Here we compare existing neocortical layer 5 pyramidal cells from modeldb

neuron simulator (compiled with pyneuron)

matplotlib

numpy

1. Traub et.al. - tuft IB Pyramidal cell - 2005
2. Hays et.al. - BAC firing model - 2011

1. Mainen et.al. - 1996
2. Larkum et.al. - 2009
3. 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

1. the number of segments and sections
2. the area of the cell
3. 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