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<!DOCTYPE html>
<html lang="en">
<head>
<meta charset="UTF-8">
<meta name="viewport" content="width=device-width, initial-scale=1.0">
<title>Publications — Embedded OME-ZARR Viewer Demo | Find Nuclei</title>
<meta name="description" content="See how journals can embed interactive OME-ZARR microscopy viewers directly in publication pages. Two lines of HTML — no install, no iframe.">
<link rel="icon" type="image/svg+xml" href="./favicon.svg">
<link rel="icon" type="image/x-icon" href="./favicon.ico">
<style>
* { margin: 0; padding: 0; box-sizing: border-box; }
/* Reason: Hide browser scrollbar while keeping scroll functional.
The page still scrolls normally — only the visual bar is hidden. */
html { scrollbar-width: none; }
html::-webkit-scrollbar { display: none; }
body {
min-height: 100vh;
background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
font-family: -apple-system, BlinkMacSystemFont, 'Segoe UI', Roboto, 'Helvetica Neue', Arial, sans-serif;
color: #333;
padding: 2rem;
}
.page-container {
max-width: 960px;
margin: 0 auto;
background: white;
border-radius: 16px;
box-shadow: 0 20px 60px rgba(0, 0, 0, 0.2);
overflow: hidden;
}
/* ── Header ── */
.page-header {
background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
padding: 2.5rem 2rem;
color: white;
text-align: center;
}
.page-header h1 {
font-size: 2rem;
font-weight: 700;
margin-bottom: 0.5rem;
}
.page-header p {
opacity: 0.9;
font-size: 0.9375rem;
max-width: 560px;
margin: 0 auto;
line-height: 1.6;
}
.page-body {
padding: 0 2.5rem 3rem;
}
/* ── Tabs ── */
.tabs {
display: flex;
flex-wrap: wrap;
border-bottom: 2px solid #e5e7eb;
margin-bottom: 2rem;
gap: 0;
overflow: hidden;
}
.tab {
padding: 1rem 1.5rem;
font-size: 0.9375rem;
font-weight: 600;
color: #6b7280;
cursor: pointer;
border-bottom: 2px solid transparent;
margin-bottom: -2px;
white-space: nowrap;
transition: color 0.15s ease, border-color 0.15s ease;
background: none;
border-top: none;
border-left: none;
border-right: none;
font-family: inherit;
}
.tab:hover {
color: #374151;
}
.tab.active {
color: #667eea;
border-bottom-color: #667eea;
}
/* ── Study panels ── */
.study-panel {
display: none;
}
.study-panel.active {
display: block;
}
.study-meta {
margin-bottom: 1.5rem;
}
.study-meta h2 {
font-size: 1.25rem;
color: #1f2937;
margin-bottom: 0.5rem;
}
.study-meta .study-id {
display: inline-block;
font-size: 0.6875rem;
font-weight: 700;
text-transform: uppercase;
letter-spacing: 0.05em;
color: #667eea;
background: #f0f4ff;
padding: 0.2rem 0.5rem;
border-radius: 4px;
margin-bottom: 0.75rem;
}
.study-meta p {
color: #4b5563;
font-size: 0.9375rem;
line-height: 1.7;
}
.study-meta a {
color: #667eea;
text-decoration: none;
}
.study-meta a:hover {
text-decoration: underline;
}
.study-tags {
display: flex;
flex-wrap: wrap;
gap: 0.5rem;
margin-top: 0.75rem;
margin-bottom: 1.5rem;
}
.study-tag {
font-size: 0.75rem;
color: #6b7280;
background: #f9fafb;
border: 1px solid #e5e7eb;
padding: 0.2rem 0.6rem;
border-radius: 100px;
}
/* ── Viewer container ── */
.viewer-section {
margin-bottom: 2rem;
}
.viewer-section h3 {
font-size: 0.875rem;
color: #9ca3af;
text-transform: uppercase;
letter-spacing: 0.05em;
margin-bottom: 0.75rem;
font-weight: 600;
}
.viewer-wrap {
border-radius: 12px;
overflow: hidden;
border: 1px solid #e5e7eb;
}
/* ── Code snippet ── */
.code-section {
margin-top: 2rem;
}
.code-section h3 {
font-size: 0.875rem;
color: #9ca3af;
text-transform: uppercase;
letter-spacing: 0.05em;
margin-bottom: 0.75rem;
font-weight: 600;
}
.code-block {
background: #1e1e2e;
color: #cdd6f4;
padding: 1.25rem 1.5rem;
border-radius: 12px;
font-family: 'SF Mono', Monaco, 'Cascadia Code', 'Roboto Mono', monospace;
font-size: 0.8125rem;
line-height: 1.7;
overflow-x: auto;
position: relative;
}
.code-block .tag { color: #89b4fa; }
.code-block .attr { color: #a6e3a1; }
.code-block .val { color: #f9e2af; }
.code-block .comment { color: #6c7086; }
.copy-btn {
position: absolute;
top: 0.75rem;
right: 0.75rem;
background: rgba(255, 255, 255, 0.1);
border: none;
color: #cdd6f4;
font-size: 0.75rem;
padding: 0.3rem 0.6rem;
border-radius: 4px;
cursor: pointer;
font-family: inherit;
transition: background 0.15s ease;
}
.copy-btn:hover {
background: rgba(255, 255, 255, 0.2);
}
/* ── CTA ── */
.page-cta {
text-align: center;
margin-top: 2.5rem;
padding-top: 2rem;
border-top: 1px solid #e5e7eb;
}
.page-cta p {
color: #4b5563;
font-size: 0.9375rem;
margin-bottom: 0.75rem;
line-height: 1.6;
}
.page-cta .cta-button {
display: inline-block;
background: linear-gradient(135deg, #667eea 0%, #764ba2 100%);
color: white;
text-decoration: none;
font-weight: 600;
font-size: 1rem;
padding: 0.75rem 2rem;
border-radius: 8px;
transition: opacity 0.2s ease, transform 0.2s ease;
}
.page-cta .cta-button:hover {
opacity: 0.9;
transform: translateY(-1px);
}
.page-cta .cta-button-secondary {
background: transparent;
border: 2px solid #667eea;
color: #667eea;
margin-left: 0.75rem;
}
.page-cta .cta-button-secondary:hover {
background: rgba(102, 126, 234, 0.08);
border-color: #764ba2;
color: #764ba2;
}
.page-cta .cta-sub {
margin-top: 0.75rem;
font-size: 0.8125rem;
color: #9ca3af;
}
.page-back {
display: inline-block;
margin-top: 2rem;
color: #667eea;
text-decoration: none;
font-weight: 600;
font-size: 0.9375rem;
}
.page-back:hover { text-decoration: underline; }
/* ── Responsive ── */
@media (max-width: 640px) {
body { padding: 1rem; }
.page-body { padding: 0 1.25rem 2rem; }
.page-header h1 { font-size: 1.5rem; }
.tab { padding: 0.75rem 1rem; font-size: 0.8125rem; }
}
</style>
</head>
<body>
<div class="page-container">
<div class="page-header">
<h1>Embedded Viewer for Publications</h1>
<p>
Two lines of HTML. No iframe. No install.
See how journals can embed interactive OME-ZARR microscopy data directly in their pages.
</p>
</div>
<div class="page-body">
<!-- Tabs -->
<div class="tabs">
<button class="tab active" data-panel="idr0062">IDR-0062</button>
<button class="tab" data-panel="idr0066">IDR-0066</button>
<button class="tab" data-panel="idr0073">IDR-0073</button>
<button class="tab" data-panel="idr0079">IDR-0079</button>
<button class="tab" data-panel="howto">How It Works</button>
</div>
<!-- ─── IDR-0062 ─── -->
<div class="study-panel active" id="panel-idr0062">
<div class="study-meta">
<span class="study-id">IDR-0062</span>
<h2>NesSys: Accurate Nuclear Segmentation in 3D</h2>
<p>
Blin G et al. (2019) <em>PLoS Biology</em>.
Automated detection and segmentation of nuclei within intact mouse tissues
and dense 3D cultures using confocal microscopy.
<a href="https://idr.openmicroscopy.org/study/idr0062/" target="_blank" rel="noopener">View on IDR →</a>
·
<a href="/?url=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr" target="_blank" rel="noopener">Open in Find Nuclei Viewer →</a>
</p>
<div class="study-tags">
<span class="study-tag">Mus musculus</span>
<span class="study-tag">Confocal 3D</span>
<span class="study-tag">Nuclear segmentation</span>
<span class="study-tag">Multi-channel</span>
</div>
</div>
<div class="viewer-section">
<h3>Interactive Viewer</h3>
<div class="viewer-wrap">
<find-nuclei-viewer
url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"
labels="on"
width="100%"
height="500"
></find-nuclei-viewer>
</div>
</div>
<div class="code-section">
<h3>Embed Code</h3>
<div class="code-block" id="code-idr0062">
<button class="copy-btn" onclick="copyCode('code-idr0062')">Copy</button>
<span class="comment"><!-- Load once in <head> --></span>
<span class="tag"><script</span> <span class="attr">src</span>=<span class="val">"https://find-nuclei.github.io/embed/v1/viewer.js"</span><span class="tag">></script></span>
<span class="comment"><!-- Place anywhere in your article --></span>
<span class="tag"><find-nuclei-viewer</span>
<span class="attr">url</span>=<span class="val">"https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr"</span>
<span class="attr">labels</span>=<span class="val">"on"</span>
<span class="attr">width</span>=<span class="val">"100%"</span>
<span class="attr">height</span>=<span class="val">"500"</span>
<span class="tag">></find-nuclei-viewer></span>
</div>
</div>
</div>
<!-- ─── IDR-0066 ─── -->
<div class="study-panel" id="panel-idr0066">
<div class="study-meta">
<span class="study-id">IDR-0066</span>
<h2>mesoSPIM: Open-Source Light-Sheet Microscopy for Cleared Tissue</h2>
<p>
Voigt FF et al. (2019) <em>Nature Methods</em>.
Mesoscale light-sheet imaging of large cleared tissue specimens including
chicken embryo vasculature.
<a href="https://idr.openmicroscopy.org/study/idr0066/" target="_blank" rel="noopener">View on IDR →</a>
·
<a href="/?url=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpD_chicken_embryo_MIP.ome.zarr" target="_blank" rel="noopener">Open in Find Nuclei Viewer →</a>
</p>
<div class="study-tags">
<span class="study-tag">Chicken embryo</span>
<span class="study-tag">Light-sheet (mesoSPIM)</span>
<span class="study-tag">Cleared tissue</span>
<span class="study-tag">MIP</span>
</div>
</div>
<div class="viewer-section">
<h3>Interactive Viewer</h3>
<div class="viewer-wrap">
<find-nuclei-viewer
url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpD_chicken_embryo_MIP.ome.zarr"
width="100%"
height="500"
></find-nuclei-viewer>
</div>
</div>
<div class="code-section">
<h3>Embed Code</h3>
<div class="code-block" id="code-idr0066">
<button class="copy-btn" onclick="copyCode('code-idr0066')">Copy</button>
<span class="comment"><!-- Load once in <head> --></span>
<span class="tag"><script</span> <span class="attr">src</span>=<span class="val">"https://find-nuclei.github.io/embed/v1/viewer.js"</span><span class="tag">></script></span>
<span class="comment"><!-- Place anywhere in your article --></span>
<span class="tag"><find-nuclei-viewer</span>
<span class="attr">url</span>=<span class="val">"https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0066/ExpD_chicken_embryo_MIP.ome.zarr"</span>
<span class="attr">width</span>=<span class="val">"100%"</span>
<span class="attr">height</span>=<span class="val">"500"</span>
<span class="tag">></find-nuclei-viewer></span>
</div>
</div>
</div>
<!-- ─── IDR-0073 ─── -->
<div class="study-panel" id="panel-idr0073">
<div class="study-meta">
<span class="study-id">IDR-0073</span>
<h2>Graph-Based Description of Tertiary Lymphoid Organs</h2>
<p>
Schaadt NS et al. (2020) <em>PLoS Computational Biology</em>.
Neighborhood graph analysis of immune infiltrates in human tissue sections
(breast cancer, kidney, lung) using bright-field immunohistochemistry.
<a href="https://idr.openmicroscopy.org/study/idr0073/" target="_blank" rel="noopener">View on IDR →</a>
·
<a href="/?url=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0073A/9798462.zarr" target="_blank" rel="noopener">Open in Find Nuclei Viewer →</a>
</p>
<div class="study-tags">
<span class="study-tag">Homo sapiens</span>
<span class="study-tag">Bright-field histology</span>
<span class="study-tag">Immunohistochemistry</span>
<span class="study-tag">Tertiary lymphoid organs</span>
</div>
</div>
<div class="viewer-section">
<h3>Interactive Viewer</h3>
<div class="viewer-wrap">
<find-nuclei-viewer
url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0073A/9798462.zarr"
width="100%"
height="500"
></find-nuclei-viewer>
</div>
</div>
<div class="code-section">
<h3>Embed Code</h3>
<div class="code-block" id="code-idr0073">
<button class="copy-btn" onclick="copyCode('code-idr0073')">Copy</button>
<span class="comment"><!-- Load once in <head> --></span>
<span class="tag"><script</span> <span class="attr">src</span>=<span class="val">"https://find-nuclei.github.io/embed/v1/viewer.js"</span><span class="tag">></script></span>
<span class="comment"><!-- RGB images auto-detect white background, or set explicitly --></span>
<span class="tag"><find-nuclei-viewer</span>
<span class="attr">url</span>=<span class="val">"https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0073A/9798462.zarr"</span>
<span class="attr">background</span>=<span class="val">"white"</span>
<span class="attr">width</span>=<span class="val">"100%"</span>
<span class="attr">height</span>=<span class="val">"500"</span>
<span class="tag">></find-nuclei-viewer></span>
</div>
</div>
</div>
<!-- ─── IDR-0079 ─── -->
<div class="study-panel" id="panel-idr0079">
<div class="study-meta">
<span class="study-id">IDR-0079</span>
<h2>Cellular Architecture in the Developing Lateral Line Primordium</h2>
<p>
Hartmann J et al. (2020) <em>eLife</em>.
3D cell shape and organization analysis in the zebrafish posterior lateral line
primordium using AiryScan confocal microscopy and automated segmentation.
<a href="https://idr.openmicroscopy.org/study/idr0079/" target="_blank" rel="noopener">View on IDR →</a>
·
<a href="/?url=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr" target="_blank" rel="noopener">Open in Find Nuclei Viewer →</a>
</p>
<div class="study-tags">
<span class="study-tag">Danio rerio</span>
<span class="study-tag">AiryScan confocal</span>
<span class="study-tag">3D segmentation</span>
<span class="study-tag">Z-stack</span>
</div>
</div>
<div class="viewer-section">
<h3>Series 0</h3>
<div class="viewer-wrap">
<find-nuclei-viewer
url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr"
image="0"
labels="on"
x="500" y="350" zoom="-0.5"
width="100%"
height="400"
></find-nuclei-viewer>
</div>
</div>
<div class="viewer-section">
<h3>Series 1</h3>
<div class="viewer-wrap">
<find-nuclei-viewer
url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr"
image="1"
width="100%"
height="400"
></find-nuclei-viewer>
</div>
</div>
<div class="viewer-section">
<h3>Series 2</h3>
<div class="viewer-wrap">
<find-nuclei-viewer
url="https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr"
image="2"
labels="on"
width="100%"
height="400"
></find-nuclei-viewer>
</div>
</div>
<div class="code-section">
<h3>Embed Code</h3>
<div class="code-block" id="code-idr0079">
<button class="copy-btn" onclick="copyCode('code-idr0079')">Copy</button>
<span class="comment"><!-- Load once in <head> --></span>
<span class="tag"><script</span> <span class="attr">src</span>=<span class="val">"https://find-nuclei.github.io/embed/v1/viewer.js"</span><span class="tag">></script></span>
<span class="comment"><!-- Use the image attribute to select a series --></span>
<span class="tag"><find-nuclei-viewer</span>
<span class="attr">url</span>=<span class="val">"https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0079A/idr0079_images.zarr"</span>
<span class="attr">image</span>=<span class="val">"0"</span>
<span class="attr">width</span>=<span class="val">"100%"</span>
<span class="attr">height</span>=<span class="val">"400"</span>
<span class="tag">></find-nuclei-viewer></span>
</div>
</div>
</div>
<!-- ─── How It Works ─── -->
<div class="study-panel" id="panel-howto">
<div class="study-meta">
<h2>Embed in Two Steps</h2>
<p>
Any journal, data portal, or institutional repository can add interactive
OME-ZARR viewers to their pages. No backend, no API key, no build step.
</p>
</div>
<div class="code-section" style="margin-top: 0;">
<h3>Step 1 — Load the script (once per page)</h3>
<div class="code-block">
<span class="tag"><script</span> <span class="attr">src</span>=<span class="val">"https://find-nuclei.github.io/embed/v1/viewer.js"</span><span class="tag">></script></span>
</div>
</div>
<div class="code-section">
<h3>Step 2 — Place the viewer</h3>
<div class="code-block">
<span class="tag"><find-nuclei-viewer</span>
<span class="attr">url</span>=<span class="val">"https://your-s3-bucket.com/dataset.ome.zarr"</span>
<span class="attr">width</span>=<span class="val">"100%"</span>
<span class="attr">height</span>=<span class="val">"500"</span>
<span class="tag">></find-nuclei-viewer></span>
</div>
</div>
<div class="code-section">
<h3>Optional — Customize channels and Z-slice</h3>
<div class="code-block">
<span class="tag"><find-nuclei-viewer</span>
<span class="attr">url</span>=<span class="val">"https://..."</span>
<span class="attr">z</span>=<span class="val">"15"</span>
<span class="attr">channels</span>=<span class="val">"0:on:00FF00:100:4000,1:on:FF0000:50:2000"</span>
<span class="attr">theme</span>=<span class="val">"light"</span>
<span class="attr">controls</span>=<span class="val">"minimal"</span>
<span class="tag">></find-nuclei-viewer></span>
</div>
</div>
<div class="code-section">
<h3>Attributes Reference</h3>
<div style="overflow-x: auto;">
<table style="width: 100%; border-collapse: collapse; font-size: 0.875rem; margin-top: 0.5rem;">
<thead>
<tr style="border-bottom: 2px solid #e5e7eb; text-align: left;">
<th style="padding: 0.5rem 1rem; color: #374151;">Attribute</th>
<th style="padding: 0.5rem 1rem; color: #374151;">Required</th>
<th style="padding: 0.5rem 1rem; color: #374151;">Default</th>
<th style="padding: 0.5rem 1rem; color: #374151;">Description</th>
</tr>
</thead>
<tbody>
<tr style="border-bottom: 1px solid #f3f4f6;">
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">url</code></td>
<td style="padding: 0.5rem 1rem;">Yes</td>
<td style="padding: 0.5rem 1rem;">—</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;">ZARR store URL (HTTP or S3)</td>
</tr>
<tr style="border-bottom: 1px solid #f3f4f6;">
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">z</code></td>
<td style="padding: 0.5rem 1rem;">No</td>
<td style="padding: 0.5rem 1rem;">middle</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;">Initial Z-slice index</td>
</tr>
<tr style="border-bottom: 1px solid #f3f4f6;">
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">channels</code></td>
<td style="padding: 0.5rem 1rem;">No</td>
<td style="padding: 0.5rem 1rem;">auto</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;">Channel config: <code style="font-size:0.75rem">idx:on/off:hex:min:max,...</code></td>
</tr>
<tr style="border-bottom: 1px solid #f3f4f6;">
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">width</code></td>
<td style="padding: 0.5rem 1rem;">No</td>
<td style="padding: 0.5rem 1rem;">100%</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;">CSS width (pixels or %)</td>
</tr>
<tr style="border-bottom: 1px solid #f3f4f6;">
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">height</code></td>
<td style="padding: 0.5rem 1rem;">No</td>
<td style="padding: 0.5rem 1rem;">16:9 auto</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;">CSS height (pixels or %)</td>
</tr>
<tr style="border-bottom: 1px solid #f3f4f6;">
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">controls</code></td>
<td style="padding: 0.5rem 1rem;">No</td>
<td style="padding: 0.5rem 1rem;">minimal</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;"><code>minimal</code> or <code>none</code></td>
</tr>
<tr style="border-bottom: 1px solid #f3f4f6;">
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">theme</code></td>
<td style="padding: 0.5rem 1rem;">No</td>
<td style="padding: 0.5rem 1rem;">dark</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;"><code>dark</code> or <code>light</code></td>
</tr>
<tr>
<td style="padding: 0.5rem 1rem;"><code style="background:#f0f4ff;color:#667eea;padding:0.1em 0.3em;border-radius:3px;">token</code></td>
<td style="padding: 0.5rem 1rem;">No</td>
<td style="padding: 0.5rem 1rem;">—</td>
<td style="padding: 0.5rem 1rem; color: #4b5563;">Bearer token for auth sources</td>
</tr>
</tbody>
</table>
</div>
</div>
</div>
<!-- CTA -->
<div class="page-cta">
<p>Want to embed interactive microscopy in your journal or data portal?</p>
<a href="/" class="cta-button">Try the Full Viewer →</a>
<a href="/docs/guides/embedding.html" target="_blank" rel="noopener noreferrer" class="cta-button cta-button-secondary">Read the Embedding Guide →</a>
<p class="cta-sub">Free to use · No account required · No install</p>
</div>
<a href="/" class="page-back">← Back to Find Nuclei Viewer</a>
</div>
</div>
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<script>
// Tab switching
document.querySelectorAll('.tab').forEach(tab => {
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tab.classList.add('active');
const panelId = 'panel-' + tab.dataset.panel;
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});
});
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const text = temp.textContent?.trim() || '';
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const btn = block.querySelector('.copy-btn');
if (btn) {
btn.textContent = 'Copied!';
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}
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