manifest.bioimage.io.yaml

format_version: 0.2.0
config:
  id: bioimage.io
  name: BioImage.IO
  tags: []
  logo: 🦒
  icon: 🦒
  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 Github
    - Link models to datasets and applications
  explore_button_text: Start Exploring
  background_image: static/img/zoo-background.svg
  resource_types:
    - model
    - application
    - notebook
    - dataset
  url_root: https://raw.githubusercontent.com/bioimage-io/bioimage-io-models/master

collection:
  - id: zero
    source: https://raw.githubusercontent.com/HenriquesLab/ZeroCostDL4Mic/master/manifest.bioimage.io.yaml
  - id: deepimagej
    source: https://raw.githubusercontent.com/deepimagej/models/master/manifest.bioimage.io.yaml
  - id: fiji
    source: https://raw.githubusercontent.com/bioimage-io/fiji-bioimage-io/master/manifest.bioimage.io.yaml

application:
  - id: Ilastik Model Preview
    source: src/Ilastik-app.imjoy.html
  - id: Fiji Model Preview
    source: src/Fiji-app.imjoy.html
  - id: HPA-Classification
    source: https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/apps/HPA-Classification.imjoy.html
  - id: Kaibu
    source: src/Kaibu-app.imjoy.html

dataset:
  - id: dummy_zarr
    source: https://gist.githubusercontent.com/oeway/3dcbd79cd29da42be13a7e3bc0f9ca12/raw/dummy_zarr.dataset.yaml

notebook:
  - id: vitessce-image-viewer
    source: https://gist.githubusercontent.com/oeway/582856630a0aed4d4d221e54df1b3ece/raw/vitessce-image-viewer.notebook.yaml

model:
  - id: HPAShuffleNetV2
    source: https://raw.githubusercontent.com/bioimage-io/tfjs-bioimage-io/master/models/HPAShuffleNetV2/HPAShuffleNetV2.model.yaml
    links:
      - HPA-Classification

  - id: UNet2DNucleiBroad
    source: https://raw.githubusercontent.com/bioimage-io/pytorch-bioimage-io/v0.1.1/specs/models/unet2d/nuclei_broad/UNet2DNucleiBroad.model.yaml
    links:
      - Ilastik Model Preview
    download_url: https://github.com/bioimage-io/pytorch-bioimage-io/releases/download/v0.1.1/UNet2DNucleiBroad.model.zip

  - id: UNet3DArabidopsisOvules
    source: https://raw.githubusercontent.com/fynnbe/pytorch-3dunet/eabf146079c5829f6c6fe0488595838e54887c06/bioimage-io/UNet3DArabidopsisOvules.model/UNet3DArabidopsisOvules.model.yaml
    links:
      - Ilastik Model Preview
    download_url: https://github.com/wolny/pytorch-3dunet/releases/download/1.2.6/UNet3DArabidopsisOvules.model.zip

  - id: UNet3DPlatyCellProbs
    source: https://raw.githubusercontent.com/platybrowser/platybrowser/3711f1c26e5db8c38c3faff4cccb3110560e3c67/segmentation/cells/UNet3DPlatyCellProbs.model/UNet3DPlatyCellProbs.model.yaml
    links:
      - Ilastik Model Preview
    download_url: https://github.com/platybrowser/platybrowser/releases/download/1.0.0/UNet3DPlatyCellProbs.model.zip

  - id: UNetDA
    source: https://raw.githubusercontent.com/subeeshvasu/hbp-DL-seg-codes/0.1.2/UNetDA.model.yaml
    links:
      - Ilastik Model Preview
    download_url: https://github.com/subeeshvasu/hbp-DL-seg-codes/releases/download/0.1.2/UNetDA.model.zip

  - id: 2sUNetDA
    source: https://raw.githubusercontent.com/subeeshvasu/hbp-DL-seg-codes/0.1.2/2sUNetDA.model.yaml
    links:
      - Ilastik Model Preview
    download_url: https://github.com/subeeshvasu/hbp-DL-seg-codes/releases/download/0.1.2/2sUNetDA.model.zip