Welcome to the BioImage Model Zoo

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# Welcome to the BioImage Model Zoo

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    Caterina Fuster-Barceló</a>
  
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### <i class="far fa-question-circle" aria-hidden="true"></i><span class="visually-hidden">question</span> Questions

- What can be found in the BioImage Model Zoo?

- Why is it worth trying?

- How does it work?

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### <i class="fas fa-bullseye" aria-hidden="true"></i><span class="visually-hidden">objectives</span> Objectives

- Overview

- Content

- Models

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## What you can find:

- Pretrained AI models to perform bioimage analysis tasks.
- Reference datasets used to train the models (and to test them!)
- Python notebooks to train or fine-tune your models.

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In the Bioimage Model Zoo you can find pretrained models to perform different bioimage analysis tasks as well as reference datasets used to train the models.
Between many different tools and softwares, you can also find python notebooks to train or fine-tune your models easily.

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## Why is it worth trying?

You can easily run any of the models in user-friendly tools such as Ilastik, deepImageJ, ZeroCostDL4Mic, ImJoy, Fiji, Icy, QuPath or more.

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You can easily run any of the models in user-friendly tools such as Ilastik, deepImageJ, ZeroCostDL4Mic, ImJoy, Fiji, Icy, QuPath or more.

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### BioImage Model Zoo: Overview

<figure id="figure-1" style="max-width: 90%;"><img src="../../images/welcome-bioimageio-01.png"  alt="Consumer Software of Bioimageio. "  width="961" height=721 loading="lazy"><a target="_blank" href="../../images/welcome-bioimageio-01.png" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/><figcaption><span class="figcaption-prefix"><strong>Figure 1</strong>:</span> Consumer software of the Bioimageio</figcaption></figure>

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If you access the BioImage Model Zoo webpage you can find all consumer software that can run the bioimage io models.

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### BioImage Model Zoo: Overview

<figure id="figure-2" style="max-width: 90%;"><img src="../../images/welcome-bioimageio-02.png"  alt="Choose a category. "  width="961" height=721 loading="lazy"><a target="_blank" href="../../images/welcome-bioimageio-02.png" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/><figcaption><span class="figcaption-prefix"><strong>Figure 2</strong>:</span> Choose a category</figcaption></figure>

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Depending on the task you wish to perform, you may cohose the type of card you are looking for. It will depend on the model, application or dataset you wish to use.

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### BioImage Model Zoo: Overview

<figure id="figure-3" style="max-width: 90%;"><img src="../../images/welcome-bioimageio-03.png"  alt="Search bar. "  width="961" height=721 loading="lazy"><a target="_blank" href="../../images/welcome-bioimageio-03.png" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/><figcaption><span class="figcaption-prefix"><strong>Figure 3</strong>:</span> Search bar</figcaption></figure>

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In the search bar you can write an image processing task, the name of a model or a bioimaging modality. It will suggest you the existing choices.

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### BioImage Model Zoo: Content

<figure id="figure-4" style="max-width: 90%;"><img src="../../images/welcome-bioimageio-04.png"  alt="BioImage Model Zoo Content. "  width="906" height=500 loading="lazy"><a target="_blank" href="../../images/welcome-bioimageio-04.png" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/><figcaption><span class="figcaption-prefix"><strong>Figure 4</strong>:</span> BioImage Model Zoo Content</figcaption></figure>

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The content of bioimage io such as models, datasets and applications are provided as cards.

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### BioImage Model Zoo: Models

<figure id="figure-5" style="max-width: 90%;"><img src="../../images/welcome-bioimageio-05.png"  alt="BioImage Model Zoo Model Cards. "  width="1073" height=615 loading="lazy"><a target="_blank" href="../../images/welcome-bioimageio-05.png" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/><figcaption><span class="figcaption-prefix"><strong>Figure 5</strong>:</span> BioImage Model Zoo Model Cards</figcaption></figure>

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In each model card you can find interactive buttons and the description of the model itself. These buttons will provide you some of the features of that model such as the training dataset or the license.
You can also choose the consumer software to run the model, share this model, download it and more.

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### BioImage Model Zoo: Models

<figure id="figure-6" style="max-width: 90%;"><img src="../../images/welcome-bioimageio-06.png"  alt="BioImage Model Zoo Model Download. "  width="950" height=516 loading="lazy"><a target="_blank" href="../../images/welcome-bioimageio-06.png" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/><figcaption><span class="figcaption-prefix"><strong>Figure 6</strong>:</span> BioImage Model Zoo Model Download</figcaption></figure>

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If you want, you can click on the download button to download the method and click on the consumer software you chose.
It will download automatically.

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### BioImage Model Zoo: Models

If you want to know more about the Bioimage Model Zoo, check out the documentation or contact us!

<figure id="figure-7" style="max-width: 90%;"><img src="../../images/welcome-bioimageio-07.png"  alt="BioImage Model Zoo Documentation. "  width="961" height=721 loading="lazy"><a target="_blank" href="../../images/welcome-bioimageio-07.png" rel="noopener noreferrer"><small>Open image in new tab</small></a><br/><br/><figcaption><span class="figcaption-prefix"><strong>Figure 7</strong>:</span> BioImage Model Zoo Documentation</figcaption></figure>

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If you want to know more about the Bioimage Model Zoo, check our documentation or contact us!

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## Thank You!

This material is the result of a collaborative work. Thanks to the [Galaxy Training Network](https://training.galaxyproject.org) and all the contributors!

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