README CK Overstreet 12/18/2012 This folder contains NEURON code used to determine the extracellular stimulation threshold for several interneurons found in the somatosensory cortex of cats. Below is a listing of the files in this folder and the steps necessary to run this code. To obtain the threshold maps, first compile xtra.mod, then edit initxcstim to select the appropriate anat_type file and corresponding moveandstim files. Then run initxcstim. The moveandstim file for each neuron type repeatedly moves the extracellular electrode within the square area containing the entire neuron and approximately a 250 micron border around the cell. The moveandstim files included in this code are not intended to be run as written - they represent the total area that an electrode must be moved within to accurately capture the effects of extracellular stimulation on that type of neuron. Because many of these neurons are large and/or sparse, it will be more efficient to break up these simulations into multiple files and concatenate the results. Several files in this folder are modified versions of the extracellular_stim_and_rec download available at http://www.neuron.yale.edu/ftp/ted/neuron/extracellular_stim_and_rec.zip calcrxc.hoc field.hoc fixnseg.hoc interpxyz.hoc setpointers.hoc stim.hoc stimbipolar.hoc rigc.ses vrecc.ses xtra.mod Additionally, the ion channel dynamics used in this work are from McIntyre CC, Richardson AG, and Grill WM. Modeling the excitability of mammalian nerve fibers: influence of afterpotentials on the recovery cycle. Journal of Neurophysiology 87:995-1006, 2002. This code is available on ModelDB at http://senselab.med.yale.edu/modeldb/ShowModel.asp?model=3810 AXNODE.mod The major characteristics of cell bodies and axons were reconstructed by hand from: H.D. Schwark, The distribution of intrinsic cortical axons in area 3b of cat primary somatosensory cortex, Experimental Brain Research, vol. 78, no. 3, pp. 501-513, Aug. 1989. Each anat_type file contains a different cell type. anat_type9 - Layer II Broad anat_type10 - Layer III Intermediate anat_type11 - Layer III Broad External anat_type12 - Layer IV Intermediate anat_type13 - Layer IV Narrow anat_type14 - Layer V Intermediate anat_type15 - Layer VI Narrow We generated separate "symmetrical" neuron models for cell types that had branches with strong directional preferences but moderate rotational symmetry about the vertical axis. These sym models were used for calculating the stimulation threshold in areas outside the plane of the directional branches. 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. initpulsecomp - moves electrode away from the axon and determines the stimulation threshold for monopolar and bipolar stimuli initstrdur - clarifies the relationship between pulse duration and stimulation threshold at multiple distances from the axon.