Community index

.github/workflows/community.yml

@@ -0,0 +1,40 @@
+name: Community
+
+on:
+  push:
+    paths:
+      - 'community/**'
+      - '.github/workflows/community.yml'
+  pull_request:
+    paths:
+      - 'community/**'
+      - '.github/workflows/community.yml'
+  schedule:
+    # Weekly link-rot check against the default branch (Mondays, 12:00 UTC).
+    - cron: '0 12 * * 1'
+  workflow_dispatch:
+
+jobs:
+  validate:
+    name: Validate entries
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - run: pip install pyyaml
+      - name: Validate schema and check the index is in sync
+        run: python community/validate.py
+
+  links:
+    name: Check links
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v4
+      - uses: actions/setup-python@v5
+        with:
+          python-version: '3.11'
+      - run: pip install pyyaml
+      - name: Check that every linked URL resolves
+        run: python community/validate.py --links-only

.github/workflows/ruff.yml

@@ -1,8 +1,13 @@
 name: Ruff
-on: [ push, pull_request ]
+
+on: [push, pull_request]
+
 jobs:
   ruff:
     runs-on: ubuntu-latest
     steps:
       - uses: actions/checkout@v4
-      - uses: astral-sh/ruff-action@v3
+
+      - uses: astral-sh/ruff-action@v3
+        with:
+          version: "0.9.4"

README.md

@@ -78,12 +78,16 @@ model = Merlin(RadiologyReport=True)
 
 #### For a code-first walkthrough of the Merlin codebase, please check out this [blog](https://urldefense.com/v3/__https://passthetorch.dev/posts/deep-dive-into-merlin/__;!!G92We9drHetJ8EofZw!Z0a3-_4uuVWoAUwvJWSw5kj19m15l0bkqc64EveKRMXUceD7ezETrpV2weXxJe6wgUyoYxLFRY3u75ykWYnClE9L$).
 
-## 📂  Merlin Abdominal CT Dataset
+## 📂 Merlin Abdominal CT Dataset
 
 We are excited to release the **Merlin Abdominal CT Dataset** to the community!
 
 For details on accessing and using the dataset, please see the [download documentation](documentation/download.md)!
 
+## 🤝 Community
+
+Models, datasets, and tools built on Merlin by the community are indexed in [`community/`](community). Please see here on [how to add yours](community/CONTRIBUTING.md).
+
 ## 📎 Citation
 
 If you find this repository useful for your work, please cite the cite the [Nature paper](https://www.nature.com/articles/s41586-026-10181-8):

community/CONTRIBUTING.md

@@ -0,0 +1,43 @@
+# Adding your project to the Merlin community index
+
+The community index points people to work derived from Merlin: fine-tuned models, derived datasets, embeddings, benchmarks, and tutorials. You keep hosting and maintaining your artifact wherever you like. This index just makes it discoverable.
+
+## How to add an entry
+
+1. Fork this repository.
+1. Copy [`template.yaml`](template.yaml) to `community/entries/<your-project-name>.yaml`. The filename must be lowercase, e.g. `merlin-nnunet.yaml`.
+1. Fill in the fields (see the reference below) and delete the optional ones you do not need.
+1. Regenerate the index table and check your links:
+   ```bash
+   pip install pyyaml
+   python community/validate.py --write --check-links
+   ```
+1. Commit both your YAML file and the updated `community/README.md`, then open a pull request.
+
+CI re-runs the same validation on every pull request that touches `community/`, so if you skip step 4 the check will tell you what to fix.
+
+## Field reference
+
+| Field | Required | Notes |
+| --- | --- | --- |
+| `name` | yes | Display name, 80 characters max. Must be unique in the index. |
+| `description` | yes | One or two sentences, 300 characters max, single line. |
+| `category` | yes | One of `model`, `dataset`, `tool`, `benchmark`, `tutorial`, `other`. |
+| `authors` | yes | List of `name`, with optional `affiliation` and `email`. |
+| `license` | yes | License of your artifact, e.g. `MIT`, `Apache-2.0`, `CC BY-NC 4.0`, or the name of your data use agreement. |
+| `links` | yes | Mapping with a required `homepage`, plus optional `code`, `data`, `paper`, `demo`, `docs`. All must be public http(s) URLs. |
+| `added` | yes | Date (`YYYY-MM-DD`) you added the entry. |
+| `merlin_components` | no | Which parts of Merlin you build on, e.g. `image encoder`, `Merlin Abdominal CT Dataset`. |
+| `tags` | no | Free-form keywords. |
+| `citation` | no | BibTeX for your work, as a YAML `\|` block. |
+| `contact` | no | Email or URL for questions and link-rot follow-up. Recommended. |
+
+## What we ask
+
+- **Host your own artifacts.** This repository does not store models or data. If you are sharing data, point to a host that can serve it, for example Hugging Face, Zenodo, or an institutional repository.
+- **Links must be public.** URLs that require a login cannot be checked and will fail CI. A landing page describing how to request access is fine; a private URL is not.
+- **Be clear about licensing and provenance.** State the license of what you are sharing, and make sure you have the right to share it. Derived data carries the obligations of the source data — if your work uses the Merlin Abdominal CT Dataset, its [data use agreement](../documentation/download.md) still applies to anything you redistribute.
+- **No patient-identifiable data.** Anything you link must be appropriately de-identified.
+- **Keep it working.** A weekly CI job re-checks every link. If yours goes dead we will open an issue and, if we cannot reach you, remove the entry. To update or remove your own entry, just open a pull request.
+
+Questions about an entry are best raised as a [GitHub issue](https://github.com/StanfordMIMI/Merlin/issues).

community/README.md

@@ -0,0 +1,33 @@
+# Merlin Community Projects 🤝
+
+Work built on top of Merlin, which include models, datasets, tools, benchmarks, and tutorials contributed by the community.
+
+Everything listed here is **hosted and maintained by its own authors**. This directory is an index: each project is described by a small YAML file in [`entries/`](entries), and the table below is generated from those files. Nothing is stored in this repository, and a listing is not an endorsement or a validation of clinical safety.
+
+**Want to add your project?** See [CONTRIBUTING.md](CONTRIBUTING.md), copy [`template.yaml`](template.yaml), fill in the fields, and open a pull request.
+
+## Projects
+
+<!-- COMMUNITY_TABLE:START -->
+
+| Project | Type | Description | License |
+| --- | --- | --- | --- |
+| [Merlin-nnUNet](https://github.com/ashwinkumargb/Merlin-nnUNet) | model | Integrates the Merlin image encoder into the nnU-Net framework for 3D abdominal CT segmentation, with setup and inference instructions. | Apache-2.0 |
+
+<details>
+<summary><b>Merlin-nnUNet</b> — model</summary>
+
+- **Description:** Integrates the Merlin image encoder into the nnU-Net framework for 3D abdominal CT segmentation, with setup and inference instructions.
+- **Authors:** Ashwin Kumar (Stanford University)
+- **Links:** [Code](https://github.com/ashwinkumargb/Merlin-nnUNet)
+- **License:** Apache-2.0
+- **Builds on:** image encoder
+- **Tags:** `segmentation`, `abdominal-ct`, `nnU-Net`
+- **Contact:** akkumar@stanford.edu
+- **Added:** 2026-09-11 · **Entry:** [`merlin-nnunet.yaml`](entries/merlin-nnunet.yaml)
+
+</details>
+
+<!-- COMMUNITY_TABLE:END -->
+
+<sub>The table and the expandable entries above are generated by [`validate.py`](validate.py) from the files in [`entries/`](entries). Therefore, you should edit your YAML file, not this section.</sub>

community/entries/merlin-nnunet.yaml

@@ -0,0 +1,20 @@
+name: Merlin-nnUNet
+description: >
+  Integrates the Merlin image encoder into the nnU-Net framework for 3D
+  abdominal CT segmentation, with setup and inference instructions.
+category: model
+authors:
+  - name: Ashwin Kumar
+    affiliation: Stanford University
+license: Apache-2.0
+links:
+  homepage: https://github.com/ashwinkumargb/Merlin-nnUNet
+  code: https://github.com/ashwinkumargb/Merlin-nnUNet
+added: 2026-09-11
+merlin_components:
+  - image encoder
+tags:
+  - segmentation
+  - abdominal-ct
+  - nnU-Net
+contact: akkumar@stanford.edu

community/template.yaml

@@ -0,0 +1,58 @@
+# Copy this file to entries/<your-project-name>.yaml and fill it in.
+# Validate locally with:  python community/validate.py --write --check-links
+# Field reference: community/CONTRIBUTING.md
+
+# Required. Display name of your project, as you want it listed.
+name: My Merlin Project
+
+# Required. One or two sentences, 300 characters max. Plain text, single line.
+description: >
+  A short summary of what your project does and how it builds on Merlin.
+
+# Required. One of: model, dataset, tool, benchmark, tutorial, other
+category: tool
+
+# Required. Everyone you want credited. 'affiliation' and 'email' are optional.
+authors:
+  - name: Your Name
+    affiliation: Your Institution
+
+# Required. The license your artifact is released under, e.g. MIT, Apache-2.0,
+# CC BY 4.0, CC BY-NC 4.0, or a Stanford AIMI data use agreement.
+license: MIT
+
+# Required. 'homepage' is required; the rest are optional. All must be http(s)
+# URLs that work without a login. Merlin does not host artifacts — these point
+# to wherever you host yours.
+links:
+  homepage: https://github.com/your-org/your-project
+  code: https://github.com/your-org/your-project
+  data: https://huggingface.co/datasets/your-org/your-dataset
+  paper: https://arxiv.org/abs/0000.00000
+  demo: https://huggingface.co/spaces/your-org/your-demo
+  docs: https://your-project.readthedocs.io
+
+# Required. ISO date (YYYY-MM-DD) you are adding this entry.
+added: 2026-09-01
+
+# Optional. Which parts of Merlin your work builds on.
+merlin_components:
+  - image encoder
+  - Merlin Abdominal CT Dataset
+
+# Optional. Free-form keywords.
+tags:
+  - segmentation
+  - abdominal-ct
+
+# Optional. How people should cite your work, as BibTeX.
+citation: |
+  @article{yourname2026project,
+    author  = {Your Name},
+    title   = {My Merlin Project},
+    journal = {Journal},
+    year    = {2026}
+  }
+
+# Optional. Email or URL for questions and follow-up.
+contact: you@example.edu