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.
In addition to this collection, an evaluation of selected tools/libraries is available on https://ome.github.io/ome-ngff-tools/.
Dataset Viewers#
Name |
Link |
Description |
|---|---|---|
AGAVE |
|
A desktop application for viewing multichannel volume data. |
ITKWidgets |
|
A Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry. |
Microscopy Nodes |
|
A Blender add-on for visualizing high-dimensional microscopy data. |
MoBIE/BDV |
|
A Fiji plugin for exploring and sharing big multi-modal image and associated tabular data. |
napari |
|
A fast, interactive, multi-dimensional image viewer for Python that supports OME-Zarr with the napari-ome-zarr plugin. |
Neuroglancer |
|
A WebGL-based viewer for volumetric data. |
n5-ij |
|
A Fiji plugin for loading and saving image data to OME-Zarr and other formats supported by the N5 API. |
Viv (Avivator, Vizarr, Vitessce, …) |
|
A WebGL-powered 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 built with React and WebGL (Three.js). |
WEBKNOSSOS |
|
An open-source tool for annotating and exploring large 3D image datasets. |
Dataset Conversion#
Many of the tools in the File Reading/Writing section below also support format 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. |
nf-omezarr |
|
A Nextflow pipeline for converting directories of images to OME-Zarr using bioformats2raw |
NGFF-Converter |
|
A GUI application for conversion of bioimage formats into OME-Zarr or OME-TIFF. |
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. |
EuBI-Bridge |
|
A tool for distributed conversion of microscopic image collections into the OME-Zarr format. |
Dataset Reading/Writing#
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 |
|
(formerly AICSImageIO AllenCellModeling/aicsimageio) Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in pure Python. Requires bioio-ome-zarr |
iohub |
|
Pythonic and parallelizable I/O for N-dimensional imaging data with OME metadata |
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. |
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. |
Various libraries for reading/writing OME-Zarr files in Python were evaluated as part of the BioVisionCenter “Next generation bioimage analysis workflows hackathon” 2023 in Zurich, Switzerland: https://github.com/jwindhager/ome-ngff-readers-writers/.
Dataset Validation#
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#
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. |
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. |