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 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) |
|
MoBIE is a FIJI plug-in for exploring and sharing big multi-modal image and associated tabular data |
FIJI (BigDataViewer) |
BigDataViewer ships with FIJI and opens local or remote OME-Zarr via its HDF5/N5/Zarr/OME-NGFF Viewer, with support for multiscale pyramids and labels |
|
FIJI (BigVolumeBrowser) |
FIJI plugin for 3D vieweing and rendering of multiple (local and remote) multiscale datasets and labels, via n5-viewer and ome-zarr-fiji backends. |
|
FIJI (n5-ij) |
n5-ij is a FIJI plug-in for loading and saving image data to OME-Zarr and other formats supported by the N5 API |
|
FIJI (ome-zarr-fiji) |
ome-zarr-fiji is a FIJI plug-in offering drag & drop / copy & paste handlers for OME-Zarrs data. |
|
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) |
|
clearscale |
|
Python library for handling OME metadata without learning the spec |
ez-zarr |
|
A Python and R package for reading and plotting OME-Zarr images. |
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 |
|---|---|---|
OMEZarrTileSource |
|
An OpenSeadragon tile source for the OME-Zarr bioimage file format. |
ome-zarr.js |
|
A JavaScript library for simple rendering of thumbnails and images. |
idetik |
|
A library for building web-based image viewers. |