cytomining · gwaybio · May 15, 2026 · May 15, 2026 · May 15, 2026 · May 15, 2026
diff --git a/.gitignore b/.gitignore
@@ -158,3 +158,7 @@ cython_debug/
 #  and can be added to the global gitignore or merged into this file.  For a more nuclear
 #  option (not recommended) you can uncomment the following to ignore the entire idea folder.
 #.idea/
+
+# Hugo build output
+public/
+resources/_gen/
diff --git a/assets/css/custom.css b/assets/css/custom.css
@@ -1,3 +1,19 @@
+/* Page entrance animation — single pages use <article>, list/section pages use <header>+<section> */
+#main-content > article {
+  animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.1s both;
+}
+#main-content > header {
+  animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.1s both;
+}
+#main-content > section {
+  animation: fadeUp 0.6s cubic-bezier(0.22,1,0.36,1) 0.25s both;
+}
+
+/* Global font size reduction */
+html {
+  font-size: 90%;
+}
+
 /* Logo dark/light switching.
    Congo toggles a .dark class on <html> via JS — the native
    prefers-color-scheme media query inside <picture> tags does not respond
@@ -63,11 +79,14 @@ html.dark .v2-pipeline-step-green {
   from { opacity: 0; transform: translateY(28px); }
   to   { opacity: 1; transform: translateY(0); }
 }
-.hero-fade-1 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.15s both; }
-.hero-fade-2 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.30s both; }
-.hero-fade-3 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.45s both; }
-.hero-fade-4 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.60s both; }
-.hero-fade-5 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.75s both; }
+.hero-fade-1 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.10s both; }
+.hero-fade-2 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.22s both; }
+.hero-fade-3 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.34s both; }
+.hero-fade-4 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.46s both; }
+.hero-fade-5 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.58s both; }
+.hero-fade-6 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.70s both; }
+.hero-fade-7 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.82s both; }
+.hero-fade-8 { animation: fadeUp 0.7s cubic-bezier(0.22,1,0.36,1) 0.94s both; }
 
 /* List view logos */
 .list-logo-light { display: block; }

diff --git a/config/_default/params.toml b/config/_default/params.toml
@@ -1,7 +1,7 @@
 colorScheme = "ocean"
 defaultAppearance = "light"
 autoSwitchAppearance = true
-enableSearch = true
+enableSearch = false
 enableCodeCopy = false
 
 [homepage]

diff --git a/content/_index.md b/content/_index.md
@@ -2,90 +2,3 @@
 title: "Cytomining"
 description: "Open-source tools for single-cell image-based profiling"
 ---
-
-<div class="not-prose" style="text-align: center; padding: 3rem 0 2rem;">
-
-  <!-- Logo -->
-  <div class="hero-fade-1" style="margin-bottom: 1.5rem;">
-    <img
-      src="https://avatars.githubusercontent.com/u/19327357?v=4"
-      alt="Cytomining"
-      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);"
-    >
-    <h1 style="font-size: 2.5rem; font-weight: 800; letter-spacing: -0.02em; margin: 0;">Cytomining</h1>
-  </div>
-
-  <!-- Tagline -->
-  <div class="hero-fade-2" style="margin-bottom: 2.5rem;">
-    <p style="font-size: 1.2rem; color: #6b7280; max-width: 540px; margin: 0 auto; line-height: 1.6;">
-      Open-source tools for every stage of the<br>single-cell image-based profiling workflow.
-    </p>
-  </div>
-
-  <!-- Pipeline visualization -->
-  <div class="hero-fade-3" style="margin-bottom: 2.5rem; overflow-x: auto; padding: 0.5rem 0;">
-    <div style="display: inline-flex; align-items: center; gap: 0.4rem; flex-wrap: wrap; justify-content: center; padding: 0 1rem;">
-
-      <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;">
-        🔬 Raw Images
-      </div>
-
-      <span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
-
-      <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;">
-        iceberg-bioimage
-      </a>
-
-      <span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
-
-      <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;">
-        CytoTable
-      </a>
-
-      <span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
-
-      <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;">
-        coSMicQC
-      </a>
-
-      <span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
-
-      <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;">
-        pycytominer
-      </a>
-
-      <span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">→</span>
-
-      <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;">
-        copairs
-      </a>
-
-      <span style="color: #9ca3af; font-size: 1.1rem; font-weight: 300;">/</span>
-
-      <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;">
-        buscar
-      </a>
-
-    </div>
-    <p style="font-size: 0.72rem; color: #9ca3af; margin-top: 0.75rem;">ingest &nbsp;·&nbsp; quality control &nbsp;·&nbsp; process &nbsp;·&nbsp; evaluate</p>
-  </div>
-
-  <!-- CTA -->
-  <div class="hero-fade-4" style="margin-bottom: 2.5rem; display: flex; gap: 0.75rem; justify-content: center; flex-wrap: wrap;">
-    <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;">
-      Explore tools →
-    </a>
-    <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;">
-      Profiling handbook
-    </a>
-  </div>
-
-  <!-- Community + get started links -->
-  <div class="hero-fade-5" style="font-size: 0.85rem; color: #6b7280; display: flex; gap: 1.25rem; justify-content: center; flex-wrap: wrap;">
-    <a href="https://github.com/cytomining/profiling-recipe" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">Profiling recipe</a>
-    <a href="https://forum.image.sc/" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">image.sc forum</a>
-    <a href="https://github.com/orgs/cytomining/people" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">Contributors</a>
-    <a href="https://www.cytodata.org/" target="_blank" style="color: #6b7280; text-decoration: none; border-bottom: 1px dashed #d1d5db;">CytoData community</a>
-  </div>
-
-</div>
diff --git a/layouts/_partials/article-link.html b/layouts/_partials/article-link.html
@@ -31,11 +31,11 @@
     </div>
   {{- end }}
   <div>
-    {{/* Small icon above title */}}
-    {{ with .Params.logoUrl }}
-      <img src="{{ . }}" alt="{{ $.Title }} icon" style="height: 28px; width: 28px; object-fit: contain; display: block; margin-bottom: 0.4rem; border-radius: 4px;">
-    {{ end }}
     <h3 class="flex items-center text-xl font-semibold">
+      {{/* Inline icon before title */}}
+      {{ with .Params.logoUrl }}
+        <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;">
+      {{ end }}
       {{ with .Params.externalUrl }}
         <div>
           <a