AI4Life Community Event Workshop 1

Session 1: Creating, Uploading, Deploying and Containerizing BioImage Model Zoo Models

This repository provides materials for Session 1. It includes code and resources to help you learn how to work with the BioImage Model Zoo using Python and Jupyter notebooks.

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🚀 Quick Start

The notebook can be used in Google Colab or locally, after setting up the environment. To open the notebook in Google click here: Otherwise, follow the installation steps below.

1. Install Conda

If you don't have Conda installed, download and install Miniconda or Anaconda for your operating system.

2. Create and Activate the Conda Environment

Open a terminal (Anaconda Prompt on Windows or Terminal on Mac/Linux) and create a new environment called bioimageio with Python 3.10 by running:

conda create --name bioimageio python=3.10
conda activate bioimageio

3. Install Required Packages

Install the main dependencies from the conda-forge channel:

conda install -c conda-forge bioimageio.core pytorch jupyterlab matplotlib devtools

• bioimageio.core: Core library for working with BioImage Model Zoo models.
• pytorch: Deep learning framework.
• jupyterlab: Interactive notebook environment.
• matplotlib: Plotting library.

4. Clone this Repository

git clone https://github.com/bioimage-io/AI4Life_CommunityEvent_W1S2.git
cd AI4Life_CommunityEvent_W1S2

5. Launch JupyterLab

Start JupyterLab to explore and run the notebooks:

jupyter lab

This will open JupyterLab in your browser. You can now open and run the notebooks provided in this repository.