Simulation and fitting of two-compartment (active soma, passive dendrite)
for different classes of cortical neurons.
The fitting technique indirectly matches neuronal currents derived from
somatic membrane potential data rather than fitting the voltage traces
directly. The method uses an analytic solution for the somatic ion channel
maximal conductances given approximate models of the channel kinetics,
membrane dynamics and dendrite. This approach is tested on model-derived
data for various cortical neurons.
The fitting method and models are described in
Lepora N., Overton P. and Gurney K.
Efficient fitting of conductance-based model neurons from somatic current
Journal Computational Neuroscience 2011
The models are two compartment versions of the single compartment cortical
neuron models described in (see also modelDB entry)
Pospischil, M., Toledo-Rodriguez, M., Monier, C., Piwkowska, Z.,
Bal, T., Fregnac, Y., Markram, H. and Destexhe, A.
Minimal Hodgkin-Huxley type models for different classes of
cortical and thalamic neurons.
Biological Cybernetics 99: 427-441, 2008.
Intrinsic currents: INa, IKd for action potentials, IM for spike-frequency
adaptation, ICaL for high-threshold calcium current, ICaT for the
low-threshold calcium current.
Requires GENESIS 2.3 in linux/unix. GENESIS must run from the command line.
Extract zipped folder and navigate to within the directory demo_modelDB.
Run fig1_tar.m in MATLAB to simulate the neurons, for generating the target
data. Then run fig1.m in MATLAB to run the fitting routines and output jpg
plots of the fits. The figure is based on fig1 in the paper (with a longer
time-step to hasten running speed and minimize RAM use).
The properties of the simulated neurons and fit routine parameters can be
changed by editing these two files.
Note that most of the figures in the paper were generated from compiled
versions of this software on a small cluster.
Tested on three different installations (VMware Ubuntu, and two clusters
with Scientific Linux).
If you have problems:
1) Can you run GENESIS from the command prompt in the extracted directory
If not you need the appropriate path (see GENESIS instructions).
2) Do you have enough RAM?
The routines are quite RAM intensive. Try commenting out some of the
simulations and editing the code to use a larger time-step.