Understanding OME-ZARR

OME-NGFF (Open Microscopy Environment - Next Generation File Format) is a specification for storing bioimaging data in a cloud-ready, analysis-friendly format based on Zarr.

What is OME-ZARR?

OME-ZARR defines conventions for storing multi-dimensional microscopy images with:

Multiscale pyramids: Multiple resolution levels for efficient visualization at different zoom levels
Labeled axes: Named dimensions (t, c, z, y, x) with types (time, channel, space)
Coordinate transformations: Scale and translation metadata for physical coordinates
Labels/segmentations: Associated segmentation masks stored alongside images
HCS plates: High-content screening data with well-plate structures

Resources

Specification

OME-NGFF Specification - The official specification document
Specification GitHub Repository - Specification source
NGFF website repository - Source for NGFF website and place for discussions about the format

Zarr Format

Zarr Documentation - The underlying storage format
Zarr v3 Specification - Latest zarr format

Tools

A comprehensive list of tools to generate, convert, view or work with ome-zarr images in general is provided on the ngff website

Community

Image.sc Forum - Community discussions about OME-NGFF
OME Website - Open Microscopy Environment