Learning and Teaching Material#
This section provides additional resources related to NGFF and OME-Zarr intended for both new and experienced users.
Introductory Guide#
An Introduction to OME-Zarr for Big Bioimaging Data. Book explaining the theory and practice behind handling large bioimaging datasets using the OME-Zarr data format.
Hands-on Tutorials, Worked Examples and Training Materials#
Working with OME-Zarr NGFF. Tutorials with Zarr-python and ngff-zarr (Python). Source code is licensed under the Apache License 2.0 and documentation, images, and other non-code assets are licensed under Creative Commons Attribution 4.0 International (CC BY 4.0).
Jupyter notebook on how to read Zarr Images. Uses Zarr-python. Done under License BSD 2-Clause by University of Dundee for the EMBL-EBI Course 2025.
NEUBIAS OME-Zarr Training Materials. A collection of explanations and practical exercises on OME-Zarr developed by the NEUBIAS community. Examples using ome-ngff-validator, minio-cleient, ome_zarr_py, zarr-python, MoBIE, n5-ij, n5-viewer, napari, vizarr, neuroglancer, WebKnossos, ITK viewer, BioImage Archive tools, and BatchConverter.
Jupyter notebook on Loading Zarr Image from a public S3 store and analyzing it in parallel. Done under License BSD 2-Clause by University of Dundee.
Load Zarr Image with labels from a public S3 repository, analyze using Cellpose and compare results. Done under License BSD 2-Clause by University of Dundee.
Basic example of using OME-Zarr in a Nextflow pipeline. This tutorial contains an example on how to create new gaussian blurred ome-zarr image, segment this image and measure segment shape features. Uses Nextflow (CLI).
How to open OME-Zarr in Fiji. Instructions on how to use the N5-ij plugin to open OME-Zarr datasets in Fiji.
N5 API Tutorial. A tutorial on using the N5 API for reading and writing OME-Zarr data in Java.
ome-zarr models library tutorial. Tutorial on how to use the ome-zarr-models library to read and write OME-Zarr data.
Talks and Demos#
Title |
Speaker(s) |
Event |
Link |
|---|---|---|---|
Tooling Around the Next-Generation File Format OME-Zarr |
Buğra Özdemir |
Workshop ‘Euro-BioImaging’s Guide to FAIR Bioimage Data 2024’ |
|
Introduction to OME-NGFF next generation file format |
Christian Tischer |
EMBL - Global BioImaging (2022) |
|
Towards open and standardised imaging data: an introduction to Bio Formats, OME-TIFF, and OME-Zarr |
Josh Moore |
EMBL-EBI Webinar (2025) |
|
Exploration and Analysis of Image Data using OME-Zarr |
Joel Luethi & Buğra Özdemir |
Euro-BioImaging Virtual Pub (2023) |
|
Introduction to next-generation file formats and how to work with OME-Zarr |
Buğra Özdemir |
Euro-BioImaging Image Data Community Days 2025 |