Tighten website content and add details on org structures (#16)

* minor fixes to tighten

* remove old file

* add view on github

* respond to comments and pass check

* fix link check

* setup hugo first

Author: gwaybio

.github/workflows/link-check.yaml

@@ -11,20 +11,33 @@ jobs:
     steps:
       - name: Checkout
         uses: actions/checkout@v6
+        with:
+          submodules: true
+
+      - name: Setup Hugo
+        uses: peaceiris/actions-hugo@v3
+        with:
+          hugo-version: latest
+          extended: true
+
+      - name: Build site
+        run: hugo --minify
 
       - name: Check links with lychee
         uses: lycheeverse/lychee-action@v2
         with:
-          # Check all Markdown files in content/ and the root-level docs
+          # Check all Markdown files; --root-dir resolves root-relative links against built site
           args: >-
             --verbose
             --no-progress
+            --root-dir ./public
             --exclude-path node_modules
             --exclude "^https://forum\\.image\\.sc/"
             --exclude "^https://www\\.broadinstitute\\.org/"
             --exclude "^https://www\\.eu-openscreen\\.eu/"
             --exclude "^https://doi\\.org/"
             --exclude "^https://gohugo\\.io/installation/"
+            --exclude "^https://sbi2\\.org/"
             'content/**/*.md'
             '*.md'
           fail: true

assets/css/custom.css

@@ -138,6 +138,39 @@ 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; }
 
+/* Inline code: remove Congo's visible backtick pseudo-elements, style like standard markdown */
+.prose :where(code):not(:where([class~="not-prose"],[class~="not-prose"] *))::before,
+.prose :where(code):not(:where([class~="not-prose"],[class~="not-prose"] *))::after {
+  content: "" !important;
+}
+.prose :where(code):not(:where(pre *, [class~="not-prose"], [class~="not-prose"] *)) {
+  background: #f3f4f6;
+  color: #374151;
+  padding: 0.15em 0.4em;
+  border-radius: 3px;
+  font-weight: 400;
+  font-size: 0.875em;
+}
+html.dark .prose :where(code):not(:where(pre *, [class~="not-prose"], [class~="not-prose"] *)) {
+  background: #374151;
+  color: #e5e7eb;
+}
+
+/* Publication card dark mode */
+html.dark .publication-card {
+  background: #1f2937 !important;
+  border-color: #374151 !important;
+}
+html.dark .publication-card p[style*="color: #374151"] {
+  color: #e5e7eb !important;
+}
+html.dark .publication-card p[style*="color: #6b7280"] {
+  color: #9ca3af !important;
+}
+html.dark .publication-card a {
+  color: #93c5fd !important;
+}
+
 /* Header breakpoint override:
    Use hamburger menu up to 900px (instead of Congo's default 640px). */
 @media (max-width: 900px) {

content/about/_index.md

@@ -7,29 +7,29 @@ showAuthor: false
 
 Cytomining is an open-source software ecosystem for single-cell image-based profiling — the practice of measuring thousands of cell morphology features from microscopy images to understand how cells respond to genetic, chemical, or environmental perturbations.
 
-Core tools are maintained under the [cytomining GitHub organization](https://github.com/cytomining) by [contributors](https://github.com/orgs/cytomining/people) from the [Way Lab](https://www.waysciencelab.com/) at the University of Colorado Anschutz Medical Campus and beyond.
+Core tools are maintained under the [Cytomining GitHub organization](https://github.com/cytomining) by [contributors](https://github.com/orgs/cytomining/people) from the [Way Lab](https://www.waysciencelab.com/) at the University of Colorado Anschutz Medical Campus and beyond.
 Experimental and emerging tools are developed under the [WayScience GitHub organization](https://github.com/WayScience) before graduating into the core ecosystem.
 
 ## Impact
 
 Cytomining tools have been adopted across academia and industry for large-scale drug discovery and functional genomics.
-`Pycytominer` underpins some of the largest publicly available image-based profiling datasets, including the [JUMP Cell Painting dataset](https://jump-cellpainting.broadinstitute.org/) (over 136,000 chemical and genetic perturbations profiled across 12 partner sites) the [LINCS Drug Repurposing](https://github.com/broadinstitute/lincs-cell-painting) Cell Painting dataset, and the [EU-OPENSCREEN](https://www.eu-openscreen.eu/) Bioactive Compound Set profiled across multiple imaging sites.
+[`Pycytominer`](/tools/pycytominer/) underpins some of the largest publicly available image-based profiling datasets, including the [JUMP Cell Painting dataset](https://jump-cellpainting.broadinstitute.org/) (over 136,000 chemical and genetic perturbations profiled across 12 partner sites) the [LINCS Drug Repurposing](https://github.com/broadinstitute/lincs-cell-painting) Cell Painting dataset, and the [EU-OPENSCREEN](https://www.eu-openscreen.eu/) Bioactive Compound Set profiled across multiple imaging sites.
 It has also processed many of the 31+ datasets in the [Cell Painting Gallery](https://broadinstitute.github.io/cellpainting-gallery/).
 
 The foundational [Caicedo et al. 2017](https://doi.org/10.1038/nmeth.4397) review has accumulated over 670 citations, and individual tool papers have together been cited more than 150 times since 2024.
 Packages are downloaded thousands of times per month via [PyPI] download statistics (https://pypistats.org/).
 
 ## History
 
-The ecosystem traces its roots to the [Imaging Platform](https://www.broadinstitute.org/imaging) at the Broad Institute, where early contributors including Anne Carpenter, Shantanu Singh, Allen Goodman, and others developed `cytominer`, an R package for processing high-content imaging data.
+The ecosystem traces its roots to the [Imaging Platform](https://www.broadinstitute.org/imaging) at the Broad Institute, where early contributors including Anne Carpenter, Shantanu Singh, Allen Goodman, and others developed [`cytominer`](https://github.com/cytomining/cytominer), an R package for processing high-content imaging data.
 
 In 2016, members of this community co-founded the [CytoData Society](https://www.cytodata.org/) to unite researchers across academia and industry around image-based profiling.
 The following year, the team contributed the landmark [Caicedo et al. 2017](https://doi.org/10.1038/nmeth.4397) review in _Nature Methods_ that established the field's foundational analysis standards.
 
-Since 2021, the [Way Lab](https://www.waysciencelab.com/) has driven a major expansion of the ecosystem — migrating from R to Python with `Pycytominer` and building a modern infrastructure stack including `CytoTable` and `coSMicQC`.
+Since 2021, the [Way Lab](https://www.waysciencelab.com/) has driven a major expansion of the ecosystem — migrating from R to Python with [`Pycytominer`](/tools/pycytominer/) and building a modern infrastructure stack including [`CytoTable`](/tools/cytotable/), [`coSMicQC`](/tools/cosmicqc/), and others.
 In 2026, members of the CytoData community published an updated review, [Serrano et al.](https://doi.org/10.1038/s44320-026-00197-7) in _Molecular Systems Biology_, surveying progress and new challenges in image-based profiling.
 Today, Cytomining tools are used by research groups worldwide for drug discovery, functional genomics, and cell biology.
 
-## Community
+## Communities
 
-We are proud members of the [CytoData](https://www.cytodata.org/) community, which hosts an annual symposium bringing together researchers and developers working on image-based profiling.
+We are proud members of the [CytoData Society](https://www.cytodata.org/) and [The Society of Biomolecular Imaging and Informatics](https://sbi2.org/), which hosts an annual symposium bringing together researchers and developers working on image-based profiling.

content/contact/_index.md

@@ -3,6 +3,8 @@ title: Contact
 description: Get in touch with the Cytomining community.
 ---
 
-- 💬 Join the conversation on our [Discourse forums](https://forum.image.sc/)
+- 🎮 Join us on [Discord](https://discord.gg/dgEDz6xzfJ)
+- 💬 Ask a question at [image.sc](https://forum.image.sc/)
 - 📫 Subscribe to the [CytoData mailing list](https://www.cytodata.org/contact/)
+- 🔬 Join the [SBI2 community](https://sbi2.org/)
 - 🐛 Report issues on [GitHub](https://github.com/cytomining)

content/experimental/buscar.md

@@ -8,11 +8,14 @@ logoUrl: "https://raw.githubusercontent.com/WayScience/buscar/main/logo/just-ico
 githubRepo: "WayScience/buscar"
 ---
 
+<a href="https://github.com/WayScience/buscar" target="_blank" rel="external">
 <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">
+</a>
 
 {{< tool-badges >}}
 
+
 `buscar` scores perturbations directly on single-cell distributions using Earth Mover's Distance, preserving heterogeneity throughout hit calling.
 
 **Problem:** Population-level hit calling averages away biologically meaningful cell-to-cell variation, making heterogeneous responses and rare subpopulations invisible to standard metrics.
@@ -23,6 +26,6 @@ githubRepo: "WayScience/buscar"
 - 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
+- Integrates directly with [`Pycytominer`](/tools/pycytominer/), [`coSMicQC`](/tools/cosmicqc/), and [`CytoTable`](/tools/cytotable/) workflows
 
 **[View on GitHub →](https://github.com/WayScience/buscar)**

content/experimental/iceberg-bioimage.md

@@ -8,10 +8,13 @@ logoUrl: "https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/doc
 githubRepo: "WayScience/iceberg-bioimage"
 ---
 
+<a href="https://github.com/WayScience/iceberg-bioimage" target="_blank" rel="external">
 <img src="https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/docs/src/_static/iceberg-bioimage-logo.png" alt="iceberg-bioimage logo" width="400">
+</a>
 
 {{< tool-badges >}}
 
+
 `iceberg-bioimage` scans any image store into a versioned Apache Iceberg catalog that directly exports Cytomining-compatible Parquet warehouses.
 
 **Problem:** Raw bioimaging archives have no standard catalog — finding, versioning, and joining images to downstream data requires bespoke scripts per lab.

content/experimental/ome-arrow.md

@@ -8,10 +8,13 @@ logoUrl: "https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_
 githubRepo: "WayScience/OME-arrow"
 ---
 
+<a href="https://github.com/WayScience/OME-arrow" target="_blank" rel="external">
 <img src="https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/ome-arrow-with-text.png?raw=true" alt="OME-arrow logo" width="400">
+</a>
 
 {{< tool-badges >}}
 
+
 `OME-arrow` embeds images as first-class columns in Apache Arrow tables, so features, metadata, and pixel data travel together and can be queried or exported as tensors.
 
 **Problem:** Images and feature tables live in separate systems — linking a numeric outlier back to its source cell requires error-prone manual joins across formats.

content/experimental/zedprofiler.md

@@ -8,11 +8,14 @@ logoUrl: "https://raw.githubusercontent.com/WayScience/ZedProfiler/main/logo/log
 githubRepo: "WayScience/zedprofiler"
 ---
 
+<a href="https://github.com/WayScience/ZedProfiler" target="_blank" rel="external">
 <img class="logo-light" src="https://raw.githubusercontent.com/WayScience/ZedProfiler/main/logo/with-text-for-light-bg.png" alt="ZEDprofiler logo" width="400">
 <img class="logo-dark" src="https://raw.githubusercontent.com/WayScience/ZedProfiler/main/logo/with-text-for-dark-bg.png" alt="ZEDprofiler logo" width="400">
+</a>
 
 {{< tool-badges >}}
 
+
 `ZEDprofiler` extracts morphological features directly from 3D volumetric images, including anisotropic voxel spacing correction — no GPU required.
 
 **Problem:** Classical profiling tools extract only 2D features, leaving organoid, cleared-tissue, and z-stack experiments without a CPU-efficient extractor.

content/media/_index.md

@@ -42,24 +42,24 @@ showAuthor: false
 
 #### Peer-reviewed
 
-- **CytoTable ([tool page](https://cytomining.github.io/tools/cytotable/)):** Bunten, D. et al. Scalable data harmonization for single-cell image-based profiling with CytoTable.
+- **CytoTable ([tool page](https://cytomining.github.io/tools/cytotable/) · [GitHub](https://github.com/cytomining/CytoTable)):** Bunten, D. et al. Scalable data harmonization for single-cell image-based profiling with CytoTable.
   *Patterns* **7**, 101514 (2026).
   [doi:10.1016/j.patter.2026.101514](https://doi.org/10.1016/j.patter.2026.101514)
-- **Pycytominer ([tool page](https://cytomining.github.io/tools/pycytominer/)):** Serrano, E. et al. Reproducible image-based profiling with Pycytominer.
+- **Pycytominer ([tool page](https://cytomining.github.io/tools/pycytominer/) · [GitHub](https://github.com/cytomining/pycytominer)):** Serrano, E. et al. Reproducible image-based profiling with Pycytominer.
   *Nat. Methods* **22**, 677–680 (2025).
   [doi:10.1038/s41592-025-02611-8](https://doi.org/10.1038/s41592-025-02611-8)
-- **copairs ([tool page](https://cytomining.github.io/tools/copairs/)):** Kalinin, A.A. et al. A versatile information retrieval framework for evaluating profile strength and similarity.
+- **copairs ([tool page](https://cytomining.github.io/tools/copairs/) · [GitHub](https://github.com/cytomining/copairs)):** Kalinin, A.A. et al. A versatile information retrieval framework for evaluating profile strength and similarity.
   *Nat. Commun.* **16**, 5181 (2025).
   [doi:10.1038/s41467-025-60306-2](https://doi.org/10.1038/s41467-025-60306-2)
-- **DeepProfiler ([tool page](https://cytomining.github.io/tools/deepprofiler/)):** Moshkov, N. et al. Learning representations for image-based profiling of perturbations.
+- **DeepProfiler ([tool page](https://cytomining.github.io/tools/deepprofiler/) · [GitHub](https://github.com/cytomining/DeepProfiler)):** Moshkov, N. et al. Learning representations for image-based profiling of perturbations.
   *Nat. Commun.* **15**, 1594 (2024).
   [doi:10.1038/s41467-024-45999-1](https://doi.org/10.1038/s41467-024-45999-1)
 
 #### Preprints
 
-- **buscar ([tool page](https://cytomining.github.io/experimental/buscar/)):** Serrano, E., Li, W.S. & Way, G.P. Single-cell hit calling in high-content imaging screens with Buscar.
+- **buscar ([tool page](https://cytomining.github.io/experimental/buscar/) · [GitHub](https://github.com/WayScience/buscar)):** Serrano, E., Li, W.S. & Way, G.P. Single-cell hit calling in high-content imaging screens with Buscar.
   *bioRxiv* (2026).
   [doi:10.64898/2026.04.15.718737](https://doi.org/10.64898/2026.04.15.718737)
-- **coSMicQC ([tool page](https://cytomining.github.io/tools/cosmicqc/)):** Tomkinson, J. et al. Stellar quality control for single-cell image-based profiling with coSMicQC.
+- **coSMicQC ([tool page](https://cytomining.github.io/tools/cosmicqc/) · [GitHub](https://github.com/cytomining/coSMicQC)):** Tomkinson, J. et al. Stellar quality control for single-cell image-based profiling with coSMicQC.
   *bioRxiv* (2025).
   [doi:10.1101/2025.10.14.682427](https://doi.org/10.1101/2025.10.14.682427)

content/people/_index.md

@@ -19,9 +19,9 @@ We welcome issues, bug reports, documentation improvements, and pull requests fr
 ## Governance
 
 Cytomining uses a lightweight governance model centered on maintainers and public decision-making.
-We keep policy concise and bias toward transparent, repository-native workflows over heavy process.
+We keep policy concise and transparent.
 
-- **Stewardship:** Repositories are maintained by designated maintainers in the `Cytomining` organization.
+- **Stewardship:** Repositories are maintained by designated maintainers in the [`Cytomining`](https://github.com/cytomining) organization.
 - **Decision-making:** Day-to-day technical decisions happen in public issues, pull requests, and our public [Discord](https://discord.gg/dgEDz6xzfJ).
 - **Consensus first:** Maintainers seek rough consensus from active contributors before merging impactful changes.
 - **Escalation path:** When consensus is unclear, maintainers make a final call, document rationale, and revisit with new evidence.
@@ -31,6 +31,31 @@ We keep policy concise and bias toward transparent, repository-native workflows
 
 This reflects how the organization operates today and is intentionally compact so contributors can understand how decisions get made without navigating a large policy surface.
 
+### Organizational structure
+
+The Cytomining ecosystem currently spans two GitHub organizations with distinct roles.
+
+The [**cytomining**](https://github.com/cytomining) organization hosts production-ready tools that have reached stable APIs, published documentation, test coverage, and community adoption.
+Tools here are maintained collaboratively by contributors from the [Way Lab](https://www.waysciencelab.com/) at the University of Colorado Anschutz and the broader image-based profiling community.
+
+The [**WayScience**](https://github.com/WayScience) organization serves as an incubator for next-generation tools under active development.
+It is the primary home for roadmap work: tools here are experimental, may have unstable APIs, and have not yet graduated into [`Cytomining`](https://github.com/cytomining).
+
+The two organizations are complementary.
+[`WayScience`](https://github.com/WayScience) is where new ideas are prototyped and validated; [`Cytomining`](https://github.com/cytomining) is where they become community infrastructure.
+Core production tools ([`Pycytominer`](/tools/pycytominer/), [`CytoTable`](/tools/cytotable/), [`coSMicQC`](/tools/cosmicqc/), [`copairs`](/tools/copairs/), [`DeepProfiler`](/tools/deepprofiler/), [`CytoDataFrame`](/tools/cytodataframe/)) live in [`Cytomining`](https://github.com/cytomining).
+Roadmap tools ([`buscar`](/experimental/buscar/), [`OME-arrow`](/experimental/ome-arrow/), [`iceberg-bioimage`](/experimental/iceberg-bioimage/), [`ZEDprofiler`](/experimental/zedprofiler/)) live in [`WayScience`](https://github.com/WayScience) until they are ready to graduate.
+
+### Graduation process
+
+A tool is considered ready to migrate from [`WayScience`](https://github.com/WayScience) (or any other repository from other organizations) into [`Cytomining`](https://github.com/cytomining) when it meets the following criteria:
+
+- **Within scope** — the tool must be purpose-built for scientists who perform image-based profiling.
+- **Stable API** — no breaking changes anticipated in the near term; a versioned release has been tagged
+- **Documentation** — a published documentation site covering installation, usage, and API reference
+- **Test coverage** — a CI-passing test suite with meaningful coverage (>80%) of core functionality
+- **Publication or preprint** — a citable reference describing the tool's design and validation
+
 ## Code of Conduct
 
 Participation in Cytomining spaces is expected to follow the organization-wide Code of Conduct: