Add Missing Community Partner Documentation in Guide

[cfusterbarcelo]

Description:

The guide on using BioImage Model Zoo models in different software currently lacks documentation for several community partners. Each partner should add a short section explaining how to use their software with the BioImage Model Zoo.

Each section should include the following:

1. A brief introduction explaining the software's compatibility with BioImage Model Zoo models (e.g., supported frameworks like PyTorch, TensorFlow, etc.).
2. Installation instructions on how to set up the software to work with BioImage Model Zoo models.
3. Usage instructions on how to load and run a model downloaded from the BioImage Model Zoo.
4. Links to detailed documentation for further reference.

Here is a template in Markdown that contributors can use to create their section:

### [Software Name]
*Note: Specify compatible frameworks (e.g., PyTorch, TensorFlow) if applicable.*

1. **Install the software and necessary plugins/extensions**:
   - Include specific plugins/extensions required to run BioImage Model Zoo models.
   - Provide brief steps for installation.

2. **Download and set up a model from the BioImage Model Zoo**:
   - Include instructions on how to download models from the zoo.
   - Provide steps for importing the model into the software.

3. **Run the model**:
   - Mention any example datasets or testing workflows, if applicable.
   - Include basic steps for running the model.

4. **Learn more**:
   - Provide links to detailed tutorials or documentation.

Action Items:

• BiaPy @danifranco @iarganda
• Ilastik @FynnBe
• QuPath @petebankhead
• DL4MicEverywhere @IvanHCenalmor
• CAREamics @mese79
• SpotMax
• ...

Please point to whoever should be in charge of this.

This effort will make the guide more comprehensive and improve accessibility for users! Thank you for your contribution!

[danifranco]

Hello,

We have a dedicated section in our doc with all the explanations on how to use BMZ models in BiaPy. To not replicate the information maybe we can link in BioImage Model Zoo to this documentation?

[cfusterbarcelo]

Hi @danifranco,
That would be very helfpful. Please provide a short description of BiaPy stating that you can consume and produce models and link it to the dedicated documentation.
Thank you very much!

[danifranco]

Here is a description:

BiaPy

Note: BiaPy empowers users to train custom models or fine-tune existing ones for bioimaging tasks and upload them to the BioImage Model Zoo. BiaPy supports models exported with PyTorch.

BiaPy adapts to users of all expertise levels, offering multiple ways to run and interact with models:

• Graphical User Interface (GUI): Ideal for beginners.
• No-Coding Jupyter Notebooks: Simplified workflows for those without programming knowledge.
• Docker Containers: Ensure reproducibility and isolation.
• Command Line Interface (CLI): Perfect for advanced users.

How you interact with BioImage Model Zoo models also depends on your chosen method. Get started with the resources below:

• BiaPy Landing Page: Your gateway to all things BiaPy.
• BiaPy Documentation: In-depth guides and tutorials.
• BioImage Model Zoo in BiaPy: Learn how to work with models from the BioImage Model Zoo.

[esgomezm]

Hi there! here is the description for DL4MicEverywhere:

DL4MicEverywhere

DL4MicEverywhere is a user-friendly platform that offers long-term reproducible and cross-compatible deep learning workflows using Docker containers and user-friendly interactive notebooks. It supports easy containerization and integration of reproducible deep learning techniques following the Zoo's standards, and validation of functional containerization across operating systems.

1. Installation instructions

2. Quick start for containerised notebooks

3. Containerizing your workflow and integrating it within the Zoo's collection

4. Full DL4MicEverywhere documentation