MiRA/tutorial-brain-network.html at main · Ecological-Complexity-Lab/MiRA · GitHub

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  <title>Multilayer brain network visualization | MiRA Multilayer Network Visualization</title>
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    content="Step-by-step walkthrough for visualizing a multilayer human brain connectome in MiRA, using the structural connectome dataset (Keresztes et al. 2022) with layers as time points.">
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    <p class="crumbs"><a href="index.html">MiRA</a> › Tutorials › Brain network</p>

    <h1>How do I visualize a multilayer brain network in MiRA?</h1>
    <p class="lead">
      A <strong>multilayer connectome</strong> represents the brain as regions (nodes) linked by
      structural or functional connections, with each layer a subject, condition, or time point.
      MiRA renders this as a stacked 3D network in the browser — no installation, no code — and
      MiRA works for any unipartite multilayer network, not only ecological ones.
    </p>

    <h2>The dataset</h2>
    <p>
      The <strong>human brain structural connectome</strong>
      (<a href="https://doi.org/10.1038/s41598-022-06697-4">Keresztes et al. 2022</a>) has 3 layers,
      124 nodes, 372 state nodes, and 1,827 within-layer plus 220 between-layer links. Each layer is
      a time point; nodes are brain regions; interlayer links couple the same region across layers.
      It is undirected and unipartite.
    </p>

    <h2>Walkthrough</h2>
    <ol class="steps">
      <li>Open <a href="index.html">MiRA</a>, click <strong>Load Example Data</strong>, and choose
        <em>Human brain structural connectome</em>.</li>
      <li>In <strong>Network Mode</strong>, rotate and pan the stacked 3D view to see the three
        layers and the interlayer links coupling the same regions across time.</li>
      <li>In the <strong>Nodes</strong> panel, size nodes by degree to find hub regions, and color
        by any region attribute present in the data.</li>
      <li>Use the <strong>Intralayer Links</strong> threshold to hide weak connections and expose
        the strong structural backbone within each layer.</li>
      <li>Switch to <strong>Grid View</strong> to compare the three layers as small multiples, then
        to <strong>Meta-Network Mode</strong> for an aggregated single-layer summary of cross-layer
        connectivity.</li>
      <li>Open <strong>Dashboard Mode</strong> for degree distributions, the presence matrix, and
        the layer-similarity heatmap quantifying how connectivity changes between time points.</li>
    </ol>

    <div class="callout">
      <strong>Beyond ecology.</strong> Although MiRA was built with biology in mind, it renders any
      multilayer network. Connectomes, protein–protein interaction networks, and social networks
      all load through the same <a href="data-format.html">JSON or CSV format</a>.
    </div>

    <h2>Use your own data</h2>
    <p>
      Represent each subject, condition, or time point as a layer, couple repeated regions with
      interlayer links, and export to MiRA's <a href="data-format.html">JSON or CSV format</a>. Then
      use <strong>Load Data</strong> and follow the same steps.
    </p>

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