├── .github └── workflows │ └── validate-collection.yml ├── .gitignore ├── README.md ├── collection.bioimage.io.yaml └── requirements.txt /.github/workflows/validate-collection.yml: -------------------------------------------------------------------------------- 1 | name: Validate Collection 2 | 3 | on: 4 | push: 5 | branches: [ main ] 6 | pull_request: 7 | branches: [ main ] 8 | 9 | jobs: 10 | run: 11 | runs-on: ubuntu-latest 12 | steps: 13 | - name: checkout 14 | uses: actions/checkout@v2 15 | - name: install bioimageio.spec 16 | run: pip install bioimageio.spec lxml 17 | - name: validate collection 18 | run: bioimageio validate-partner-collection collection.bioimage.io.yaml 19 | -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- 1 | .DS_Store 2 | __pycache__ 3 | *.pyc 4 | rdf.yaml 5 | 6 | # local env files 7 | .env.local 8 | .env.*.local 9 | 10 | # Log files 11 | npm-debug.log* 12 | yarn-debug.log* 13 | yarn-error.log* 14 | 15 | # Editor directories and files 16 | .idea 17 | .vscode 18 | *.suo 19 | *.ntvs* 20 | *.njsproj 21 | *.sln 22 | *.sw* 23 | manifest.bioimage.io.json -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 1 | [![Gitter](https://badges.gitter.im/bioimage-io/community.svg)](https://gitter.im/bioimage-io/community?utm_source=badge&utm_medium=badge&utm_campaign=pr-badge) 2 | 3 | # BioImage.IO Resources -------------------------------------------------------------------------------- /collection.bioimage.io.yaml: -------------------------------------------------------------------------------- 1 | format_version: 0.2.2 2 | type: collection 3 | name: BioImageIO Collection 4 | tags: [bioimage.io] 5 | description: "Resources collection for BioImgage.IO" 6 | 7 | authors: 8 | - name: "BioImageIO Team" 9 | github_user: bioimage-io 10 | 11 | maintainers: 12 | - name: "BioImageIO Team" 13 | github_user: bioimage-io 14 | 15 | config: # todo: clean up config (which of these fields are still used?) 16 | # todo: compare to https://github.com/bioimage-io/collection-bioimage-io/blob/f89e869c2f84d3589d4c7e57e6993faf76d48ed3/collection_rdf_template.yaml#L15-L24 17 | id: bioimageio 18 | name: BioImage.IO 19 | tags: [] 20 | logo: https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/public/static/img/bioimage-io-icon.svg 21 | icon: https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/public/static/img/bioimage-io-icon.svg 22 | splash_title: BioImage Model Zoo 23 | splash_subtitle: Advanced AI models in one-click 24 | splash_feature_list: 25 | - Integrate with Fiji, Ilastik, ImJoy 26 | - Try model instantly with BioEngine 27 | - Contribute your models via Zenodo 28 | - Link models to datasets and applications 29 | explore_button_text: Start Exploring 30 | background_image: static/img/zoo-background.svg 31 | resource_types: 32 | - model 33 | - application 34 | - notebook 35 | - dataset 36 | default_type: model 37 | url_root: https://raw.githubusercontent.com/bioimage-io/bioimage-io-resources/main 38 | 39 | collection: 40 | - id: stardist 41 | name: StarDist 42 | description: "Object Detection with Star-convex Shapes" 43 | format_version: 0.2.2 44 | git_repo: "https://github.com/stardist/stardist" 45 | type: application 46 | authors: 47 | - name: Uwe Schmidt 48 | github_user: uschmidt83 49 | - name: Martin Weigert 50 | github_user: maweigert 51 | maintainers: 52 | - name: Uwe Schmidt 53 | github_user: uschmidt83 54 | cite: 55 | - doi: https://doi.org/10.1007/978-3-030-00934-2_30 56 | text: Cell Detection with Star-Convex Polygons 57 | - doi: https://doi.org/10.1109/WACV45572.2020.9093435 58 | text: >- 59 | Star-convex Polyhedra for 3D Object Detection and Segmentation in 60 | Microscopy 61 | documentation: https://raw.githubusercontent.com/stardist/stardist/master/README.md 62 | covers: ["https://raw.githubusercontent.com/stardist/stardist/master/images/stardist_logo.jpg"] 63 | icon: "https://raw.githubusercontent.com/stardist/stardist/master/images/stardist_logo.jpg" 64 | tags: [stardist] 65 | - id: qupath 66 | name: QuPath 67 | description: "QuPath is an open, powerful, flexible, extensible software platform for bioimage analysis." 68 | format_version: 0.2.2 69 | git_repo: "https://github.com/qupath/qupath" 70 | type: application 71 | authors: 72 | - name: Pete Bankhead 73 | github_user: petebankhead 74 | maintainers: 75 | - name: Pete Bankhead 76 | github_user: petebankhead 77 | cite: 78 | - doi: "10.1038/s41598-017-17204-5" 79 | text: "QuPath: Open source software for digital pathology image analysis" 80 | license: "GPL-3.0-or-later" 81 | documentation: "https://raw.githubusercontent.com/qupath/qupath/main/README.md" 82 | covers: ["https://raw.githubusercontent.com/qupath/qupath/e96e7f228c2a9e27e7236108808540a4dbf503e8/qupath-gui-fx/src/main/resources/icons/QuPath_512.png"] 83 | icon: "https://raw.githubusercontent.com/qupath/qupath/e96e7f228c2a9e27e7236108808540a4dbf503e8/qupath-gui-fx/src/main/resources/icons/QuPath_64.png" 84 | tags: [qupath] 85 | -------------------------------------------------------------------------------- /requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/bioimage-io/bioimage-io-resources/f549651922eba99405e291b42bfb3440ad466670/requirements.txt --------------------------------------------------------------------------------