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overhaul (#4)
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docs/.nojekyll renamed to .hugo_build.lock

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‎assets/css/custom.css‎

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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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to this toggle, so we handle switching with CSS classes instead. */
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.logo-light {
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display: block;
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max-width: 100%;
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height: auto;
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}
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.logo-dark {
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display: none;
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max-width: 100%;
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height: auto;
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}
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html.dark .logo-light {
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display: none;
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}
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html.dark .logo-dark {
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display: block;
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}
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/* Experimental page — v2 callout and problem cards */
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html.dark .v2-callout {
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background: #1e3a5f !important;
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border-color: #3b82f6 !important;
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}
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html.dark .v2-callout p { color: #93c5fd !important; }
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html.dark .v2-callout strong { color: #bfdbfe !important; }
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html.dark .problem-card {
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background: #1f2937 !important;
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border-color: #374151 !important;
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}
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html.dark .problem-card p { color: #9ca3af !important; }
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html.dark .problem-card strong { color: #d1d5db !important; }
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html.dark .v2-pipeline-step-neutral {
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background: #1f2937 !important;
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border-color: #374151 !important;
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color: #d1d5db !important;
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}
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html.dark .v2-pipeline-step-purple {
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background: #2e1065 !important;
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border-color: #4c1d95 !important;
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color: #c4b5fd !important;
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}
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html.dark .v2-pipeline-step-blue {
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background: #1e3a5f !important;
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border-color: #1e40af !important;
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color: #93c5fd !important;
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}
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html.dark .v2-pipeline-step-yellow {
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background: #422006 !important;
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border-color: #854d0e !important;
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color: #fde68a !important;
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}
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html.dark .v2-pipeline-step-green {
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background: #052e16 !important;
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border-color: #166534 !important;
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color: #86efac !important;
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}
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/* Hero entrance animations */
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@keyframes fadeUp {
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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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/* List view logos */
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.list-logo-light { display: block; }
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.list-logo-dark { display: none; }
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html.dark .list-logo-light { display: none !important; }
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html.dark .list-logo-dark { display: block !important; }
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/* Pipeline step hover bounce (spring easing gives natural overshoot) */
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.pipeline-step {
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transition: transform 0.25s cubic-bezier(0.34, 1.56, 0.64, 1), box-shadow 0.2s ease;
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}
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.pipeline-step:hover {
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transform: translateY(-4px) scale(1.04);
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box-shadow: 0 6px 16px rgba(0,0,0,0.13);
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}
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html.dark .pipeline-step:hover {
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box-shadow: 0 6px 16px rgba(0,0,0,0.45);
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}
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/* Pill icon */
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.pill-icon {
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height: 14px;
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width: 14px;
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object-fit: contain;
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vertical-align: middle;
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margin-right: 4px;
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border-radius: 2px;
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display: inline-block;
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position: relative;
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top: -1px;
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}
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/* Hero dark mode overrides */
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html.dark .hero-tagline { color: #9ca3af !important; }
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html.dark .hero-arrow { color: #4b5563 !important; }
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html.dark .hero-stage-label { color: #6b7280 !important; }
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html.dark .hero-pill-neutral { background: #1f2937 !important; border-color: #374151 !important; color: #d1d5db !important; }
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html.dark .hero-pill-purple { background: #2e1065 !important; border-color: #4c1d95 !important; color: #c4b5fd !important; }
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html.dark .hero-pill-blue { background: #1e3a5f !important; border-color: #1e40af !important; color: #93c5fd !important; }
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html.dark .hero-pill-green { background: #052e16 !important; border-color: #166534 !important; color: #86efac !important; }
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html.dark .hero-btn-primary { background: #3b82f6 !important; }
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html.dark .hero-btn-outline { border-color: #374151 !important; color: #d1d5db !important; }
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html.dark .hero-secondary-link { color: #6b7280 !important; border-bottom-color: #374151 !important; }

‎config/_default/hugo.toml‎

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baseURL = "https://cytomining.github.io/"
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locale = "en"
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title = "Cytomining"
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theme = "congo"
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enableRobotsTXT = true
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paginate = 10
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[markup]
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[markup.goldmark]
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[markup.goldmark.renderer]
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unsafe = true

‎config/_default/languages.en.toml‎

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label = "English"
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weight = 1
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title = "Cytomining"
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[params]
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description = "Essential tools, workflows, and best practices for single-cell image-based profiling."
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[params.author]
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name = "Cytomining"

‎config/_default/menus.en.toml‎

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[[main]]
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name = "Tools"
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pageRef = "tools"
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weight = 10
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[[main]]
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name = "Experimental tools"
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pageRef = "experimental"
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weight = 20
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[[main]]
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name = "Media"
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pageRef = "media"
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weight = 30
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[[main]]
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name = "About"
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pageRef = "about"
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weight = 40
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[[main]]
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name = "History"
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pageRef = "history"
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weight = 50
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[[main]]
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name = "Contact"
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pageRef = "contact"
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weight = 60

‎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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enableCodeCopy = false
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[homepage]
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layout = "background"
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showRecent = false
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[header]
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layout = "fixed"
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[footer]
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showCopyright = true
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showThemeAttribution = false
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showAppearanceSwitcher = true
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showScrollToTop = true
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[article]
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showDate = false
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showAuthor = false
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showReadingTime = false
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showTableOfContents = true
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showRelatedContent = false
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showEdit = false
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[list]
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showCards = true
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groupByYear = false
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cardView = true
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showSummary = true

‎content/_index.md‎

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---
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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>

‎content/about/_index.md‎

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---
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title: "About"
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description: "About the Cytomining ecosystem and community."
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---
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Cytomining is an open-source software ecosystem that maintains essential tools, workflows, and best practices for single-cell image-based profiling and microscopy data analysis research.
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We are proud members of the [CytoData](https://www.cytodata.org/) scientific community.

‎content/contact/_index.md‎

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---
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title: "Contact"
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description: "Get in touch with the Cytomining community."
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---
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- 💬 Join the conversation on our [Discourse forums](https://forum.image.sc/)
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- 📫 Subscribe to the [CytoData mailing list](https://www.cytodata.org/contact/)
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- 🐛 Report issues on [GitHub](https://github.com/cytomining)

‎content/experimental/_index.md‎

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---
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title: "Experimental"
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description: "Next-generation tools under active development in the WayScience organization."
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---
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The following tools are under active development in the [WayScience](https://github.com/WayScience) organization and represent the next generation of the Cytomining ecosystem.

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