inner_product.m

plots.inner_product is a viewer which shows axon SFAPs in context with membrane currents and sensitivity curves. The name indicates the origin of the SFAP: the inner product at each moment in time between the instantaneous membrane current (computed using models.membrane_currents and saved in .mat files organized under sub~/axons/[name]/) at that moment in time, across all axon collocation points in space, and the sensitivity function

(computed using models.membrane_currents and saved in .mat files organized under sub~/eidors/)

for each of those spatial locations. This function does not actually use the output of models.axon_sfap)

plots.inner_product is part of package +plots, but shares structural similarities to models.nerve_recording.

Syntax [raw docstr]

plots.inner_product( [eidors_file], [axons_file], [model], ... )

-file 'sensitivity*.mat' : specify spatial sensitivity function (generated using models.nerve_anatomy)
-axons 'axons*.mat' : specify axon population for SFAP calculation, defaults to newest axons file in axons~/
-currents [folder] : specify root folder for membrane currents (generated using models.membrane_currents), defaults to the folder X corresponding to axons (X).mat
-model [model] : axon model (one of 'Gaines', 'MRG', 'Sundt', or 'Tigerholm') - strictly speaking the -model indicator is not necessary, but allows you to extend ViNERS with other axon models.
-fascicle [#] : which fascicle to compute SFAPs and visualise? --f is a synonym.
-elec [list] set electrodes to display (default: sequential bipolar pairs), n_electrodes x 1 or n_channels x 2 list of electrodes. Synonyms: -pair, `-
-axon [#] : which axon model should be used to compute SFAPs? By default, the median axon model is used.

Additional options:

-field {cell array of ScatteredInterpolant} : use a modified set of sensitivity functions
-nX [n] size of the grid of axon potentials to simulate. Grid is centered on fascicle cross-section and is n-by-n (ignoring axons falling outside the fascicle)
-axon-t set 3D axon trajectories (not yet implemented, may interfere with -axons?)
-delta-xy [x y] displace axons by specified amount (in µm)
-distortion apply a systemic distortion to the recorded velocities, temporal current width, and/or spatial current width (not tested in a long time). -debug-distortion illustrates the applied distortion, -debug-distortion -and-plot also generates the default output figure.
-ref [value] reference x-axis value for spike-times in raster.
-pad [value] change before/after padding for SFAP calculation (default 5x pad).
-fs [rate, default 30 kHz] set sampling rate for recorded SFAP. Synonyms: -sample-rate [rate]
-time [value, default 50 ms] set time ROI window for SFAP
-q,-quiet : suppress most output to console.
-debug-units : set up the calculation and display axon trajectories against the fascicle, useful for debugging units issues. Synonym for -preview
-smooth-n [n] apply N-point smooth to computed SFAP (default: 5-point smooth).
-smooth-k [kernel] apply convolutional filter to computed SFAP.
-index [list] select indices from the grid to display, by default the axon model producing the largest SFAP and the axon model closest to the centre of the fascicle are displayed.