collection.bioimage.io.yaml

format_version: 0.2.2
type: collection
name: BioImageIO Collection
tags: [bioimage.io]
description: "Resources collection for BioImgage.IO"

authors:
  - name: "BioImageIO Team"
    github_user: bioimage-io

maintainers:
  - name: "BioImageIO Team"
    github_user: bioimage-io

config:  # todo: clean up config (which of these fields are still used?)
  # todo: compare to https://github.com/bioimage-io/collection-bioimage-io/blob/f89e869c2f84d3589d4c7e57e6993faf76d48ed3/collection_rdf_template.yaml#L15-L24
  id: bioimageio
  name: BioImage.IO
  tags: []
  logo: https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/public/static/img/bioimage-io-icon.svg
  icon: https://raw.githubusercontent.com/bioimage-io/bioimage.io/main/public/static/img/bioimage-io-icon.svg
  splash_title: BioImage Model Zoo
  splash_subtitle: Advanced AI models in one-click
  splash_feature_list:
    - Integrate with Fiji, Ilastik, ImJoy
    - Try model instantly with BioEngine
    - Contribute your models via Zenodo
    - Link models to datasets and applications
  explore_button_text: Start Exploring
  background_image: static/img/zoo-background.svg
  resource_types:
    - model
    - application
    - notebook
    - dataset
  default_type: model
  url_root: https://raw.githubusercontent.com/bioimage-io/bioimage-io-resources/main
  
collection:
- id: stardist
  name: StarDist
  description: "Object Detection with Star-convex Shapes"
  format_version: 0.2.2
  git_repo: "https://github.com/stardist/stardist"
  type: application
  authors:
    - name: Uwe Schmidt
      github_user: uschmidt83
    - name: Martin Weigert 
      github_user: maweigert
  maintainers:
    - name: Uwe Schmidt
      github_user: uschmidt83
  cite:
  - doi: https://doi.org/10.1007/978-3-030-00934-2_30
    text: Cell Detection with Star-Convex Polygons
  - doi: https://doi.org/10.1109/WACV45572.2020.9093435
    text: >-
      Star-convex Polyhedra for 3D Object Detection and Segmentation in
      Microscopy
  documentation: https://raw.githubusercontent.com/stardist/stardist/master/README.md
  covers: ["https://raw.githubusercontent.com/stardist/stardist/master/images/stardist_logo.jpg"]
  icon: "https://raw.githubusercontent.com/stardist/stardist/master/images/stardist_logo.jpg"
  tags: [stardist]
- id: qupath
  name: QuPath
  description: "QuPath is an open, powerful, flexible, extensible software platform for bioimage analysis."
  format_version: 0.2.2
  git_repo: "https://github.com/qupath/qupath"
  type: application
  authors:
    - name: Pete Bankhead
      github_user: petebankhead
  maintainers:
    - name: Pete Bankhead
      github_user: petebankhead
  cite:
  - doi: "10.1038/s41598-017-17204-5"
    text: "QuPath: Open source software for digital pathology image analysis"
  license: "GPL-3.0-or-later"
  documentation: "https://raw.githubusercontent.com/qupath/qupath/main/README.md"
  covers: ["https://raw.githubusercontent.com/qupath/qupath/e96e7f228c2a9e27e7236108808540a4dbf503e8/qupath-gui-fx/src/main/resources/icons/QuPath_512.png"]
  icon: "https://raw.githubusercontent.com/qupath/qupath/e96e7f228c2a9e27e7236108808540a4dbf503e8/qupath-gui-fx/src/main/resources/icons/QuPath_64.png"
  tags: [qupath]