cytomining · gwaybio · May 15, 2026 · May 15, 2026
diff --git a/docs/.nojekyll → .hugo_build.lock b/docs/.nojekyll → .hugo_build.lock
diff --git a/assets/css/custom.css b/assets/css/custom.css
@@ -0,0 +1,114 @@
+/* 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
+   to this toggle, so we handle switching with CSS classes instead. */
+.logo-light {
+  display: block;
+  max-width: 100%;
+  height: auto;
+}
+.logo-dark {
+  display: none;
+  max-width: 100%;
+  height: auto;
+}
+html.dark .logo-light {
+  display: none;
+}
+html.dark .logo-dark {
+  display: block;
+}
+
+/* Experimental page — v2 callout and problem cards */
+html.dark .v2-callout {
+  background: #1e3a5f !important;
+  border-color: #3b82f6 !important;
+}
+html.dark .v2-callout p { color: #93c5fd !important; }
+html.dark .v2-callout strong { color: #bfdbfe !important; }
+html.dark .problem-card {
+  background: #1f2937 !important;
+  border-color: #374151 !important;
+}
+html.dark .problem-card p { color: #9ca3af !important; }
+html.dark .problem-card strong { color: #d1d5db !important; }
+html.dark .v2-pipeline-step-neutral {
+  background: #1f2937 !important;
+  border-color: #374151 !important;
+  color: #d1d5db !important;
+}
+html.dark .v2-pipeline-step-purple {
+  background: #2e1065 !important;
+  border-color: #4c1d95 !important;
+  color: #c4b5fd !important;
+}
+html.dark .v2-pipeline-step-blue {
+  background: #1e3a5f !important;
+  border-color: #1e40af !important;
+  color: #93c5fd !important;
+}
+html.dark .v2-pipeline-step-yellow {
+  background: #422006 !important;
+  border-color: #854d0e !important;
+  color: #fde68a !important;
+}
+html.dark .v2-pipeline-step-green {
+  background: #052e16 !important;
+  border-color: #166534 !important;
+  color: #86efac !important;
+}
+
+/* Hero entrance animations */
+@keyframes fadeUp {
+  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; }
+
+/* List view logos */
+.list-logo-light { display: block; }
+.list-logo-dark  { display: none; }
+html.dark .list-logo-light { display: none !important; }
+html.dark .list-logo-dark  { display: block !important; }
+
+/* Pipeline step hover bounce (spring easing gives natural overshoot) */
+.pipeline-step {
+  transition: transform 0.25s cubic-bezier(0.34, 1.56, 0.64, 1), box-shadow 0.2s ease;
+}
+.pipeline-step:hover {
+  transform: translateY(-4px) scale(1.04);
+  box-shadow: 0 6px 16px rgba(0,0,0,0.13);
+}
+html.dark .pipeline-step:hover {
+  box-shadow: 0 6px 16px rgba(0,0,0,0.45);
+}
+
+/* Pill icon */
+.pill-icon {
+  height: 14px;
+  width: 14px;
+  object-fit: contain;
+  vertical-align: middle;
+  margin-right: 4px;
+  border-radius: 2px;
+  display: inline-block;
+  position: relative;
+  top: -1px;
+}
+
+/* Hero dark mode overrides */
+html.dark .hero-tagline     { color: #9ca3af !important; }
+html.dark .hero-arrow       { color: #4b5563 !important; }
+html.dark .hero-stage-label { color: #6b7280 !important; }
+
+html.dark .hero-pill-neutral { background: #1f2937 !important; border-color: #374151 !important; color: #d1d5db !important; }
+html.dark .hero-pill-purple  { background: #2e1065 !important; border-color: #4c1d95 !important; color: #c4b5fd !important; }
+html.dark .hero-pill-blue    { background: #1e3a5f !important; border-color: #1e40af !important; color: #93c5fd !important; }
+html.dark .hero-pill-green   { background: #052e16 !important; border-color: #166534 !important; color: #86efac !important; }
+html.dark .hero-btn-primary  { background: #3b82f6 !important; }
+html.dark .hero-btn-outline  { border-color: #374151 !important; color: #d1d5db !important; }
+html.dark .hero-secondary-link { color: #6b7280 !important; border-bottom-color: #374151 !important; }
diff --git a/config/_default/hugo.toml b/config/_default/hugo.toml
@@ -0,0 +1,12 @@
+baseURL = "https://cytomining.github.io/"
+locale = "en"
+title = "Cytomining"
+theme = "congo"
+
+enableRobotsTXT = true
+paginate = 10
+
+[markup]
+  [markup.goldmark]
+    [markup.goldmark.renderer]
+      unsafe = true
diff --git a/config/_default/languages.en.toml b/config/_default/languages.en.toml
@@ -0,0 +1,9 @@
+label = "English"
+weight = 1
+title = "Cytomining"
+
+[params]
+  description = "Essential tools, workflows, and best practices for single-cell image-based profiling."
+
+[params.author]
+  name = "Cytomining"
diff --git a/config/_default/menus.en.toml b/config/_default/menus.en.toml
@@ -0,0 +1,29 @@
+[[main]]
+  name = "Tools"
+  pageRef = "tools"
+  weight = 10
+
+[[main]]
+  name = "Experimental tools"
+  pageRef = "experimental"
+  weight = 20
+
+[[main]]
+  name = "Media"
+  pageRef = "media"
+  weight = 30
+
+[[main]]
+  name = "About"
+  pageRef = "about"
+  weight = 40
+
+[[main]]
+  name = "History"
+  pageRef = "history"
+  weight = 50
+
+[[main]]
+  name = "Contact"
+  pageRef = "contact"
+  weight = 60
diff --git a/config/_default/params.toml b/config/_default/params.toml
@@ -0,0 +1,32 @@
+colorScheme = "ocean"
+defaultAppearance = "light"
+autoSwitchAppearance = true
+enableSearch = true
+enableCodeCopy = false
+
+[homepage]
+  layout = "background"
+  showRecent = false
+
+[header]
+  layout = "fixed"
+
+[footer]
+  showCopyright = true
+  showThemeAttribution = false
+  showAppearanceSwitcher = true
+  showScrollToTop = true
+
+[article]
+  showDate = false
+  showAuthor = false
+  showReadingTime = false
+  showTableOfContents = true
+  showRelatedContent = false
+  showEdit = false
+
+[list]
+  showCards = true
+  groupByYear = false
+  cardView = true
+  showSummary = true
diff --git a/content/_index.md b/content/_index.md
@@ -0,0 +1,91 @@
+---
+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/content/about/_index.md b/content/about/_index.md
@@ -0,0 +1,7 @@
+---
+title: "About"
+description: "About the Cytomining ecosystem and community."
+---
+
+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.
+We are proud members of the [CytoData](https://www.cytodata.org/) scientific community.
diff --git a/content/contact/_index.md b/content/contact/_index.md
@@ -0,0 +1,8 @@
+---
+title: "Contact"
+description: "Get in touch with the Cytomining community."
+---
+
+- 💬 Join the conversation on our [Discourse forums](https://forum.image.sc/)
+- 📫 Subscribe to the [CytoData mailing list](https://www.cytodata.org/contact/)
+- 🐛 Report issues on [GitHub](https://github.com/cytomining)
diff --git a/content/experimental/_index.md b/content/experimental/_index.md
@@ -0,0 +1,6 @@
+---
+title: "Experimental"
+description: "Next-generation tools under active development in the WayScience organization."
+---
+
+The following tools are under active development in the [WayScience](https://github.com/WayScience) organization and represent the next generation of the Cytomining ecosystem.
diff --git a/content/experimental/buscar.md b/content/experimental/buscar.md
@@ -0,0 +1,23 @@
+---
+title: "buscar"
+description: "Hit calling — identifies biologically active perturbations from single-cell morphological profiles using distribution-level scoring."
+showDate: false
+showAuthor: false
+logoUrl: "https://raw.githubusercontent.com/WayScience/buscar/main/logo/just-icon.png"
+---
+
+<img class="logo-light" src="https://raw.githubusercontent.com/WayScience/buscar/main/logo/with-text-for-light-bg.png" alt="buscar logo" width="400">
+<img class="logo-dark" src="https://raw.githubusercontent.com/WayScience/buscar/main/logo/with-text-for-dark-bg.png" alt="buscar logo" width="400">
+
+buscar is a Python package for reproducible hit calling in high-content screening.
+Rather than averaging cells into population-level summaries, it operates on individual cell distributions to preserve biological heterogeneity and identify perturbations with on-target morphological signatures.
+
+**Key capabilities:**
+
+- Define on-target and off-target morphology signatures from reference profiles
+- Score perturbation efficacy via Earth Mover's Distance
+- Assess specificity with off-target scoring to reduce false positives
+- Preserve single-cell heterogeneity throughout hit calling
+- Integrates directly with pycytominer, coSMicQC, and CytoTable workflows
+
+**[View on GitHub →](https://github.com/WayScience/buscar)**
diff --git a/content/experimental/iceberg-bioimage.md b/content/experimental/iceberg-bioimage.md
@@ -0,0 +1,22 @@
+---
+title: "iceberg-bioimage"
+description: "Data cataloging — scans bioimaging stores and publishes image metadata to Cytomining-compatible Parquet warehouses via Apache Iceberg."
+showDate: false
+showAuthor: false
+logoUrl: "https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/docs/src/_static/iceberg-bioimage-logo.png"
+---
+
+<img src="https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/docs/src/_static/iceberg-bioimage-logo.png" alt="iceberg-bioimage logo" width="400">
+
+iceberg-bioimage is a Python package that catalogs bioimaging data using Apache Iceberg.
+It scans image stores across formats, publishes structured metadata tables, and exports layouts compatible with the Cytomining profiling ecosystem — bridging raw image archives and downstream analysis pipelines.
+
+**Key capabilities:**
+
+- Scan image stores into canonical `ScanResult` objects
+- Publish image metadata with PyIceberg for versioned, queryable catalogs
+- Export Cytomining-compatible Parquet warehouses for profiling workflows
+- Validate profile tables against microscopy join contracts
+- Supports Zarr, OME-TIFF, and Parquet source formats
+
+**[View documentation →](https://wayscience.github.io/iceberg-bioimage/)**
diff --git a/content/experimental/ome-arrow.md b/content/experimental/ome-arrow.md
@@ -0,0 +1,22 @@
+---
+title: "OME-arrow"
+description: "Image storage — stores microscopy images alongside metadata and derived data in a unified, queryable Apache Arrow format."
+showDate: false
+showAuthor: false
+logoUrl: "https://raw.githubusercontent.com/WayScience/OME-arrow/main/docs/src/_static/ome-arrow-logo.png"
+---
+
+<img src="https://raw.githubusercontent.com/WayScience/OME-arrow/main/docs/src/_static/ome-arrow-logo.png" alt="OME-arrow logo" width="400">
+
+OME-arrow brings Open Microscopy Environment (OME) specifications to Apache Arrow, enabling microscopy images to be stored directly in data tables alongside their metadata and derived features as multilayer structs.
+This makes bioimaging data fast to query, easy to share, and compatible with modern tensor-based ML workflows.
+
+**Key capabilities:**
+
+- Store images, metadata, and derived features together in a single table
+- Support for TIFF, OME-Zarr, NumPy, and Parquet source formats
+- Lazy reading and region-of-interest (ROI) access for large datasets
+- Tensor-focused output compatible with PyTorch, JAX, and DLPack
+- Visualization integrations for matplotlib, PyVista, and Napari
+
+**[View documentation →](https://wayscience.github.io/ome-arrow/)**