Peri-Stimulus Time Histogram (PSTH) of CBGTC spike times

class analyseur.cbgtc.visual.peristimulus.VizPSTH

Bases: object

The Peri-Stimulus Time Histogram (PSTH) Class.

Methods	Return
plot()	matplotlib.pyplot.hist object
plot_in_ax()	matplotlib.pyplot.axis object

Use Case:

1. Setup

from  analyseur.cbgtc.loader import LoadSpikeTimes
from analyseur.cbgtc.visual.peristimulus import VizPSTH

loadST = LoadSpikeTimes("/full/path/to/spikes_GPi.csv")
spiketimes_superset = loadST.get_spiketrains()

2. Peri-Stimulus Time Histogram for the whole simulation window

VizPSTH.plot_pool(spiketimes_superset)

3. PSTH for desired window and bin size

VizPSTH.plot_pool(spiketimes_superset, window=(0,5), binsz=1)  # time unit in seconds
VizPSTH.plot_pool(spiketimes_superset, window=(0,5), binsz=0.05)

• PSTH gives an overall temporal pattern of population activity with a picture in both temporal and rate

• The computation is done by PSTH

---

classmethod plot_avg(spiketimes_set, binsz=0.01, window=(0, 10), neurons='all', nucleus=None, show=True)

Displays the Averaged Peri-Stimulus Time Histogram (PSTH) of the given spike times (seconds) and returns the plot figure (to save if necessary) using plot_avg_in_ax().

Parameters:

spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

Parameters:

• binsz – integer or float; 0.01 [default]

• window – Tuple in the form (start_time, end_time); (0, 10) [default]

• neurons –

  “all” [default] or scalar or range(a, b) or list of neuron ids like [2, 3, 6, 7]

  • ”all” means subset = superset

  • N (a scalar) means subset of first N neurons in the superset

  • range(a, b) or [2, 3, 6, 7] means subset of selected neurons

• nucleus – string; name of the nucleus

• show – boolean [default: True]

Returns:

object matplotlib.axes.Axes

containing matplotlib.pyplot.bar

• window controls the binning range as well as the spike counting window

• CBGT simulation was done in seconds so window (0, 10) signifies time 0 s to 10 s

---

classmethod plot_avg_in_ax(ax, spiketimes_set, binsz=None, window=None, neurons=None, nucleus=None)

Averaged PSTH (Population Activity)

Average Firing Rate (Hz)
^
|        ┬      ┬      ┬      ┬      ┬
|       ███    ███    ███    ███    ███
|       ███    ███    ███    ███    ███
|       ███    ███    ███    ███    ███
|        ┴      ┴      ┴      ┴      ┴
+--------------------------------------------------> Time (s)
0        2        4        6        8        10

Bars represent the population-average firing rate per time bin.
Error bars indicate variability across neurons (SEM).

Draws the Averaged Peri-Stimulus Time Histogram (PSTH) on the given matplotlib.pyplot.axis

Parameters:

• ax – object matplotlib.pyplot.axis`

• spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

Parameters:

• binsz – integer or float; 0.01 [default]

• window – Tuple in the form (start_time, end_time); (0, 10) [default]

• neurons –

  “all” [default] or scalar or range(a, b) or list of neuron ids like [2, 3, 6, 7]

  • ”all” means subset = superset

  • N (a scalar) means subset of first N neurons in the superset

  • range(a, b) or [2, 3, 6, 7] means subset of selected neurons

• nucleus – string; name of the nucleus

Returns:

object ax with PSTH plotting done into it

---

classmethod plot_pool(spiketimes_set, binsz=0.01, window=(0, 10), neurons='all', nucleus=None, show=True)

Displays the Pooled Peri-Stimulus Time Histogram (PSTH) of the given spike times (seconds) and returns the plot figure (to save if necessary) using plot_pool_in_ax().

Parameters:

spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

Parameters:

• binsz – integer or float; 0.01 [default]

• window – Tuple in the form (start_time, end_time); (0, 10) [default]

• neurons –

  “all” [default] or scalar or range(a, b) or list of neuron ids like [2, 3, 6, 7]

  • ”all” means subset = superset

  • N (a scalar) means subset of first N neurons in the superset

  • range(a, b) or [2, 3, 6, 7] means subset of selected neurons

• nucleus – string; name of the nucleus

• show – boolean [default: True]

Returns:

object matplotlib.axes.Axes

containing matplotlib.pyplot.bar

• window controls the binning range as well as the spike counting window

• CBGT simulation was done in seconds so window (0, 10) signifies time 0 s to 10 s

---

classmethod plot_pool_in_ax(ax, spiketimes_set, binsz=None, window=None, neurons=None, nucleus=None)

Pooled PSTH (Population Activity)

Total Spike Count
|
|        ████ █████ ████ █████ ████
|        ████ █████ ████ █████ ████
|        ████ █████ ████ █████ ████
|
+--------------------------------------------------> Time (s)
0        2        4        6        8        10

Histogram bins show spike counts aggregated across neurons.
Each bar represents the number of spikes from the pooled neuron
population within a time bin.

Draws the Pooled Peri-Stimulus Time Histogram (PSTH) on the given matplotlib.pyplot.axis

Parameters:

• ax – object matplotlib.pyplot.axis`

• spiketimes_set – Dictionary returned using get_spiketimes_superset()

or using get_spiketimes_subset()

Parameters:

• binsz – integer or float; 0.01 [default]

• window – Tuple in the form (start_time, end_time); (0, 10) [default]

• neurons –

  “all” [default] or scalar or range(a, b) or list of neuron ids like [2, 3, 6, 7]

  • ”all” means subset = superset

  • N (a scalar) means subset of first N neurons in the superset

  • range(a, b) or [2, 3, 6, 7] means subset of selected neurons

• nucleus – string; name of the nucleus

Returns:

object ax with PSTH plotting done into it

---