Services
Format Development and Ambassadorship
Learn more about data formats in bioimaging and how next generation file formats such as OME-Zarr can store large data files including metadata of your favorite microscope. We help steering and driving this development.
Who is the service recommended for?
- Life scientists: explore and reuse NGFF bioimage data and workflows
- Bioimage analysts: reuse NGFF data for workflow development
- Data format developers: reuse the public OME-Zarr bioimage data collected in the 2024 NGFF challenge to drive format development
Which infrastructure do you need?
- for conversion of monolithic file format to NGFF: workflow or tool such as the NGFF File Converter
Which expertise do you need?
- for usage of OME-Zarr: basic understanding of conventional (single file) vs next-generation (chunked) bioimage formats is recommended in case of handling of large datasets
What are next generation file formats and how can you benefit from them?
In modern microscopy, increasing size and complexity of bioimage datasets demand data formats that can better implement scalability, cloud-native workflows as well as standardized metadata to ensure FAIR principles.
So-called next-generation file formats (NGFFs) are cloud-ready, chunked, multidimensional data containers for data and metadata storage. This structure allows
- Fast random access to any part of an image through individually referenceable sub-datasets (so-called chunks)
- Partial data streaming over the web
- Parallel processing in high-performance and cloud environments
- Machine-actionable standardized metadata linked to the binary image data
OME-Zarr is a prominent NGFF that combines chunked image data with embedded metadata that meet community standards. Read more about the generic Zarr format, OME-Zarr and the OME metadata format developed by the Open Microscopy Environment team and the integration of both as OME-Zarr.
We contributed to the collaborative NGFF challenge in 2024. This project collected several hundred TB of OME-Zarr data across microscopic techniques and institutions worldwide. Explore and reuse the datasets.
If you are a software developer and interested in our work, get in touch with us and contribute to our work.
How to get started:
- Familiarize with bioimage file formats in general and next generation file formats particularly. If you have basic proficiency in python, explore how to open, convert and visualize datasets in OME-Zarr in this self-learning tutorials of Euro-BioImaging.
- Convert own datasets to next generation file formats, for example using the NGFF File Converter.
Do you know that public bioimage databases such as the BioImage Archive and the Image Data Resource (IDR) support and drive the deposition of NGFF bioimage datasets?
