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.
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 / 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) |
Microscopy Nodes |
|
Blender add-on for visualizing high-dimensional microscopy data |
napari |
napari plug-in for viewing Zarr |
|
Neuroglancer |
A browser-based volume viewer |
|
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 |
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Vol-E |
A browser-based volume viewer |
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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. |
multiscale-spatial-image |
|
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-Zarr. |
Nextflow (nf-omezarr) |
A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw |
|
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. |
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 |
ngio |
|
Python package for bject-based API for opening, exploring, and manipulating OME-Zarr images and high-content screening (HCS) plates |
ngff-zarr |
|
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation. |
ome-zarr-py |
|
A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME-Zarr spec. |
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 |
Other tools and libraries#
Tools that do not explicitly fit into any of the above categories (ex. Zarr computation workflow orchestrators)
Name |
Link |
Description |
|---|---|---|
Fileglancer |
|
A webapp for browsing, sharing, and viewing OME-Zarr images. |
Fractal |
|
A framework to process OME-Zarr data at scale with modular processing tasks and to prepare it for interactive visualization. |
Ilastik |
|
An interactive learning and segmentation toolkit |
Mastodon |
|
A large-scale tracking and track-editing framework for large, multi-view images. |
Nyxus |
|
A scalable library for calculating features from intensity-label image data. |
ome-zarr.js |
|
A JavaScript library for simple rendering of thumbnnails and images. |
SpatialData |
|
An open and universal framework for processing spatial omics data. |
Zarrcade |
|
Create searchable web-based OME-Zarr image galleries. |