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Clean and build (#6)
* overhaul * cleanup files * tweak content
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‎.gitignore‎

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# and can be added to the global gitignore or merged into this file. For a more nuclear
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# option (not recommended) you can uncomment the following to ignore the entire idea folder.
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#.idea/
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# Hugo build output
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public/
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resources/_gen/

‎assets/css/custom.css‎

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/* Page entrance animation — single pages use <article>, list/section pages use <header>+<section> */
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#main-content > article {
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animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.1s both;
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}
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#main-content > header {
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animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.1s both;
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}
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#main-content > section {
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animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.25s both;
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}
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/* Global font size reduction */
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html {
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font-size: 90%;
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}
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/* Logo dark/light switching.
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Congo toggles a .dark class on <html> via JS — the native
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prefers-color-scheme media query inside <picture> tags does not respond
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from { opacity: 0; transform: translateY(28px); }
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to { opacity: 1; transform: translateY(0); }
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}
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.hero-fade-1 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.15s both; }
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.hero-fade-2 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.30s both; }
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.hero-fade-3 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.45s both; }
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.hero-fade-4 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.60s both; }
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.hero-fade-5 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.75s both; }
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.hero-fade-1 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.10s both; }
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.hero-fade-2 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.22s both; }
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.hero-fade-3 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.34s both; }
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.hero-fade-4 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.46s both; }
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.hero-fade-5 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.58s both; }
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.hero-fade-6 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.70s both; }
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.hero-fade-7 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.82s both; }
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.hero-fade-8 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.94s both; }
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/* List view logos */
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.list-logo-light { display: block; }

‎config/_default/params.toml‎

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colorScheme = "ocean"
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defaultAppearance = "light"
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autoSwitchAppearance = true
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enableSearch = true
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enableSearch = false
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enableCodeCopy = false
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[homepage]

‎content/_index.md‎

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title: "Cytomining"
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description: "Open-source tools for single-cell image-based profiling"
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---
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<div class="not-prose" style="text-align: center; padding: 3rem 0 2rem;">
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<!-- Logo -->
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<div class="hero-fade-1" style="margin-bottom: 1.5rem;">
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<img
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src="https://avatars.githubusercontent.com/u/19327357?v=4"
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alt="Cytomining"
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style="width: 96px; height: 96px; border-radius: 50%; margin: 0 auto 1rem; display: block; box-shadow: 0 4px 20px rgba(0,0,0,0.12);"
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>
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<h1 style="font-size: 2.5rem; font-weight: 800; letter-spacing: -0.02em; margin: 0;">Cytomining</h1>
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</div>
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<!-- Tagline -->
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<div class="hero-fade-2" style="margin-bottom: 2.5rem;">
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<p style="font-size: 1.2rem; color: #6b7280; max-width: 540px; margin: 0 auto; line-height: 1.6;">
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Open-source tools for every stage of the<br>single-cell image-based profiling workflow.
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</p>
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</div>
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<!-- Pipeline visualization -->
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<div class="hero-fade-3" style="margin-bottom: 2.5rem; overflow-x: auto; padding: 0.5rem 0;">
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<div style="display: inline-flex; align-items: center; gap: 0.4rem; flex-wrap: wrap; justify-content: center; padding: 0 1rem;">
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<div class="pipeline-step" style="background: #f3f4f6; border-radius: 8px; padding: 0.45rem 0.9rem; font-size: 0.8rem; color: #374151; font-weight: 500; border: 1px solid #e5e7eb;">
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🔬 Raw Images
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</div>
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<span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
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<a href="/experimental/iceberg-bioimage/" class="pipeline-step" style="background: #ede9fe; border-radius: 8px; padding: 0.45rem 0.9rem; font-size: 0.8rem; color: #5b21b6; font-weight: 600; border: 1px solid #ddd6fe; text-decoration: none;">
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iceberg-bioimage
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</a>
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<span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
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<a href="/tools/cytotable/" class="pipeline-step" style="background: #ede9fe; border-radius: 8px; padding: 0.45rem 0.9rem; font-size: 0.8rem; color: #5b21b6; font-weight: 600; border: 1px solid #ddd6fe; text-decoration: none;">
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CytoTable
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</a>
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<span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
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<a href="/tools/cosmicqc/" class="pipeline-step" style="background: #dbeafe; border-radius: 8px; padding: 0.45rem 0.9rem; font-size: 0.8rem; color: #1e40af; font-weight: 600; border: 1px solid #bfdbfe; text-decoration: none;">
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coSMicQC
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</a>
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<span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
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<a href="/tools/pycytominer/" class="pipeline-step" style="background: #dbeafe; border-radius: 8px; padding: 0.45rem 0.9rem; font-size: 0.8rem; color: #1e40af; font-weight: 600; border: 1px solid #bfdbfe; text-decoration: none;">
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pycytominer
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</a>
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<span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
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<a href="/tools/copairs/" class="pipeline-step" style="background: #dcfce7; border-radius: 8px; padding: 0.45rem 0.9rem; font-size: 0.8rem; color: #166534; font-weight: 600; border: 1px solid #bbf7d0; text-decoration: none;">
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copairs
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</a>
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<span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">/</span>
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<a href="/experimental/buscar/" class="pipeline-step" style="background: #dcfce7; border-radius: 8px; padding: 0.45rem 0.9rem; font-size: 0.8rem; color: #166534; font-weight: 600; border: 1px solid #bbf7d0; text-decoration: none;">
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buscar
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</a>
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</div>
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<p style="font-size: 0.72rem; color: #9ca3af; margin-top: 0.75rem;">ingest &nbsp;·&nbsp; quality control &nbsp;·&nbsp; process &nbsp;·&nbsp; evaluate</p>
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</div>
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<!-- CTA -->
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<div class="hero-fade-4" style="margin-bottom: 2.5rem; display: flex; gap: 0.75rem; justify-content: center; flex-wrap: wrap;">
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<a href="/tools/" style="display: inline-block; background: #2563eb; color: white; font-weight: 600; font-size: 0.95rem; padding: 0.65rem 1.5rem; border-radius: 8px; text-decoration: none; transition: background 0.15s;">
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Explore tools →
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</a>
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<a href="https://cytomining.github.io/profiling-handbook" target="_blank" style="display: inline-block; background: transparent; color: #374151; font-weight: 600; font-size: 0.95rem; padding: 0.65rem 1.5rem; border-radius: 8px; text-decoration: none; border: 1.5px solid #d1d5db; transition: border-color 0.15s;">
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Profiling handbook
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</a>
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</div>
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<!-- Community + get started links -->
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<div class="hero-fade-5" style="font-size: 0.85rem; color: #6b7280; display: flex; gap: 1.25rem; justify-content: center; flex-wrap: wrap;">
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<a href="https://github.com/cytomining/profiling-recipe" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">Profiling recipe</a>
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<a href="https://forum.image.sc/" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">image.sc forum</a>
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<a href="https://github.com/orgs/cytomining/people" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">Contributors</a>
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<a href="https://www.cytodata.org/" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">CytoData community</a>
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</div>
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</div>

‎layouts/_partials/article-link.html‎

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</div>
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{{- end }}
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<div>
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{{/* Small icon above title */}}
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{{ with .Params.logoUrl }}
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<img src="{{ . }}" alt="{{ $.Title }} icon" style="height: 28px; width: 28px; object-fit: contain; display: block; margin-bottom: 0.4rem; border-radius: 4px;">
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{{ end }}
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<h3 class="flex items-center text-xl font-semibold">
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{{/* Inline icon before title */}}
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{{ with .Params.logoUrl }}
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<img src="{{ . }}" alt="{{ $.Title }} icon" style="height: 22px; width: 22px; object-fit: contain; border-radius: 3px; margin-right: 0.5rem; flex-shrink: 0; position: relative; top: -1px;">
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{{ end }}
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{{ with .Params.externalUrl }}
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<div>
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<a

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