Add people page, focus on roadmap, and add badges for tools (#13)

d33bs · gwaybio · web-flow · commit eec4d36d48ce · 2026-05-27T09:56:53.000-06:00
* people page

* header button with mobile display

* correct gov reference

* org security link

* orient experimental tools to the roadmap by label

* add badges to tool pages

* roadmap instead of experimental links

* Update _index.md

* Apply suggestions from code review

Co-authored-by: Gregory Way &lt;gregory.way@gmail.com&gt;

---------

Co-authored-by: Gregory Way &lt;gregory.way@gmail.com&gt;
diff --git a/assets/css/custom.css b/assets/css/custom.css
@@ -14,6 +14,12 @@ html {
   font-size: 90%;
 }
 
+/* Header logo: make site mark compact in top nav */
+a.mr-2 > img {
+  max-height: 1.75rem !important;
+  max-width: 1.75rem !important;
+}
+
 /* 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
@@ -131,3 +137,15 @@ html.dark .hero-pill-green   { background: #052e16 !important; border-color: #16
 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; }
+
+/* Header breakpoint override:
+   Use hamburger menu up to 900px (instead of Congo's default 640px). */
+@media (max-width: 900px) {
+  #menu-button {
+    display: block !important;
+  }
+
+  header nav > ul.hidden.sm\:flex {
+    display: none !important;
+  }
+}
diff --git a/assets/img/cytomining-logo.png b/assets/img/cytomining-logo.png
diff --git a/config/_default/menus.en.toml b/config/_default/menus.en.toml
@@ -4,7 +4,7 @@
   weight = 10
 
 [[main]]
-  name = "Experimental tools"
+  name = "Roadmap"
   pageRef = "experimental"
   weight = 20
 
@@ -18,6 +18,11 @@
   pageRef = "about"
   weight = 40
 
+[[main]]
+  name = "People"
+  pageRef = "people"
+  weight = 50
+
 
 [[main]]
   name = "Contact"
diff --git a/config/_default/params.toml b/config/_default/params.toml
@@ -9,7 +9,8 @@ enableCodeCopy = false
   showRecent = false
 
 [header]
-  layout = "fixed"
+  layout = "hybrid"
+  logo = "img/cytomining-logo.png"
 
 [footer]
   showCopyright = true
diff --git a/content/experimental/_index.md b/content/experimental/_index.md
@@ -1,6 +1,9 @@
 ---
-title: "Experimental"
+title: "Roadmap"
 description: "Tools under active development in the WayScience organization, forming the foundation of the next Cytomining ecosystem."
+url: /roadmap/
+aliases:
+  - /experimental/
 ---
 
 The following tools are under active development in the [WayScience](https://github.com/WayScience) organization and form the backbone of the Cytomining roadmap.
diff --git a/content/experimental/buscar.md b/content/experimental/buscar.md
@@ -5,11 +5,14 @@ problem: "Population-level hit calling averages away cell-to-cell variation, hid
 showDate: false
 showAuthor: false
 logoUrl: "https://raw.githubusercontent.com/WayScience/buscar/main/logo/just-icon.png"
+githubRepo: "WayScience/buscar"
 ---
 
 <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">
 
+{{< 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.
diff --git a/content/experimental/iceberg-bioimage.md b/content/experimental/iceberg-bioimage.md
@@ -5,10 +5,13 @@ problem: "Raw bioimaging archives have no standard catalog — finding, versioni
 showDate: false
 showAuthor: false
 logoUrl: "https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/docs/src/_static/iceberg-bioimage-logo.png"
+githubRepo: "WayScience/iceberg-bioimage"
 ---
 
 <img src="https://raw.githubusercontent.com/WayScience/iceberg-bioimage/main/docs/src/_static/iceberg-bioimage-logo.png" alt="iceberg-bioimage logo" width="400">
 
+{{< 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.
diff --git a/content/experimental/ome-arrow.md b/content/experimental/ome-arrow.md
@@ -4,10 +4,13 @@ description: "Image storage — stores microscopy images alongside metadata and
 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."
 showDate: false
 showAuthor: false
-logoUrl: "https://raw.githubusercontent.com/WayScience/OME-arrow/main/docs/src/_static/ome-arrow-logo.png"
+logoUrl: "https://raw.githubusercontent.com/wayscience/ome-arrow/main/docs/src/_static/ome-arrow-with-text.png?raw=true"
+githubRepo: "WayScience/OME-arrow"
 ---
 
-<img src="https://raw.githubusercontent.com/WayScience/OME-arrow/main/docs/src/_static/ome-arrow-logo.png" alt="OME-arrow logo" width="400">
+<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">
+
+{{< 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.
 
diff --git a/content/experimental/zedprofiler.md b/content/experimental/zedprofiler.md
@@ -5,11 +5,14 @@ problem: "Classical profiling tools only extract 2D features, leaving organoid a
 showDate: false
 showAuthor: false
 logoUrl: "https://raw.githubusercontent.com/WayScience/ZedProfiler/main/logo/logo.png"
+githubRepo: "WayScience/zedprofiler"
 ---
 
 <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">
 
+{{< 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.
diff --git a/content/people/_index.md b/content/people/_index.md
@@ -0,0 +1,51 @@
+---
+title: People
+description: Contributors, governance, code of conduct, and security stance for the Cytomining community.
+showDate: false
+showAuthor: false
+layout: simple
+---
+
+The Cytomining ecosystem is maintained by a distributed community of contributors across academia and industry.
+
+## Contributors
+
+- Browse contributors and maintainers in the [Cytomining GitHub organization](https://github.com/cytomining)
+- See organization members directly in the [People directory](https://github.com/orgs/cytomining/people)
+- Explore project-level contribution history in each repository's contributors graph
+
+We welcome issues, bug reports, documentation improvements, and pull requests from the broader community.
+
+## 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.
+
+- **Stewardship:** Repositories are maintained by designated maintainers in the `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.
+- **Scope and ownership:** Changes are reviewed by maintainers closest to the affected project area, as defined by recent commits and other relevant ecosystem initiatives.
+- **Openness:** Design direction, roadmap changes, and tradeoffs are discussed in public whenever possible.
+- **Evolution:** Governance expectations are updated incrementally as the community and project complexity grow.
+
+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.
+
+## Code of Conduct
+
+Participation in Cytomining spaces is expected to follow the organization-wide Code of Conduct:
+
+- [Cytomining Organization Code of Conduct](https://github.com/cytomining/.github/blob/main/CODE_OF_CONDUCT.md)
+
+All contributors and community members are expected to uphold a respectful, inclusive, and professional environment.
+
+## Security Stance
+
+We take security seriously across our software and community operations.
+
+- [Cytomining Organization Security Policy](https://github.com/cytomining/.github/blob/main/SECURITY.md)
+- If you discover a potential vulnerability, please report it responsibly through GitHub security reporting mechanisms where available
+- Avoid opening public issues for unpatched security vulnerabilities
+- We aim to triage and respond to credible reports quickly and transparently
+
+For repository-specific security guidance, check each project's `SECURITY.md` (when present) and GitHub Security tabs.
diff --git a/content/tools/_index.md b/content/tools/_index.md
@@ -4,3 +4,5 @@ description: Production-ready tools for image-based profiling bioinformatics.
 ---
 
 The Cytomining ecosystem provides a suite of production-ready tools for every stage of the image-based profiling workflow.
+
+For upcoming capabilities and in-progress projects, see the [Roadmap](https://cytomining.github.io/experimental/), which includes our experimental tools under active development.
diff --git a/content/tools/copairs.md b/content/tools/copairs.md
@@ -3,8 +3,12 @@ title: copairs
 description: Downstream evaluation — measures how reproducibly perturbation profiles retrieve their matched replicates, quantifying profile quality and similarity.
 showDate: false
 showAuthor: false
+pypiPackage: copairs
+githubRepo: cytomining/copairs
 ---
 
+{{< tool-badges >}}
+
 `copairs` is a Python package for evaluating the quality of morphology profiles by measuring how well a perturbation's profile can be retrieved relative to controls.
 It implements mean Average Precision (mAP) and related metrics widely used in the image-based profiling community.
 
diff --git a/content/tools/cosmicqc.md b/content/tools/cosmicqc.md
@@ -4,11 +4,15 @@ description: Quality control step — flags and removes low-quality cells before
 showDate: false
 showAuthor: false
 logoUrl: https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/just-icon.png
+pypiPackage: cosmicqc
+githubRepo: cytomining/coSMicQC
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-light-bg.png" alt="coSMicQC logo" width="400">
 <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/coSMicQC/main/media/logo/with-text-for-dark-bg.png" alt="coSMicQC logo" width="400">
 
+{{< tool-badges >}}
+
 `coSMicQC` (Single-cell Morphology Quality Control) identifies and removes low-quality cells from image-based profiling datasets before downstream analysis.
 It catches common problems such as over-segmented nuclei, poorly segmented cells, and imaging artifacts.
 
diff --git a/content/tools/cytodataframe.md b/content/tools/cytodataframe.md
@@ -4,11 +4,15 @@ description: "Interactive exploration — view and inspect morphology profiles a
 showDate: false
 showAuthor: false
 logoUrl: https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/just-icon.png
+pypiPackage: cytodataframe
+githubRepo: cytomining/CytoDataFrame
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/with-text-for-light-bg.png" alt="CytoDataFrame logo" width="400">
 <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/CytoDataFrame/main/logo/with-text-for-dark-bg.png" alt="CytoDataFrame logo" width="400">
 
+{{< tool-badges >}}
+
 `CytoDataFrame` extends the familiar pandas DataFrame interface to let researchers view and analyze single-cell morphology profiles alongside their corresponding microscopy images and segmentation masks — all within a Jupyter notebook.
 
 **Key capabilities:**
diff --git a/content/tools/cytotable.md b/content/tools/cytotable.md
@@ -4,11 +4,15 @@ description: Upstream ingestion — converts raw CellProfiler, DeepProfiler, and
 showDate: false
 showAuthor: false
 logoUrl: https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/just-icon.png
+pypiPackage: cytotable
+githubRepo: cytomining/CytoTable
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/with-text-for-light-bg.png" alt="CytoTable logo" width="400">
 <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/CytoTable/main/logo/with-text-for-dark-bg.png" alt="CytoTable logo" width="400">
 
+{{< tool-badges >}}
+
 `CytoTable` harmonizes output from different high-content image analysis tools — including CellProfiler, `DeepProfiler`, and IN Carta — into a single, analysis-ready format.
 It scales to large datasets using Apache Parquet, DuckDB, and Parsl under the hood.
 
diff --git a/content/tools/deepprofiler.md b/content/tools/deepprofiler.md
@@ -3,10 +3,13 @@ title: DeepProfiler
 description: Alternative feature extraction — deep learning embeddings from raw microscopy images, bypassing classical segmentation-and-measurement pipelines.
 showDate: false
 showAuthor: false
+githubRepo: cytomining/DeepProfiler
 ---
 
 <img src="https://raw.githubusercontent.com/cytomining/DeepProfiler/master/figures/logo/banner.png" alt="DeepProfiler logo" width="400">
 
+{{< tool-badges >}}
+
 `DeepProfiler` uses deep neural networks to extract morphological features directly from raw microscopy images, bypassing traditional segmentation-and-measurement pipelines.
 It is designed for high-throughput screens where deep learning representations outperform classical feature sets.
 
diff --git a/content/tools/pycytominer.md b/content/tools/pycytominer.md
@@ -4,11 +4,15 @@ description: "Core processing pipeline — aggregates, normalizes, and feature-s
 showDate: false
 showAuthor: false
 logoUrl: https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/just-icon.png
+pypiPackage: pycytominer
+githubRepo: cytomining/pycytominer
 ---
 
 <img class="logo-light" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/with-text-for-light-bg.png" alt="Pycytominer logo" width="400">
 <img class="logo-dark" src="https://raw.githubusercontent.com/cytomining/pycytominer/main/logo/with-text-for-dark-bg.png" alt="Pycytominer logo" width="400">
 
+{{< tool-badges >}}
+
 `Pycytominer` is the core Python package in the Cytomining ecosystem.
 It provides a clean, composable API for processing single-cell morphology profiles produced by tools like CellProfiler.
 
diff --git a/layouts/_partials/article-link.html b/layouts/_partials/article-link.html
@@ -69,6 +69,7 @@ <h3 class="flex items-center text-xl font-semibold">
         {{ partial "extend-article-link.html" . }}
       {{ end }}
     </h3>
+    {{ partial "tool-badges.html" (dict "page" . "scope" "list") }}
     <div class="text-sm text-neutral-500 dark:text-neutral-400">
       {{ partial "article-meta.html" . }}
     </div>
diff --git a/layouts/_partials/tool-badges.html b/layouts/_partials/tool-badges.html
@@ -0,0 +1,35 @@
+{{- $page := . -}}
+{{- $scope := "single" -}}
+{{- if reflect.IsMap . -}}
+  {{- $page = .page -}}
+  {{- $scope = .scope | default "single" -}}
+{{- end -}}
+{{- $isTools := eq $page.Section "tools" -}}
+{{- $isExperimental := eq $page.Section "experimental" -}}
+{{- if and (or $isTools $isExperimental) (or $page.Params.pypiPackage $page.Params.githubRepo) -}}
+  <div class="tool-badges" style="display: flex; flex-wrap: nowrap; align-items: center; gap: 3px; font-size: 0; line-height: 0;">
+    {{- if $isTools -}}
+      {{- with $page.Params.pypiPackage -}}
+        <img src="https://img.shields.io/pypi/v/{{ . }}" alt="PyPI version for {{ . }}" loading="lazy" />
+      {{- end -}}
+    {{- end -}}
+    {{- with $page.Params.githubRepo -}}
+      <img src="https://img.shields.io/github/stars/{{ . }}" alt="GitHub stars for {{ . }}" loading="lazy" />
+    {{- end -}}
+    {{- if and $isTools (ne $scope "list") -}}
+      {{- with $page.Params.pypiPackage -}}
+        <img src="https://img.shields.io/pypi/dm/{{ . }}?label=PyPI%20downloads" alt="PyPI monthly downloads for {{ . }}" loading="lazy" />
+        <img src="https://img.shields.io/pepy/dt/{{ . }}?label=total%20downloads" alt="Total downloads for {{ . }}" loading="lazy" />
+      {{- end -}}
+      {{- with $page.Params.githubRepo -}}
+        <img src="https://img.shields.io/github/forks/{{ . }}" alt="GitHub forks for {{ . }}" loading="lazy" />
+      {{- end -}}
+    {{- end -}}
+  </div>
+  <style>
+    .tool-badges img {
+      display: inline-block;
+      vertical-align: middle;
+    }
+  </style>
+{{- end -}}
diff --git a/layouts/experimental/list.html b/layouts/experimental/list.html
@@ -2,7 +2,7 @@
 <div class="mx-auto max-w-prose py-8">
 
   {{/* Header */}}
-  <h1 class="hero-fade-1 text-4xl font-extrabold mb-2">Experimental Tools</h1>
+  <h1 class="hero-fade-1 text-4xl font-extrabold mb-2">Roadmap</h1>
   <p class="hero-fade-2" style="color: #6b7280; font-size: 1.05rem; margin-bottom: 2.5rem; line-height: 1.65;">
     Next-generation tools under active development in the <a href="https://github.com/WayScience" style="color: inherit; text-decoration: underline; text-decoration-color: #d1d5db;">WayScience</a> organization,
     forming the foundation of the Cytomining roadmap.
@@ -21,7 +21,11 @@ <h1 class="hero-fade-1 text-4xl font-extrabold mb-2">Experimental Tools</h1>
 
   {{/* Tool list */}}
   <div class="hero-fade-4">
-    <h2 style="font-size: 1.15rem; font-weight: 700; margin-bottom: 0.25rem;">Tools</h2>
+    <h2 style="font-size: 1.15rem; font-weight: 700; margin-bottom: 0.25rem;">Experimental tools</h2>
+    <p style="color: #6b7280; font-size: 0.95rem; margin-bottom: 1rem;">
+      These tools are under active development in the <a href="https://github.com/WayScience" style="color: inherit; text-decoration: underline; text-decoration-color: #d1d5db;">WayScience</a> organization.
+      For production-ready tools, see the <a href="/tools/" style="color: inherit; text-decoration: underline; text-decoration-color: #d1d5db;">Tools page</a>.
+    </p>
     {{ range .Pages }}
       {{ partial "article-link.html" . }}
     {{ end }}
diff --git a/layouts/index.html b/layouts/index.html
@@ -48,7 +48,7 @@ <h1 style="font-size: 2.5rem; font-weight: 800; letter-spacing: -0.02em; margin:
       <a href="/tools/" class="hero-btn-primary" style="display: inline-block; background: #2563eb; color: white; font-weight: 600; font-size: 0.9rem; padding: 0.65rem 1.4rem; border-radius: 8px; text-decoration: none;">
         Explore tools →
       </a>
-      <a href="/experimental/" class="hero-btn-outline" style="display: inline-block; background: transparent; color: #374151; font-weight: 600; font-size: 0.9rem; padding: 0.65rem 1.4rem; border-radius: 8px; text-decoration: none; border: 1.5px solid #d1d5db;">
+      <a href="/roadmap/" class="hero-btn-outline" style="display: inline-block; background: transparent; color: #374151; font-weight: 600; font-size: 0.9rem; padding: 0.65rem 1.4rem; border-radius: 8px; text-decoration: none; border: 1.5px solid #d1d5db;">
         Experimental tools
       </a>
     </div>
diff --git a/layouts/shortcodes/tool-badges.html b/layouts/shortcodes/tool-badges.html
@@ -0,0 +1 @@
+{{ partial "tool-badges.html" (dict "page" .Page "scope" "single") }}
diff --git a/themes/congo/layouts/list.html b/themes/congo/layouts/list.html
@@ -43,11 +43,5 @@ <h2 class="mt-12 text-2xl font-bold text-neutral-700 first:mt-8 dark:text-neutra
       {{ end }}
     </section>
     {{ partial "pagination.html" . }}
-  {{ else }}
-    <section class="prose mt-10 dark:prose-invert">
-      <p class="border-t py-8">
-        <em>{{ i18n "list.no_articles" | emojify }}</em>
-      </p>
-    </section>
   {{ end }}
 {{ end }}
