BioImage.IO Usage

Step-by-Step Protocol for Using BioImage.IO

1. Access BioImage.IO: 

• Open BioImage Model Zoo in your web browser.

2. Search for models, datasets, or applications: 

• Use keywords or filters such as:

• Segmentation

• Biological structures

3. Review model information: 

• Before using a model, check the following information: 

• Model description

• Input image requirements

• Output type

• Example images

• Author(s)

• License

• Citation

• Compatible software

4. Test a model: 

• Some models can be tested directly in your browser using BioEngine. 

• Upload a compatible image.

• Run the model. 

• Review the prediction results before downloading. 

5. Download a model: 

• On the model page, click Download. 

6. Use a model in compatible software: 

• BioImage.IO models can be used in several applications, including: 

• Ilastik

• Fiji

• StarDist

• QuPath

• SpotMAX

• BiaPy

7. Use BioImage.IO models in ilastik: 

• Open ilastik.

• Create a new project with the “Neural Network Classification (local)” workflow. 

• Load your data.

• Load the BioImage.IO model in NN Prediction:

• Copy and paste a bioimage.io model DOI or nickname, or drag and drop a model.zip file.

• Click the green arrow. 

• Click “Live Predict” to generate predictions. 

• Export the results: 

• Use the Data Export applet to save your predictions.

8. Share your own model: 

• Prepare your model package: 

• Follow the BioImage.io specification at:

https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/user_docs/model_descr_latest.md

• Ensure your package includes a valid rdf.yaml file.

• Upload your model:

• You can upload your model using:

• Folder upload: recommended for large files.

• Multiple files: select all files individually.

• ZIP archive: compress all files into a ZIP.