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Calibration: Characterising and Measuring Analog Behaviour

The goal of the exercises assembled in this task is to familiarise yourself with how we characterise and measure the analog behaviour of the chip. At the end you will understand how to convert raw hardware measurements into physical units and how to relate digital calibration values to measured membrane traces.

.. only:: jupyter

   Setup
   ~~~~~
   .. include:: common_quiggeldy_setup.rst


Characterizing the MADC

Before we continue our investigations of analog neurons, we need to characterize the readout chain used for the neurons' signals. Since HICANN-X has digital communication interfaces, the analog voltage recordings of a neuron need to be digitized on chip.

Characterizing the analog-to-digital-converter (ADC) means applying a known voltage externally and recording the value returned by the ADC. Later, we will reverse this relation in order to convert measured data back to SI units.

In the following, we define a function which applies an external voltage and returns samples from the MADC. Your task is to sweep the external voltage and analyze the returned reads. Plot the characteristic and perform a linear fit to a suitable range. You will use the parameters of your fit in the following notebooks.

Low Level Hardware Access

You will not need to make changes to the function imported in the next cell. If you are curious how it is implemented you can take a look at it.

from _static.common.measure_voltage import measure_voltage

We first test the function above by setting a medium voltage, say 0.5 V. Look at the printed samples and their data type - notice the sampled value is the first entry in each tuple, accessible by the named field "value".

from dlens_vx_v3 import hxcomm

# since we're not using the PyNN frontend here, we need to define our own
# connection to the hardware. It is available as a context manager:
with hxcomm.ManagedConnection() as connection:
    result = measure_voltage(connection, 0.5)
print(result[:20])
print(result.dtype)

Exercises

  • Measure the sampled value for voltages between 0 and 1.2 V. We recommend steps of 0.05 V. For each data point, save a mean ADC value. Hint: Use something like result["value"] for calculating your mean ADC values. Complete the cell below to do so:

Hint: You can use the measure_voltage function.

.. only:: not Solution

   .. code:: ipython3

      import numpy as np

      # Measure characteristic
      voltages =  ... # volt
      results = np.zeros_like(voltages)  # mean ADC values in LSB
      errors = np.zeros_like(voltages)  # std deviation of ADC values in LSB

      with hxcomm.ManagedConnection() as connection:
            for voltage_id, voltage in enumerate(voltages):
              samples = ...
              results[voltage_id] = ...
              errors[voltage_id] = ...
          ...

  • Plot the characteristic, i.e. plot the acquired value over the external voltage.
.. only:: not Solution

    .. code:: ipython3

        import matplotlib.pyplot as plt
        plt.figure(figsize=(12, 8))

        # TODO
        ...

        plt.xlabel("Voltage [V]")
        plt.ylabel("MADC value [LSB]")

  • Perform a linear fit in a suitable range (exclude possibly saturated values on top and bottom). Hint: In order to convert sample values to voltage later, you can use the results as "x data" and the voltages as "y data" for your fit function.
.. only:: not Solution

    .. code:: ipython3

      # fit linear function to data
      from scipy.optimize import curve_fit

      # TODO

  • Plot your linear fit and save the plot.
  • Save the fit parameters for later, so you can convert ADC values to Volt.
.. only:: Solution

   .. code:: ipython3

      import numpy as np


      # Measure characteristic
      voltages = np.arange(0, 1.21, 0.05)  # volt
      results = np.zeros_like(voltages)  # mean ADC values in LSB
      errors = np.zeros_like(voltages)  # std deviation of ADC values in LSB

      with hxcomm.ManagedConnection() as connection:
          for voltage_id, voltage in enumerate(voltages):
              samples = measure_voltage(connection, voltage)
              results[voltage_id] = np.mean(samples["value"])
              errors[voltage_id] = np.std(samples["value"])

      # plot data
      import matplotlib.pyplot as plt
      plt.figure(figsize=(12, 8))
      plt.errorbar(voltages, results, yerr=errors, fmt='.', label="data")
      plt.xlabel("Voltage [V]")
      plt.ylabel("MADC value [LSB]")

      # fit linear function to data
      from scipy.optimize import curve_fit
      linear = lambda x, m, b: m * x + b

      popt, _ = curve_fit(linear, results[5:-5], voltages[5:-5])

      # plot fit
      yvalues = np.array([np.min(results), np.max(results)])
      fit_label = f"V = {popt[0]:.5f} * value " + \
        ("+" if popt[1] > 0 else "-") + f" {np.abs(popt[1]):.3f}"
      plt.plot(linear(yvalues, *popt), yvalues, label=fit_label)
      _ = plt.legend()

You can use the fit parameters you obtained to implement a madc value to voltage conversion routine like so:

def madc_to_voltage_conversion(m, b):
    def convert(value):
        return m * value + b
    return convert

madc_to_v = madc_to_voltage_conversion(*popt)

Characterizing Neuron Parameters

We now move on to a characterisation of Neuron Parameters, the goal is to relate the parameter values, which are specified in arbitrary units to the MADC measurement values. That way you will establish a correspondence between the values you specify and the membrane measurement values send back to you by the chip.

We begin by importing some commonly used calibration code

and define plotting functions

import pynn_brainscales.brainscales2 as pynn

from pynn_brainscales.brainscales2 import Population
from pynn_brainscales.brainscales2.standardmodels.cells import SpikeSourceArray
from pynn_brainscales.brainscales2.standardmodels.synapses import StaticSynapse

%matplotlib inline

import matplotlib.pyplot as plt
import numpy as np
import time

plt.style.use("_static/matplotlibrc")

def plot_membrane_dynamics(population: Population, segment_id=-1, ylim=None):
    """
    Plot the membrane potential of the neuron in a given population view. Only
    population views of size 1 are supported.
    :param population: Population, membrane traces and spikes are plotted for.
    :param segment_id: Index of the neo segment to be plotted. Defaults to
                       -1, encoding the last recorded segment.
    :param ylim: y-axis limits for the plot.
    """
    if len(population) != 1:
        raise ValueError("Plotting is supported for populations of size 1.")
    # Experimental results are given in the 'neo' data format
    mem_v = population.get_data("v").segments[segment_id].irregularlysampledsignals[0]
    spikes = population.get_data("spikes").segments[-1].spiketrains[0]

    plt.plot(mem_v.times, mem_v, alpha=0.5, color='black')

    # indicate the spikes as red dots
    plt.scatter(spikes, np.max(mem_v)*np.ones_like(spikes), color='red')
    plt.xlabel("Wall clock time [ms]")
    plt.ylabel("ADC readout [a.u.]")
    if ylim:
        plt.ylim(ylim)

The following experiment code let's you interactively explore the measurement we are about to perform:

from ipywidgets import interact, IntSlider
from functools import partial
IntSlider = partial(IntSlider, continuous_update=False)

@interact(
    neuron_idx=IntSlider(min=0, max=511, step=1, value=0),
    v_leak=IntSlider(min=0, max=1022, step=1, value=1000),
    v_threshold=IntSlider(min=0, max=500, step=1, value=500),
    v_reset=IntSlider(min=0, max=1022, step=1, value=400),
    i_bias_leak=IntSlider(min=0, max=1022, step=1, value=150),
)
def experiment(neuron_idx, v_leak, v_threshold, v_reset, i_bias_leak):
    """
    Set up a leak over threshold neuron.

    :param v_leak: Leak potential.
    :param v_threshold: Spike threshold potential.
    :param v_reset: Reset potential.
    :param i_bias_leak: Controls the leak conductance (membrane time constant).
    :param savefig: Save the experiment figure.
    """

    plt.figure()

    # everything between pynn.setup() and pynn.end()
    # below is part of one hardware run.
    pynn.setup(initial_config=calib, neuronPermutation=[neuron_idx])

    # a pynn.Population corresponds to a certain number of
    # neuron circuits on the chip
    pop = pynn.Population(1, pynn.cells.HXNeuron(
        # Leak potential, range: 400-1000
        leak_v_leak=v_leak,
        # Leak conductance, range: 0-1022
        leak_i_bias=i_bias_leak,
        # Threshold potential, range: 0-500
        threshold_v_threshold=v_threshold,
        # Reset potential, range: 300-1000
        reset_v_reset=v_reset,
        # Membrane capacitance, range: 0-63
        membrane_capacitance_capacitance=63,
        # Refractory time (counter), range: 0-255
        refractory_period_refractory_time=255,
        # Enable reset on threshold crossing
        threshold_enable=True,
        # Reset conductance, range: 0-1022
        reset_i_bias=1022,
        # Increase reset conductance
        reset_enable_multiplication=True))

    pop.record(["v", "spikes"])

    # this triggers a hardware execution
    # with a duration of 0.2 ms
    pynn.run(0.2)
    plot_membrane_dynamics(pop, ylim=(100, 800))
    plt.show()

    mem = pop.get_data("v").segments[-1].irregularlysampledsignals[0]
    spikes = pop.get_data("spikes").segments[-1].spiketrains[0]
    pynn.end()

    return mem, spikes

We now define a function which returns the measured membrane voltage trace for a given set of parameters

def get_v_mem(neuron_params: dict, neuron_idx: int) -> np.ndarray:
    pynn.setup(initial_config=calib, neuronPermutation=[neuron_idx])
    pop = pynn.Population(1, pynn.cells.HXNeuron(**neuron_params))
    pop.record(["v"])
    pynn.run(0.2)
    mem_v = pop.get_data("v").segments[0].irregularlysampledsignals[0]
    pynn.end()
    return mem_v.base

We want to perform this experiment over potentially a larger number of neurons and for specific neuron ranges

def get_data(number_of_neurons, sweep_range, sweep_neuron_param,
             filter_function, neuron_params):

    y_measured = np.zeros(shape=(number_of_neurons, len(sweep_range)))
    for neuron_idx in range(number_of_neurons):
        y_measured_local = []
        for dac_idx, dac_value in enumerate(sweep_range):
            neuron_params.update({sweep_neuron_param: dac_value})
            membrane = get_v_mem(neuron_params, neuron_idx)
            print(f"Measuring neuron {neuron_idx} for "
                  f"{sweep_neuron_param} with value: {dac_value}")
            y_measured_local.append(filter_function(membrane.magnitude))
            y_measured[neuron_idx][dac_idx] = filter_function(membrane.magnitude)

    return y_measured

This defines the main function for the parameter sweep

def main(number_of_neurons, sweep_range, param_to_be_determined):
    if param_to_be_determined == "threshold":
        neuron_params = {"leak_v_leak": 1022,
                         "reset_v_reset": 50}
        sweep_neuron_param = "threshold_v_threshold"
        filter_function = np.max

    if param_to_be_determined == "reset":
        neuron_params = {"threshold_v_threshold": 150,
                         "leak_v_leak": 1022}
        sweep_neuron_param = "reset_v_reset"
        filter_function = np.min

    if param_to_be_determined == "leak":
        neuron_params = {"threshold_v_threshold": 1022,
                         "reset_v_reset": 50}
        sweep_neuron_param = "leak_v_leak"
        filter_function = np.mean

    y_measured = get_data(number_of_neurons, sweep_range, sweep_neuron_param,
             filter_function, neuron_params)

    #
    measured_mean = np.mean(y_measured, axis=0)
    measured_err = np.std(y_measured, axis=0)
    return sweep_range, y_measured, measured_mean, measured_err

def plot_and_fit(ax, data, label):
    sweep_range, y_measured, measured_mean, measured_err = data

    number_of_neurons = y_measured.shape[0]

    ax.set_xlabel(f"set $V_{{{label}}}$ [DAC value]")
    ax.set_ylabel(f"measured $V_{{{label}}}$ [ADC value]")
    for k in range(number_of_neurons):
        ax.plot(sweep_range, y_measured[k], '-',
                 color='darkgray', linewidth=0.25, zorder=-1)

    ax.errorbar(sweep_range, measured_mean, yerr=measured_err,
                 color='red', linestyle='-', marker='None', zorder=0)

    linear_fit = np.polyfit(sweep_range, measured_mean, 1)
    ax.plot(sweep_range, linear_fit[0] * sweep_range + linear_fit[1],
             'b--', zorder=1)

    return linear_fit

The general idea is to modify the sweep range to find a suitable range for the fit for respective parameters. Start with full range and narrow down.

# for how many neurons should an average characterisation be done
num_neurons = 1

# valid range [0, 1022]
adc_sweep_range = np.arange(0, 1022, 50)

# parameter to be determined, valid "threshold", "reset" or "leak"
adc_sweep_range = np.arange(50, 301, 50)
param_name = "threshold"
threshold_data = main(num_neurons, adc_sweep_range, param_name)

adc_sweep_range = np.arange(500, 901, 100)
param_name = "leak"
leak_data = main(num_neurons, adc_sweep_range, param_name)

adc_sweep_range = np.arange(400, 901, 100)
param_name = "reset"
reset_data = main(num_neurons, adc_sweep_range, param_name)

Excercises

fig, ax = plt.subplots(1,3, sharey=True)

v_th_fit = plot_and_fit(ax[0], threshold_data, "th")
v_leak_fit = plot_and_fit(ax[1], leak_data, "leak")
v_reset_fit = plot_and_fit(ax[2], reset_data, "reset")
def linear(param):
    def fun(x):
        return param[0] * x + param[1]

    def inverse(x):
        return (x - param[1]) / param[0]

    return fun, inverse

v_th_s2m, v_th_m2s = linear(v_th_fit)
v_leak_s2m, v_leak_m2s = linear(v_leak_fit)
v_reset_s2m, v_reset_m2s = linear(v_reset_fit)
@interact(
    neuron_idx=IntSlider(min=0, max=511, step=1, value=0),
    v_leak=IntSlider(min=v_leak_s2m(0), max=v_leak_s2m(1022), step=1, value=v_leak_s2m(1000)),
    v_threshold=IntSlider(min=v_leak_s2m(0), max=v_th_s2m(500), step=1, value=v_th_s2m(500)),
    v_reset=IntSlider(min=v_reset_s2m(0), max=v_reset_s2m(1022), step=1, value=v_reset_s2m(400)),
    i_bias_leak=IntSlider(min=0, max=1022, step=1, value=150),
)
def experiment(neuron_idx, v_leak, v_threshold, v_reset, i_bias_leak):
    """
    Set up a leak over threshold neuron.

    :param v_leak: Leak potential.
    :param v_threshold: Spike threshold potential.
    :param v_reset: Reset potential.
    :param i_bias_leak: Controls the leak conductance (membrane time constant).
    :param savefig: Save the experiment figure.
    """

    v_leak = v_leak_m2s(v_leak)
    v_threshold = v_th_m2s(v_threshold)
    v_reset = v_reset_m2s(v_reset)

    plt.figure()

    # everything between pynn.setup() and pynn.end()
    # below is part of one hardware run.
    pynn.setup(initial_config=calib, neuronPermutation=[neuron_idx])

    # a pynn.Population corresponds to a certain number of
    # neuron circuits on the chip
    pop = pynn.Population(1, pynn.cells.HXNeuron(
        # Leak potential, range: 400-1000
        leak_v_leak=v_leak,
        # Leak conductance, range: 0-1022
        leak_i_bias=i_bias_leak,
        # Threshold potential, range: 0-500
        threshold_v_threshold=v_threshold,
        # Reset potential, range: 300-1000
        reset_v_reset=v_reset,
        # Membrane capacitance, range: 0-63
        membrane_capacitance_capacitance=63,
        # Refractory time (counter), range: 0-255
        refractory_period_refractory_time=255,
        # Enable reset on threshold crossing
        threshold_enable=True,
        # Reset conductance, range: 0-1022
        reset_i_bias=1022,
        # Increase reset conductance
        reset_enable_multiplication=True))

    pop.record(["v", "spikes"])

    # this triggers a hardware execution
    # with a duration of 0.2 ms
    pynn.run(0.2)
    plot_membrane_dynamics(pop, ylim=(100, 800))
    plt.axhline(v_th_s2m(v_threshold))
    plt.axhline(v_reset_s2m(v_reset))
    plt.axhline(v_leak_s2m(v_leak), color='green')

    plt.show()

    mem = pop.get_data("v").segments[-1].irregularlysampledsignals[0]
    spikes = pop.get_data("spikes").segments[-1].spiketrains[0]
    pynn.end()

    return mem, spikes

Calibrating Neuron Parameters

def membrane2dac(voltage, slope, offset):
    return int((voltage - offset) / slope)


# set voltages
# threshold must be according to:
v_leak = 350
v_reset = 200
v_th = v_leak - (v_leak - v_reset) / np.exp(1)

# enter your fit results from task a) into the membrane2dac calls
neuron_params = {"leak_i_bias": 400,
                 "reset_i_bias": 1022,
                 "leak_enable_division": True,
                 "threshold_enable": True,
                 "reset_enable_multiplication": True,
                 "membrane_capacitance_capacitance": 63,
                 "refractory_period_refractory_time": 150,
                 "leak_v_leak": membrane2dac(v_leak, 0.79, -180),
                 "reset_v_reset": membrane2dac(v_reset, 0.88, -250),
                 "threshold_v_threshold": membrane2dac(v_th, 0.99, 60)
                 }

# the leak conductance g_leak is set by I_bias
# each entry refers to a different neuron
# must be adjusted for identical firing rates!
I_bias = [400, 400, 400, 400]
assert len(I_bias) > 3, "You need to look at least on 4 neurons."

Gather spikes an membrane trace for different neurons

# as we can only readout the membrane of one neuron at a time we need to
# repeat the measurement for each neuron

result = []
for nrnidx, bias in enumerate(I_bias):
    pynn.setup()

    pop = pynn.Population(len(I_bias),
                          pynn.cells.HXNeuron(**neuron_params))
    pop.set(leak_i_bias=bias)

    # a population view is a subset of a population
    p_view = pynn.PopulationView(pop, [nrnidx])
    p_view.record(["v", "spikes"])

    pynn.run(2)
    spikes = p_view.get_data("spikes").segments[0].spiketrains[0]

    # # FIXME spike readout fails some times
    # if len(spikes) <= 1:
    #     raise RuntimeError("not enough spikes recorded")

    mem_v = p_view.get_data("v").segments[0].irregularlysampledsignals[0]

    pynn.end()

    result.append((spikes, mem_v))

Analyse and plot neuron output

membrane = []
spikes = []
isi = []

for nrnidx, (spike, v) in enumerate(result):
    spikes.append(spike)
    membrane.append(v)
    isi.append(np.diff(spikes[nrnidx]))

num_plots = len(I_bias)
# -> play around with figsize to modify plot resolution
_, axes = plt.subplots(
    num_plots, 1, sharex=True, sharey=True, figsize=(8, 5))
axes = axes.flatten()

for nrnidx in range(num_plots):
    max_v = np.max(membrane[nrnidx])
    print(f'neuron {nrnidx}')
    print(f"max. membrane potential: {max_v:.3f} V")
    print(f"firing rate: {np.mean(1 / isi[nrnidx]):.4} "
            f"+- {np.std(1 / isi[nrnidx]):.2f} MHz")

    axes[nrnidx].plot(membrane[nrnidx].times, membrane[nrnidx])
    axes[nrnidx].plot(
        spikes[nrnidx],
        [max_v for i in range(len(spikes[nrnidx]))],
        '.', color='red')

axes[0].set_xlim(0, 0.2)
axes[2].set_ylabel("V [V]", fontsize=12)
axes[-1].set_xlabel("t [ms]", fontsize=12)

figname = f'fp_task2b_4membranes_{time.strftime("%Y%m%d-%H%M%S")}.png'
plt.savefig(figname)
print(f"plot saved {figname}")

Calibrating Membrane Time Constant

In this optional task you create a calibration routine to calibrate the leak potential of all neurons.

def membrane2dac(voltage, slope, offset):
    return int((voltage - offset) / slope)


# set voltages in volt
# threshold must be according to:
v_leak = 350
v_reset = 200
v_th = v_leak - (v_leak - v_reset) / np.exp(1)

# enter your fit results from task a) into the voltage2dac calls
neuron_params = {"leak_i_bias": 400,
                 "reset_i_bias": 38,
                 "leak_enable_division": True,  # set False for freq > 40
                 "threshold_enable": True,
                 "reset_enable_multiplication": True,
                 "membrane_capacitance_capacitance": 63,
                 "refractory_period_refractory_time": 150,
                 "leak_v_leak": membrane2dac(v_leak, 0.79, -180),
                 "reset_v_reset": membrane2dac(v_reset, 0.88, -250),
                 "threshold_v_threshold": membrane2dac(v_th, 0.99, 60)
                }

targetrate = 30.0  # in kHz

# strength of calibration
# choose value between 0 and 1
calib_param = 0.7
def get_data(i_bias, iteration):
    rates = []
    gleaks = []

    # capacitance from DAC value (63 equals 2.2pF)
    c_m = 2.2 * 10e-12 * neuron_params["membrane_capacitance_capacitance"] / 63

    # tau_ref from DAC value with f_clock = 10MHz
    tau_ref = neuron_params["refractory_period_refractory_time"] / (10e6) * 1e3

    pynn.setup()

    pop = pynn.Population(len(i_bias), pynn.cells.HXNeuron(**neuron_params))
    pop.set(leak_i_bias=i_bias)
    pop.record(["spikes"])

    pynn.run(2)
    all_spikes = pop.get_data("spikes").segments[0].spiketrains

    pynn.end()

    for nrnidx, spikes in enumerate(all_spikes):
        # if not enough spikes are recorded, the neuron is skipped
        if len(spikes) <= 1:
            rates.append(-1)
            gleaks.append(-1)

            print("not enough spikes recorded for neuron ", nrnidx)
        else:
            # calculate the firing rate from the spike array
            isi = np.array(np.diff(spikes))
            rates.append(1 / np.mean(isi))

            # calculate gleak from the interspike interval
            tau_m = np.mean(isi) - tau_ref
            gleaks.append(c_m / tau_m)

            # print(f"data obtained for neuron {nrnidx}")

    print(f"The average firing rate is {np.mean(rates):.4} "
          f"+- {np.std(rates):.3} kHz")
    print(f"The average leak conductance is {np.mean(gleaks):.4} "
          f"+- {np.std(gleaks):.3} S")

    # save results for plotting
    np.savetxt(f"fp_task2c_rates_iteration{iteration}.txt", rates)
    np.savetxt(f"fp_task2c_gleaks_iteration{iteration}.txt", gleaks)
def calibrate_neurons(i_bias, num_iterations):

    for iteration in range(num_iterations):
        get_data(i_bias, iteration)
        rates = np.loadtxt(f"fp_task2c_rates_iteration{iteration}.txt")
        for nrnidx, _ in enumerate(i_bias):
            if rates[nrnidx] != -1:
                # TODO: Check code here
                scaling = (calib_param * (targetrate / rates[nrnidx] - 1) + 1)
                i_bias[nrnidx] = int(scaling * i_bias[nrnidx])
                if i_bias[nrnidx] > 1022:
                    print(f"Reached max i_bias for neuron {nrnidx}")
                    i_bias[nrnidx] = 1022
                if i_bias[nrnidx] < 0:
                    print(f"Reached min i_bias for neuron {nrnidx}")
                    i_bias[nrnidx] = 0

Definition of visualization

def plot_histogram(num_iterations):
    # read data and filter failed runs
    rates_pre = np.loadtxt("fp_task2c_rates_iteration0.txt")
    rates_pre = rates_pre[rates_pre >= 0]
    gleaks_pre = np.loadtxt("fp_task2c_gleaks_iteration0.txt")
    gleaks_pre = gleaks_pre[gleaks_pre >= 0]
    rates_post = np.loadtxt(f"fp_task2c_rates_iteration{num_iterations-1}.txt")
    rates_post = rates_post[rates_post >= 0]
    gleaks_post = np.loadtxt(
        f"fp_task2c_gleaks_iteration{num_iterations-1}.txt")
    gleaks_post = gleaks_post[gleaks_post >= 0]
    bins = min(len(rates_pre), 20)

    # plot two histograms
    fig = plt.figure()
    ax_rate = fig.add_subplot(221)
    ax_rate.set_title("Uncalibrated firing rates")
    ax_rate.set_xlabel("rates [kHz]")
    ax_rate.set_ylabel("number of neurons")
    ax_rate.hist(rates_pre, bins=bins)

    ax_gleak = fig.add_subplot(222)
    ax_gleak.set_title("Uncalibrated leak conductance")
    ax_gleak.set_xlabel("$g_{leak}$ [S]")
    ax_gleak.set_ylabel("number of neurons")
    ax_gleak.yaxis.tick_right()
    ax_gleak.yaxis.set_label_position("right")
    ax_gleak.hist(gleaks_pre, bins=bins)

    rates_range = [min(np.min(rates_pre), np.min(rates_post)),
                   max(np.max(rates_pre), np.max(rates_post))]
    ax_rate = fig.add_subplot(223, sharex=ax_rate)
    ax_rate.set_title("Calibrated firing rates")
    ax_rate.set_xlabel("rates [kHz]")
    ax_rate.set_ylabel("number of neurons")
    ax_rate.hist(rates_post,
                 bins=bins,
                 range=rates_range)

    gleak_ranges = [min(np.min(gleaks_pre, initial=0.),
                        np.min(gleaks_post, initial=0.)),
                    max(np.max(gleaks_pre, initial=0.),
                        np.max(gleaks_post, initial=0.))]
    ax_gleak = fig.add_subplot(224, sharex=ax_gleak)
    ax_gleak.set_title("Calibrated leak conductance")
    ax_gleak.set_xlabel("$g_{leak}$ [S]")
    ax_gleak.set_ylabel("number of neurons")
    ax_gleak.yaxis.tick_right()
    ax_gleak.yaxis.set_label_position("right")
    ax_gleak.hist(gleaks_post,
                  bins=bins,
                  range=gleak_ranges)

    plt.subplots_adjust(left=0.1, right=0.9, bottom=0.1, top=0.9,
                        wspace=0.2, hspace=0.5)
    figname = f'fp_task2c_histo_{time.strftime("%Y%m%d-%H%M%S")}.png'
    plt.savefig(figname)

    print(f"plots saved {figname}")

Execution

# choose neurons you want to observe
# the default is range(0,128)
num_neurons = 100

# number of iterations for calibration
num_iterations = 20

# the leak conductance g_leak is set by I_bias
# will be adjusted for identical firing rates
i_bias = [400] * num_neurons

# calibrate neurons for same firing rate
calibrate_neurons(i_bias, num_iterations)

# plot histograms for uncalibrated and calibrated neurons
plot_histogram(num_iterations)

Exercises

  • Please complete the missing code in the cells above
  • Execute all cells, determine sensible parameter characterization ranges
  • Document the results that you have obtained and the plots that you have created below

Solution

Please insert your results here...