Instructions to generate threshold maps and cortical slice simulations

Open and run PyrPlotSimpleComplete.m

This calls several functions:
	- importfile.m - imports data files generated by NEURON
	- getImgData.m - plots stimulation threshold maps
	- PyrPlotLines.m - generates line drawings of cell models
	- Pyrcalcprobs3D.m - generates cortical slab and recruitment
          estimates for a single cell type
	- plotcellsliceactivation.m - generates videos of cell
          recruitment and separation histograms
	- Pyrnumsdepth.m - generates combined recruitment estimates
          for all cell types

We performed some additional characterization of the response of
neurons to bipolar stimuli and monopolar stimuli of varying duration.
We used an isolated side branch of the Layer II Broad (anat_type9)
neuron model for these simulations.

To generate these figures, run:
	- strengthdurationplot.m
	- PyrPulseComp.m