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ngio workshop

Hands-on workshop materials to get started with ngio. ngio is a Python library designed to simplify bioimage analysis workflows, offering an intuitive interface for working with OME-Zarr files.

Each notebook is self-contained: it declares its own dependencies inline and marimo uses uv to create an isolated environment automatically.

Running locally

Prerequisites

On Unix-like systems (Linux, macOS):

curl -LsSf https://astral.sh/uv/install.sh | sh

and, on Windows:

powershell -ExecutionPolicy ByPass -c "irm https://astral.sh/uv/install.ps1 | iex"

Running a notebook

uvx marimo edit --sandbox notebooks/<notebook>.py

On first run uv will create an isolated environment for the notebook and install its dependencies. This takes a minute; subsequent runs are instant.

Running in the cloud (no installation)

Click the Open in molab badge next to any notebook in the table below to run it in your browser via molab. No local setup required — a free molab account is needed to execute cells.

Warning: we observed some issues when leaving a molab notebook idle for a long time, or when going in and out of the notebook. If you encounter errors close tha tab re-open the notebook.

Following along with the static documentation

A static version of the notebooks is available in the documentation. You can follow along with the examples there, but you won't be able to modify and execute cells.

Workshop modules

Module Topic Open in molab Static HTML
1 — Introduction OME-Zarr containers, images, labels, and tables Open in molab View
2 — Iterators Declarative image processing iterators Open in molab View

Slides

You can find the slides for the workshop as PDF here.