Next-Generation File Formats (NGFF) + OME-Zarr#

Welcome to the Next-Generation File Formats (NGFF) main page! This site is dedicated to providing resources for the NGFF community and those that are interested in getting started with OME-Zarr.

In summary, OME-Zarr allows you to store, share and stream large images like these 500 GB:

You can find more samples of such data from the Image Data Resource at https://idr.github.io/ome-ngff-samples/.

NGFF vs OME-Zarr, what is the difference?#

OME-Zarr is the file format that the NGFF community has settled on to address issues of scalability and interoperability described below.

NGFF is the community-driven process for designing the next generation of bioimaging formats. NGFF brings together the community to define shared specifications, metadata standards, and best practices. OME-Zarr implements those decisions, providing a practical, open, and scalable way to store and share modern microscopy data. As the NGFF specifications evolve, OME-Zarr evolves with them — ensuring the format reflects the needs and experience of the wider community.

What is an OME-Zarr?#

An OME-Zarr is a file format optimized for storying, viewing, & sharing large images. There are two parts to an OME-Zarr:

  • The “Zarr” part describes how the pixel data for the images are laid out

  • The “OME”, which stands for Open Microscopy Environment, part describes metadata about the pixel data. This includes metadata such as:

    • spatial relationships

    • high content screening data

    • well data

    • and more!

Why would I use OME-Zarr?#

OME-Zarr files have two major benefits:

  • Chunking is inherent to “Zarr” files. This means “Zarr” files are stored in independently-accessible blocks.

    • Storage: Microscopy images can be quite large and can therefore reach Cloud system storage limits for individual files; the chunked nature of a Zarr can alleviate this issue. Some storage systems may also duplicate byte-equivalent files, so a chunked file like Zarr may save storage space.

    • Viewing: Viewers can target specific chunks to load based upon the current view, reducing lag, & enabling massive images to be viewed within browsers.

    • Cost: When viewing or reading data, the total cost of accessing a Zarr file on the cloud may be less than a more monolithic file format due to the more efficient data access patterns. Ex. A viewer can just access the chunks of the image it needs to display rather than the entire image.

  • “OME-Zarr” is a “Zarr” with embedded standardized metadata in the Open Microscopy Environment (OME) format.

    • Sharing: A standardized imaging metadata format can ease cross-organization file sharing and can therefore aid organizational collaboration and data sharing.

    • Interoperability: Standardized metadata can also enable the interoperability of tools.

When would I not use OME-Zarr?#

  • If your file isn’t very big and you’re working with local data, the current specification of OME-Zarr can be less convenient than a single-file format and the benefits are limited. Planned expansions to the OME-Zarr specification will make it more convenient to work with it in these scenarios (e.g. single-file Zarrs) and add features that might make it beneficial to use OME-Zarr even in these scenarios (e.g. transformations).

  • If your original file is lossy compressed, you will see a large increase in file size as the images are decompressed into OME-Zarr. There is not yet support for transferring lossy compressed image tiles to OME-Zarr. This currently impacts most whole slide image (WSI) formats such as SVS, CZI, and NDPI, which are lossy JPEG compressed by default and see about a 10x size increase into OME-Zarr.

Who is using OME-Zarr?#

These are some of the organizations (and their dataset pages) that are using OME-Zarr for their data.

How do I use OME-Zarr?#

Have other questions?#

Check out the pages below, including the FAQ page.