Update BioImage Model Zoo Documentation #441
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docs/guides/developers-guide.md
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| To upload a model to the BioImage Model Zoo, the model must adhere to the specifications of the BioImage.IO format. This ensures compatibility and standardization across the platform. You can find the [latest specifications here](https://github.com/bioimage-io/spec-bioimage-io/blob/gh-pages/user_docs/model_descr_latest.md). Creating a model involves exporting or packaging it into a specific format with defined characteristics. Below are the various ways to create a model in the BioImage.IO format. | ||
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| #### 1. Using the `bioimageio.core` Python Library | ||
| This is the most recommended and streamlined method. The library provides tools for automatic export and validation of models. |
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I guess our recommendation depends on the usecase
docs/guides/developers-guide.md
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| Use the library to export your model programmatically in Python. See the example code in this [Jupyter Notebook](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/example/model_creation.ipynb). | ||
| The primary function for building a model is `bioimageio.core.build_model`. Check its input parameters to understand what is required. Here you can also find an [example notebook](https://github.com/bioimage-io/core-bioimage-io-python/blob/main/presentations/create_ambitious_sloth.ipynb) that demonstrates how to create a model description from scratch. | ||
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| - **Manual Generation:** |
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this section shouldn't be under "Using the bioimageio.core Python Library"
| ``` | ||
| - **Dynamic Validation:** Test the model’s deployment to ensure it generates the expected output. Example: | ||
| ```bash | ||
| bioimageio test-model --weights tensorflow_saved_model_bundle --device cpu /path/to/rdf.yaml |
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the command is only called bioimageio test by now and it does include the static validation... So we shouldn't recommend to do static and then dynamic, but rather just the core test...
We should point to https://github.com/bioimage-io/core-bioimage-io-python?tab=readme-ov-file#-use-the-command-line-interface here instead of reproducing it (making it prone to be outdated)
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here it is also left out how to install (for that reference https://github.com/bioimage-io/core-bioimage-io-python?tab=readme-ov-file#get-started)
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Could you write it shortly and add the refernece? I get a bit confused because I just rewrote and added some new references because this was already there...
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made a separate PR for this: #441
docs/guides/developers-guide.md
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| 1. Visit the [bioimageio](https://bioimage.io) website and click the "Upload" button to access the model upload page. | ||
| 2. Log in using your Google or GitHub account. | ||
| 3. Upload a resource file, which can be a single zip archive containing all necessary files, or you can select/drag and drop individual files. The 'rdf.yaml' file needed for uploading can be created in the next step. | ||
| 4. Automatically once added the yaml file, you will have to "Review and Edit Your Model", to do this, provide all necessary metadata to create the 'rdf.yaml' file if it was not done yet. Ensure to give a descriptive name and description, and add the maintainer responsible for the upload. See the Model Documentation below for details such as how to name your model. |
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Automatically ... ?
part of the sentence before?
Maybe add a screenshot?
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When you upload the yaml file, you are redirected automatically to the "Reivew and Edit Your Model section.
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I see. I don't think that comes across intuitively with the current formulation
Co-authored-by: Fynn Beuttenmüller <[email protected]>
Co-authored-by: Fynn Beuttenmüller <[email protected]>
Co-authored-by: Fynn Beuttenmüller <[email protected]>
Co-authored-by: Fynn Beuttenmüller <[email protected]>
Co-authored-by: Fynn Beuttenmüller <[email protected]>
This PR updates multiple sections of the BioImage Model Zoo documentation following recent discussions and feedback from the community. The changes aim to improve clarity, provide more detailed instructions, and ensure that the documentation reflects the latest specifications and tools available.
Summary of changes