hnn_core.extracellular.ExtracellularArray¶
- class hnn_core.extracellular.ExtracellularArray(positions, *, conductivity=0.3, method='psa', min_distance=0.5, times=None, voltages=None)[source]¶
Class for recording extracellular potential fields with electrode array
Note that to add an electrode array to a simulation, you should use the
hnn_core.Network.add_electrode_array()
-method. After simulation, the network will contain a dictionary ofExtracellularArray
-objects innet.rec_arrays
(each array must be added with a unique name). AnExtracellularArray
contains the voltages at each electrode contact, along with the time points at which the voltages were sampled.- Parameters:
- positionstuple | list of tuple
The (x, y, z) coordinates (in um) of the extracellular electrodes.
- conductivityfloat
Extracellular conductivity, in S/m, of the assumed infinite, homogeneous volume conductor that the cell and electrode are in.
- methodstr
Approximation to use.
'psa'
(point source approximation) treats each segment junction as a point extracellular current source.'lsa'
(line source approximation) treats each segment as a line source of current, which extends from the previous to the next segment center point: /—x—/, where x is the current segment flanked by /.- min_distancefloat (default: 0.5; unit: um)
To avoid numerical errors in calculating potentials, apply a minimum distance limit between the electrode contacts and the active neuronal membrane elements that act as sources of current. The default value of 0.5 um corresponds to 1 um diameter dendrites.
- timesarray-like, shape (n_times,) | None
Optionally, provide precomputed voltage sampling times for electrodes at positions.
- voltagesarray-like, shape (n_trials, n_electrodes, n_times) | None
Optionally, provide precomputed voltages for electrodes at
positions
.
Notes
The length of an
ExtracellularArray
is equal to the number of trials of data it contains. Slicing anExtracellularArray
returns acopy
of the corresponding trials:array[:5]
returns a new array of length 5, etc.See Table 5 in https://doi.org/10.1152/jn.00122.2010 for measured values of conductivity in rat cortex (note units there are mS/cm)
- Attributes:
- timesarray, shape (n_times,)
The time points the extracellular voltages are sampled at (ms)
- voltagesarray, shape (n_trials, n_electrodes, n_times)
The measured extracellular voltages
sfreq
floatReturn the sampling rate of the extracellular data.
Methods
copy
()Return a copy of the ExtracellularArray instance
plot_csd
([vmin, vmax, interpolation, sink, ...])Plot laminar current source density (CSD) estimation
plot_lfp
(*[, trial_no, contact_no, tmin, ...])Plot laminar local field potential time series.
smooth
(window_len)Smooth extracellular waveforms using Hamming-windowed convolution
to_dict
()Converts an object of ExtracellularArray class to a dictionary.
- copy()[source]¶
Return a copy of the ExtracellularArray instance
- Returns:
- array_copyinstance of ExtracellularArray
A copy of the array instance.
- plot_csd(vmin=None, vmax=None, interpolation='spline', sink='b', colorbar=True, ax=None, show=True)[source]¶
Plot laminar current source density (CSD) estimation
- Parameters:
- vmin: float, optional
lower bound of the color axis. Will be set automatically of None.
- vmax: float, optional
upper bound of the color axis. Will be set automatically of None.
- sinkstr
If set to ‘blue’ or ‘b’, plots sinks in blue and sources in red, if set to ‘red’ or ‘r’, sinks plotted in red and sources blue.
- interpolationstr | None
If ‘spline’, will smoothen the CSD using spline method, if None, no smoothing will be applied.
- colorbarbool
If the colorbar is presented.
- axinstance of matplotlib figure | None
The matplotlib axis.
- showbool
If True, show the plot.
- Returns:
- figinstance of matplotlib Figure
The matplotlib figure handle.
- plot_lfp(*, trial_no=None, contact_no=None, tmin=None, tmax=None, ax=None, decim=None, color='cividis', voltage_offset=50, voltage_scalebar=200, show=True)[source]¶
Plot laminar local field potential time series.
One plot is created for each trial. Multiple trials can be overlaid with or without (default) and offset.
- Parameters:
- trial_noint | list of int | slice
Trial number(s) to plot
- contact_noint | list of int | slice
Electrode contact number(s) to plot
- axinstance of matplotlib figure | None
The matplotlib axis
- decimint | list of int | None (default)
Optional (integer) factor by which to decimate the raw dipole traces. The SciPy function
decimate()
is used, which recommends values <13. To achieve higher decimation factors, a list of ints can be provided. These are applied successively.- colorstring | array of floats | matplotlib.colors.ListedColormap
The color to use for plotting (optional). The usual Matplotlib standard color strings may be used (e.g., ‘b’ for blue). A color can also be defined as an RGBA-quadruplet, or an array of RGBA-values (one for each electrode contact trace to plot). An instance of
ListedColormap
may also be provided.- voltage_offsetfloat | None (optional)
Amount to offset traces by on the voltage-axis. Useful for plotting laminar arrays.
- voltage_scalebarfloat | None (optional)
Height, in units of uV, of a scale bar to plot in the top-left corner of the plot.
- showbool
If True, show the figure
- Returns:
- figinstance of plt.fig
The matplotlib figure handle into which time series were plotted.
- property sfreq¶
Return the sampling rate of the extracellular data.
- smooth(window_len)[source]¶
Smooth extracellular waveforms using Hamming-windowed convolution
Note that this method operates in-place, i.e., it will alter the data. If you prefer a filtered copy, consider using the
copy()
-method.- Parameters:
- window_lenfloat
The length (in ms) of a
hamming
window to convolve the data with.
- Returns:
- extracellular_copyinstance of ExtraCellularArray
The modified ExtraCellularArray instance.