membrane_currents.mat

Axon membrane currents data files

axons~/[Name]/[Type]/index.mat and axons~/[Name]/[Type]/n_%d.mat contain the membrane currents (and membrane potentials) generated by models.membrane_currents for each sub-type of axon specified in an axons.mat file. This is a distributed representation which allows downstream model steps (e.g. models.nerve_recording) to load only the data needed by each parallel process inside of each process.

The variables saved in an `index.mat` file are:

Variable	Type	Description
`pop`	struct	Data about this axon population, see axons.mat for details about the `pop` structure. Each population which uses the model `Type` is grouped together. In addition, some extra data columns are defined:
`pop.population_id`	integer (nAxons x 1)	To which original population does each axon in this pop structure belong?
`results`	struct array (1 x nGroups)	Structure array with fields `threshold` (in nA, current clamp threshold), `velocity` (in m/s), and `spiketime` (in ms post-stimulus-onset).
`sam`	struct	struct with information about the sub-group sampling.
`sam.axon`	integer sum(nAxons) x 1	vector of all myelinated or all unmyelinated subtype_IDs. Not very useful.
`sam.count`	integer nGroups x 1	number of axons per subtype across all populations.
`sam.fibre_diam`	double nGroups x 1	sample median fibre (outer) diameter.
`sam.axon_diam`	double nGroups x 1	sample median axon (inner) diameter.
`sam.g_ratio`	double nGroups x 1	g-ratio
`sam.subtype_id`	double nGroups x 1	should equal `1:nG` unless some subgroups were empty

The variables saved in an `n000_out.mat` file are:

Variable	Type	Description
`dt_dx`	double scalar	what time step corresponds to a shift in the membrane current by one node? related to reciprocal of conduction velocity.
`I_membrane`	double nTime x nExamples	What is $I_m$ at each time-step for each of the selected NEURON segments? (see `segment`)
`I_unit`	char `'nA'`	`I_membrane` is in units of nA
`index`	int 1 x nExamples	indices of selected NEURON segments in `length`
`length`	double 1 x nSegments	length-coordinate of each NEURON segment, in mm (for myelinated axons, in order NODE, MYSA, FLUT, STIN)
`length_unit`	char `'mm'`	`length` is in units of mm
`parameters`	cell `{name1 value1; name2 value2; ...}`	inputs to models.axon_model after parsing of input arguments. These are the name,value pairs which are passed to tools.make_from_template to generate the specific axon model for this subclass from the template.
`result`	double 1x3	threshold, internal current. conduction velocity, m/s. Actual simulated axon length, mm.
`segment`	cell {nExamples x 1} of char	names of the NEURON segments saved in `I_membrane` and `V_example`. the first element is always the spike initiation point (in the case of models.membrane_currents, the distal end of the axon) and the remainder are a complete NODE and set of inter-nodal points (MYSA, FLUT, and STIN)
`shift`	function_handle (as char)	basic equation for how to compute the membrane current at any time and node from the saved data
`spiketimes`	double	time of arrival of the propagating action potential at the example node
`stimuli`	struct	stimulus time-course. See plots.preview_stimulus
`time`	double nTime x 1	time vector for membrane currents, in milliseconds
`time_unit`	char `'ms'`	`time` is in units of ms
`V_example`	double nTime x nExamples	What is $V_m$ at each time-step for each of the selected NEURON segments? (see `segment`)
`V_unit`	char `'mV'`	`V_example` is in units of mV.