Here we compare existing neocortical layer 5 pyramidal cells from modeldb
neuron simulator (compiled with pyneuron)
matplotlib
numpy
- Traub et.al. - tuft IB Pyramidal cell - 2005
- Hays et.al. - BAC firing model - 2011
- Mainen et.al. - 1996
- Larkum et.al. - 2009
- Kole et.al. - 2008
You will need to compile the mod files.
> nrnivmodl mod_hay/
if you want to run the Hay cell model or
>nrnivmodl mod_traub/
if you want to run the Traub cell model
[TODO] Having to compile each time user wants to run the scrips is annoying - find a better way to do this.
> python morph_compare.py [option1$] [option2]
$ - necessary
Available option1 - Model name
‘Hay’
‘Traub’
Available option2 - To show in matplotlib or not?
True (default)
False
Shows the morphology of the cell in matplotlib 3D.
Prints the following in terminal
- the number of segments and sections
- the area of the cell
- length of the cell
> python viz_cond.py [option1$]
$ - necessary
Available option1
‘Hay’
‘Traub’
Available option2
‘g_pas’ (default)
‘cm’
etc.
Shows the colormapped morphology of a given parameter in 3D.
This script is useful to map the channel conductances over the cell body