Spike Timing Reliability

Reliability of spike timing.

See e.g. Mainen & Sejnowski (1995) for experimental results in vitro.

Here: a constant current is injected in all trials.

// non_reliability.py
from brian2 import *

N = 24
tau = 20*ms
sigma = .015
eqs_neurons = '''
dx/dt = (1.1 - x) / tau + sigma * (2 / tau)**.5 * xi : 1 (unless refractory)
'''
neurons = NeuronGroup(N, model=eqs_neurons, threshold='x > 1', reset='x = 0',
                      refractory=5*ms, method='euler')


spikes = SpikeMonitor(neurons)
run(500*ms,  report='text', report_period=0.1*second)

<!-- non_reliability.html -->
<!DOCTYPE html>
<html lang="en-us">
  <head>
    <meta charset="utf-8" />
    <meta http-equiv="Content-Type" content="text/html; charset=utf-8" />
    <title>Reliability of spike timing</title>
    <script src="brian.js"></script>
    <script>
      function myplot(event) {
        console.log("before results fetch");

        const brian_results = event.data.results;
        console.log(brian_results);

        // Extract the spike data
        const spikes_t = brian_results["spikemonitor"].t;
        const spikes_i = brian_results["spikemonitor"].i;

        // Create scatter plot data points
        let scatterData = [];
        if (spikes_t && spikes_i && spikes_t.length === spikes_i.length) {
          for (let idx = 0; idx < spikes_t.length; idx++) {
            scatterData.push({
              x: spikes_t[idx] * 1000, // Convert to milliseconds
              y: spikes_i[idx],
            });
          }
        } else {
          console.error("Spike data format is not as expected");
        }

        const ctx = document.getElementById("brian_canvas");

        // Clear any existing chart
        Chart.getChart(ctx)?.destroy();

        new Chart(ctx, {
          type: "scatter",
          data: {
            datasets: [
              {
                data: scatterData,
                backgroundColor: "black",
                pointRadius: 2,
                pointHoverRadius: 4,
                showLine: false,
              },
            ],
          },
          options: {
            responsive: true,
            maintainAspectRatio: false,
            plugins: {
              legend: { display: false },
              tooltip: {
                enabled: true,
                callbacks: {
                  label: function (context) {
                    return `Neuron: ${
                      context.raw.y
                    }, Time: ${context.raw.x.toFixed(2)} ms`;
                  },
                },
                backgroundColor: "rgba(0, 0, 0, 0.7)",
                titleFont: {
                  size: 14,
                },
                bodyFont: {
                  size: 14,
                },
                padding: 10,
              },
            },
            scales: {
              x: {
                type: "linear",
                position: "bottom",
                title: {
                  display: true,
                  text: "Time (ms)",
                },
                ticks: {
                  stepSize: 100,
                },
              },
              y: {
                type: "linear",
                title: {
                  display: true,
                  text: "Neuron index",
                },
              },
            },
            elements: {
              point: {
                radius: 2,
                backgroundColor: "black",
                hoverBackgroundColor: "#d17930",
                hoverBorderColor: "black",
                hoverBorderWidth: 1,
              },
            },
            interaction: {
              mode: "nearest",
              intersect: true,
              axis: "xy",
            },
            animation: false,
          },
        });
      }

      var brian_sim = new BrianSimulation(
        (result_plots = [{ type: "custom", func: myplot }])
      );

      // wait until the website is fully defined
      window.onload = (event) => {
        brian_sim.init();
      };
    </script>
    <link
      rel="stylesheet"
      href="https://fonts.googleapis.com/css2?family=Inter:wght@300;400;600&display=swap"
    />
    <script src="https://cdn.jsdelivr.net/npm/chart.js"></script>
    <style>
      body {
        font-family: "Inter", sans-serif;
        font-size: 1.2rem;
        padding: 20px;
      }
      h1 {
        color: #333e63;
      }
      .btn--runSimulation {
        background-color: #344683;
        color: white;
        font-size: 1.2rem;
        padding: 10px 20px;
        border: none;
        border-radius: 8px;
        cursor: pointer;
        transition: background-color 0.3s ease, transform 0.2s ease;
      }
      .btn--runSimulation:hover {
        background-color: #283252;
        transform: scale(1.05);
      }
      .btn--runSimulation:active {
        background-color: #313e68;
        transform: scale(0.98);
      }
      .slider-container {
        max-width: 40%;
        margin: 15px 0;
      }
      .slider-label {
        display: flex;
        justify-content: space-between;
        font-size: 1rem;
        margin-bottom: 5px;
      }
      input[type="range"] {
        width: 100%;
        cursor: pointer;
      }
      #brian_canvas {
        margin: 32px 0;
      }
    </style>
  </head>
  <body>
    <h1>Reliability of spike timing.</h1>
    <p>See e.g. Mainen & Sejnowski (1995) for experimental results in vitro.</p>
    <p>Here: a constant current is injected in all trials.</p>

    <button onclick="brian_sim.run(); return false;" class="btn--runSimulation">
      Run Simulation
    </button>

    <progress
      id="brian_progress_bar"
      max="1.0"
      value="0.0"
      style="width: 20em"
    ></progress>

    <div style="width: 90%; height: 400px">
      <canvas id="brian_canvas"></canvas>
    </div>
    <div id="brian_progress_text"></div>
  </body>
</html>

python - m brian2wasm non_reliability.py

Output

../_images/result_non_reliability.png