The xtools package

This document describes the xtools package. xtools is MATLAB package that contains usefull tools that are stand-alone functions. Since they exist inside a special folder that begins with a +, MATLAB knows that it is a "package", and you can access any function using dot notation:

xtools.FunctionName()

Functions


V2metrics

Syntax

options = xtools.V2metrics
metrics = xtools.V2metrics(V)
metrics = xtools.V2metrics(V, options)
metrics = xtools.V2metrics(V, 'PropertyName', PropertyValue, ...)

Description

Computes metrics from a raw time series of voltage, which can be experimental or simulated data.

If called without arguments or outputs, a struct containing fields for all optional arguments, options, is created.

V2metrics can be called using a struct to specify options, or with individual options specified as name, value keyword pairs. Options with a NaN value are ignored and the default option value is used instead.

Option Name Default Value Units
sampling_rate 20 1/ms
ibi_thresh 300 ms
spike_threshold 0 mV
debug false
Metric Name Default Value Units
firing_rate NaN ?
burst_period NaN ?
ibi_mean NaN ?
ibi_std NaN ?
isi_std NaN ?
burst_period_std NaN ?
isi_std NaN ?
duty_cycle_mean NaN ?
n_spikes_per_burst_mean NaN ?
n_spikes_per_burst_std NaN ?
min_V_mean NaN ?
min_V_std NaN ?
min_V_in_burst_mean NaN ?
min_V_in_burst_std NaN ?
spike_peak_mean NaN ?
spike_peak_std NaN ?

binCost

Syntax

c = xfit.binCost(allowed_range, actual_value)

Description

A static method that computes a quadratic cost when actual_value is outside of the minimum and maximum set by the 2-vector allowed_range, and returns zero otherwise.

This method can be used as part of a simulation function when it is important for neurocomputational properties of interest to fit within a given range, rather than necessarily fit a value perfectly.


findBurstMetrics

Syntax

xtools.findBurstMetrics(V, Ca)
[burst_metrics, spike_times, Ca_peaks, Ca_troughs] = xtools.findBurstMetrics(V, Ca)
[burst_metrics, spike_times, Ca_peaks, Ca_troughs] = xtools.findBurstMetrics(V, Ca, Ca_peak_similarity)
[burst_metrics, spike_times, Ca_peaks, Ca_troughs] = xtools.findBurstMetrics(V, Ca, Ca_peak_similarity, burst_duration_variability)
[burst_metrics, spike_times, Ca_peaks, Ca_troughs] = xtools.findBurstMetrics(V, Ca, Ca_peak_similarity, burst_duration_variability, on_off_thresh)

Description

Computes burst metrics, spike times, and peaks and troughs of calcium wave.

Arguments

V is an n x 1 vector describing the membrane potential of a compartment over time.

Ca is an n x 1 vector describing the intracellular calcium concentration of the same compartment over time.

Optional Positional Argument Default Value
Ca_peak_similarity 0.3
burst_duration_variability 0.1
on_off_thresh 0

Ca_peak_similarity sets the maximum acceptable coefficient of variation (CV) between the intracellular calcium peaks. This function will exit with an error code if this limit is exceeded. To ignore this limit, set it to Inf.

burst_duration_variability sets the maximum acceptable CV between the burst periods. This function will exit with an error code if this limit is exceeded. To ignore this limit, set it to Inf.

on_off_thresh determines the horizontal crossing line (in units of mV) at which spikes should be counted. For example, if the on_off_thresh is set to 10 mV, then only when the membrane potential crosses 10 mV will a spike be counted.

Outputs

With no outputs, the burst period, mean number of spikes per burst, and duty cycle are printed to the command window.

burst-metrics is a 10x1 vector which contains the

  1. burst period (in units of dt)
  2. mean number of spikes per burst (unitless)
  3. time of first spike within a burst relative to the burst's Ca peak (in units of dt)
  4. time of last spike within a burst relative to the burst's Ca peak (in units of dt)
  5. mean of calcium peaks ()
  6. mean of Calcium troughs ()
  7. variability of Calcium peaks (coefficient of variation)
  8. variability of burst periods (coefficient of variation)
  9. duty cycle (unitless)
  10. error code

The error code is a digit between 0 and 4 that describes the success of the function.

  1. No error
  2. Fewer than 5 Calcium peaks
  3. Calcium peaks not similar enough
  4. Burst periods too variable
  5. No spikes

spike_times is an n x 1 vector containing the times (in units of dt) of each spike in the trace defined by V.

Ca_peaks is an n x 1 vector containing the times (in units of dt) of each peak of the calcium wave.

Ca_troughs is an n x 1 vector containing the times (in units of dt) of each trough of the calcium wave.

Dependencies

This function requires the Signal Processing Toolbox for MATLAB.


findNSpikeTimes

Syntax

spike_times = xtools.findNSpikeTimes(V, n_spikes, on_off_thresh)

Description

Computes the number of spikes in a voltage trace. V is an n x 1 voltage trace Spikes are defined as voltage crossings across a threshold, on_off_thresh (default = 0 mV).


findNSpikes

Syntax

N = xtools.findNSpikes(V);
N = xtools.findNSpikes(V, on_off_thresh)

Description

Computes the number of spikes in a voltage trace. V is an n x 1 voltage trace and on_off_thresh is a membrane potential threshhold at which spikes should be counted (default = 0 mV).


matrixCost

Syntax

C = xtools.matrixCost(M1, M2)

Description

Compute the norm-squared distance between two matrices. If the matrices are LeMasson matrices, which represent discretized probability distributions of a derivative-embedded attractor of a voltage trace, then this distance serves as a measure of how dissimilar the two voltage traces are.


voltageCost

Syntax

C = xtools.voltageCost(V1, V2, N)

Description

embeds two voltage traces w.r.t to their derivatives, and measures the distance between the two embeddings. The traces are first subsampled to N points, which speeds up the computation. The subsampling is handled by fast C++ accelerated code