Tools#
A list of tools and libraries with OME-Zarr support. These are developed by various members of the OME-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/.
Image viewers with OME-Zarr support#
AGAVE#
A desktop application for viewing multichannel volume data.
ITKWidgets#
InsightSoftwareConsortium/itkwidgets
A Python interface for visualization on the web platform to interactively generate insights into multidimensional images, point sets, and geometry.
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.
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.
WEBKNOSSOS#
An open-source tool for annotating and exploring large 3D image datasets.
AICS Image Viewer#
allen-cell-animated/website-3d-cell-viewer
A browser-based volume viewer built with React and WebGL (Three.js).
Tools for converting image files to OME-Zarr#
bioformats2raw#
glencoesoftware/bioformats2raw
Java application to convert image file formats, including .mrxs, to an intermediate Zarr structure compatible with the OME-NGFF specification.
NGFF-Converter#
glencoesoftware/NGFF-Converter
A GUI application for conversion of bioimage formats into OME-NGFF (Next-Generation File Format) or OME-TIFF.
stack_to_multiscale_ngff#
CBI-PITT/stack_to_multiscale_ngff
A tool for converting multi-terabyte stacks of images into a multiscale OME-NGFF Zarr.
BatchConvert#
A Nextflow based command-line tool that wraps bioformats2raw for parallelised conversion of image data collections to OME-Zarr.
Libraries for reading/writing OME-Zarr files#
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/.
AICSImageIO#
Image Reading, Metadata Conversion, and Image Writing for Microscopy Images in pure Python.
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.
ngff-zarr#
A lean and kind Open Microscopy Environment (OME) Next Generation File Format (NGFF) Zarr implementation.
multiscale-spatial-image#
spatial-image/multiscale-spatial-image
Generate a multiscale, chunked, multi-dimensional spatial image data structure that can serialized to OME-NGFF.
ome-zarr-py#
A Python library for reading and writing multi-resolution images stored as Zarr filesets, according to the OME NGFF spec.
ITKIOOMEZarrNGFF#
InsightSoftwareConsortium/ITKIOOMEZarrNGFF
An ITK external module for IO of images stored in Zarr-backed OME-NGFF file format.
Other tools and libraries#
Fractal#
fractal-analytics-platform/fractal
A framework to process high content screening data at scale and to prepare it for interactive visualization.
Nyxus#
A scalable library for calculating features from intensity-label image data.
ome-ngff-validator#
Web page for validating OME-NGFF files.
SpatialData#
An open and universal framework for processing spatial omics data.
tensorstore#
Library for reading and writing large multi-dimensional arrays (e.g., Zarr).