Halfway to I2K 2025: OME-ZARR basics

Welcome to the guide pages for the OME-ZARR basics workshop. To prepare for the course, please follow the instructions below.

Link to Slides

Installation¶

If you haven’t already installed Python on your device, please do so by following the instructions for your respective platform.

Next, we are going to create a separate Python environment for the stuff we need in this course. To do so, install uv, which is our package manager of choice for this course:

pip install uv

Next, clone this repository and its contents:

git clone https://github.com/jo-mueller/halfway-to-i2k-2025-ome-zarr-tutorial.git
cd halfway-to-i2k-2025-ome-zarr-tutorial

Then, create a new virtual environment to separate this course’s dependencies from your other Python projects:

uv venv

Use the appropriate command for your operating system:

.venv\Scripts\activate

source .venv/bin/activate

Lastly, install everything needed for the workshop:

uv pip install -e .

Open Jupyter lab to interact with the provided notebooks like this:

jupyter lab

That’s it - you’re good to go!

Contents¶

We will do three basic things in this course:

• Generate some ome-zarr data: Write some Python code to convert microscopy data into the OME-ZARR format.
• Upload the data to cloud storage: Upload the generated OME-ZARR data to an S3-compatible cloud storage service.
• View the data from the web: Use a web-based viewer to access and visualize the data directly from the cloud.