Welcome to the NGFF Workshop!
This workshop covers several key steps for working with OME-Zarr datasets, including converting, inspecting, validating, opening, saving, and visualizing OME-Zarr data.
The sections given below are intended to guide you through working with OME-Zarr datasets using a variety of tools and libraries. Each section is designed to cover a specific task and introduces some of the existing tools to address that particular task.
It is important to note that this workshop covers OME-Zarr version 0.4. With transition to the version 0.5, many changes have been implemented in the specifications. These changes are, however, not covered or discussed here.
Prerequisites
Data
The workshop will use several example image datasets. Please download the zip file and extract the datasets to a convenient directory.
Installation of the tools
The easiest way to install the required tools is via mamba.
Installing Mamba
If you do not already have mamba, you can acquire it via Miniforge. Follow the instructions here to set up Miniforge on your system.
- Unix-based systems (Linux/macOS): Installing Miniforge will make the mamba command available in your terminal.
- Windows: Miniforge installation will set up a new command prompt called Miniforge Prompt. You can find it by typing "Miniforge" in the Windows search bar. The mamba command will be available in this prompt.
Setting Up the Workshop Environment
Once mamba is installed, run the following commands to clean up any existing package cache and create the environment:
mamba clean --all
mamba create -n ngff_workshop -c conda-forge -c euro-bioimaging eubi-bridge napari-ome-zarr pyqt=5.*
Fiji Installation
Ensure that an up-to-date version of Fiji is installed on your system.