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 optionaldend*[]
for dendritic sectionsapic*[]
for apical dendrite sectionsaxon*[]
for axonal sections
- Sections must be defined as types Section or SectionList (as
soma[1]
orsoma
)
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
:
/* ----------------------------------------------------
example_morphology.hoc
This hoc file creates a neuron of the following shape:
\
\
\ /
\ /
V
|
|
|
O
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 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 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¶
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.
Contributors¶
LFPy was developed by:
- Henrik Lindén https://lindenh.wordpress.com
- Espen Hagen http://www.mn.uio.no/fysikk/english/?vrtx=person-view&uid=espehage
- Szymon Łęski http://www.neuroinf.pl/Members/szleski
- Eivind Norheim
- Klas H. Pettersen http://www.med.uio.no/imb/english/?vrtx=person-view&uid=klashp
- Gaute T. Einevoll https://www.nmbu.no/ans/gaute.einevoll