Tools#

A list of tools and libraries with OME-Zarr support. These are developed by various members of the NGFF community. If you think your tool/library should be listed here, please open a pull request.

For tools supporting the core Zarr specification, agnostic to NGFF, see the Zarr documentation.

While some tools would fit multiple categories, we assigned each tool to a single candidate best matching category.

Contents#

Tools

Tools with a graphical interface#

Zarr viewers#

Want to view a Zarr? Use one of these.

Check this out to see viewer compatibility with various OME-Zarr features & versions.

Name	Link	Description
AGAVE		Desktop application for viewing multichannel volume data powered by your GPU
FIJI (MoBIE / BigDataViewer)		FIJI plug-in for exploring and sharing big multi-modal image and associated tabular data
FIJI (n5-ij)		FIJI plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API
ITKWidgets		Python tool for interactively viewing images (ex. in Jupyter)
Kiln		A WebGPU-native out-of-core rendering system for virtualized volumetric data
Microscopy Nodes		Blender add-on for visualizing high-dimensional microscopy data
napari		napari plug-in for viewing Zarr
Neuroglancer		A browser-based volume viewer
Odon		A spatial proteomics OME-Zarr viewer built in Rust.
QuPath		Open source software for digital pathology image analysis
syGlass		A VR desktop application for visualizing and segmenting 3D image data, with OME-Zarr streaming support.
Viv (Avivator, Vizarr, Vitessce, …)		A toolkit for interactive visualization of high-resolution, multiplexed bioimaging datasets. The viv toolkit is used by the Avivator, Vizarr and Vitessce image viewers, among others
Vol-E		A browser-based volume viewer
WEBKNOSSOS		An open-source tool for annotating and exploring large 3D image datasets

Zarr converters (with a UI)#

Want to convert your file to Zarr? Use one of these tools that has a user interface.

Name	Link	Description
NGFF-Converter		A desktop application for conversion of bioimage formats into OME-Zarr or OME-TIFF.

Tools for the programmatically inclined#

Zarr converters#

Want to convert from a different file format to a Zarr? Use one of these tools.

Check out the readers and writers below to interact with Zarrs in others ways as well conversion.

Name	Link	Description
BatchConvert		A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr.
bioformats2raw		Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-Zarr specification.
BioIO Conversion		CLI & scripting tool for easily converting images to OME-Zarr. Requires bioio-ome-zarr
EuBI-Bridge		A tool for distributed conversion of microscopic image collections into the OME-Zarr format.
ITKIOOMEZarrNGFF		An ITK external module for IO of images stored in OME-Zarr file format.
kfb2zarr		Convert KFBio whole slide images (.kfb, .kfbf) to OME-Zarr.
multiscale-spatial-image		Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr.
nd2		A Python library for reading nd2 files with native export to OME-Zarr, supporting multi-well plates and complete metadata preservation.
Nextflow (nf-omezarr)		A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw
PyMIF		A modular Python package to read, visualize, and convert multiscale microscopy image data from various microscope platforms to OME-Zarr.
stack-to-chunk		A Python library to convert stacks of 2D images to OME-Zarr with minimal memory use and maximum concurrency.
stack_to_multiscale_ngff		A tool for converting multi-terabyte stacks of images into a multiscale OME-Zarr.

Zarr readers & writers#

Want to read or write a Zarr? Use one of these tools.

Check this out to see reader/writer compatibility with various OME-Zarr features & versions.

Name	Link	Description
bfio		A Python interface to Bioformats using jpype for direct access to the library.
bia-zarr		A Python library for reading, writing, and manipulating OME-Zarr datasets, including thumbnail generation and OME-Zarr type detection.
Bio-Formats		A standalone Java library for reading and writing life sciences image file formats. Requires OMEZarrReader
BioIO		Image/Metadata Reading Writing for Microscopy Images in pure Python. Requires bioio-ome-zarr (formerly AICSImageIO)
iohub		Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata
ngff-zarr		A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
ngio		Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates
ome-writers		A Python library for streaming acquisition data to OME-Zarr or OME-TIFF, supporting multiple array backends.
ome-zarr-py		A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec.
Zarr.NET		A native .NET library for reading and writing Zarr microscopy data.

Zarr validation#

Want to validate a Zarr? Use one of these.

Name	Link	Description
ome-ngff-validator		Web page for validating OME-Zarr files.
ome-zarr-models		Python package and command line interface that can validate OME-Zarr files
yaozarrs		Bottom-up python library with models and CLI for creating & validating OME-Zarr groups and documents with optional extras for array-backend-agnostic I/O

Rendering libraries#

Libraries that support the rendering and navigation of OME-Zarr data, but that are not themselves applications with a graphical user interface.

Name	Link	Description