.

NEURON convention for creating morphology files in hoc:

/* ----------------------------------------------------

This hoc file creates a neuron of the following shape:

              \   /
               \ /

Note the conventions:
 - soma needs to be a list (soma[0], not soma),
 - use soma for the soma compartment,
 - use a name starting with dend 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 file formats is added, but consider this experimental and is poorly tested. If there is something wrong with the files, strange behaviour may occur or LFPy may even fail to load the desired morphology at all.

Using NEURON mechanisms

Custom NEURON mechanisms can be loaded from external .hoc- or .py-files - see and 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 Mac OS).

These model specific declarations is typically run after the Cell-class try to read the morphology file, and before optionally running the _set_nsegs() and _collect_geometry() procedures.


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

What Unit
Potential [mV]
Current [nA]
Conductance [S/cm2]
Capacitance [μF/cm2]
Dimension [μm]
Syn. weight [µS]

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.


If you want to contact us with questions, bugs and comments, you can send us an email to either Espen or Henrik. We are of course happy to receive feedback of any kind.