Ecosystem#
Workflows and data formats that adopt OME-Zarr and build upon it for extended capabilities and interoperabilitieswith additional systems.
It extends the tools section by including projects that are not necessarily tools for viewing, writing, reading, converting, validating or processing OME-Zarr data, but that are still part of a ecosystem of projects with first-class, dedicated support for OME-Zarr.
It fits microscope acquisition software, analysis pipelines, standards and extensions, gallery-like displays, integrative workflows, and the like.
Standards and extensions#
Name |
Link |
Description |
Status |
|---|---|---|---|
SpatialData |
|
An open and universal framework for processing spatial omics data. |
|
BIDS |
|
A community-developed standard for organizing and describing neuroscientific data, currently adding support for OME-Zarr. |
Gallery-like displays#
Tooling for sharing collections of OME-Zarr datasets in different ways.
Name |
Link |
Description |
|---|---|---|
BioFileFinder |
|
A platform from the Allen Institute for Cell Science to browse lists of files, with first-class OME-Zarr support. |
Fileglancer |
|
A webapp for browsing, sharing, and viewing OME-Zarr images. |
Zallery |
|
A React-based gallery for browsing OME-Zarr datasets, developed by the SSBD (RIKEN). |
Zarrcade |
|
Searchable web-based OME-Zarr image galleries developed by Janelia. |
Zowser |
|
A gallery template for sharing sets of images built upon the ome2024-ngff-challenge. |
Microscope acquisition software#
Name |
Link |
Description |
|---|---|---|
mesoSPIM-control |
|
Python/PyQt acquisition software for mesoSPIM light-sheet microscopes with OME-Zarr multi-scale output support. |
Squid |
|
An open-source confocal microscope with software to acquire and write OME-Zarr data. |
Integrative workflows#
Tools that integrate OME-Zarr into workflows that support OME-Zarr as either as an input, output or intermediate format for processing/management pipelines.
Name |
Link |
Description |
|---|---|---|
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 |
Nyxus |
|
A scalable library for calculating features from intensity-label image data. |
Mastodon |
|
A large-scale tracking and track-editing framework for large, multi-view images. |
multiview-stitcher |
Python package for aligning, fusing, and stitching large 2D/3D image datasets, with first-class support for OME-Zarr workflows. |
|
NL-BIOMERO |
|
An OMERO integration for in-place OME-Zarr import and remote execution of containerized bioimage workflows on HPC systems directly from OMERO.web. |
omero-zarr-pixel-buffer |
|
An OMERO server extension for reading OME-Zarr data from local or S3 storage. |
Data sharing#
Platforms with dedicated support for sharing OME-Zarr datasets, open to public data submission.
Name |
Link |
Description |
|---|---|---|
BioImage Archive |
|
A public repository for bioimaging data, with support for submissions of OME-Zarr datasets. |
HuggingFace Hub |
A platform for sharing machine-learning datasets, with ongoing updates for first-class support for OME-Zarr datasets. |
Of course, many other platforms support sharing OME-Zarr datasets, but don’t necessarily parse the OME metadata or provide any kind of custom support.One may share OME-Zarr datasets and get a DOI (but no S3-like access) in platforms like Zenodo, Figshare, Dryad, etc.
Conversely, one may not get a DOI, but may be able to share datasets with S3-like access for streaming/testing in platforms like HuggingFace Buckets, Cloudflare R2, AWS S3, Google Cloud Storage, Microsoft Azure Blob Storage, etc. Some of them offer free tiers for small and medium public datasets, as well as programs for supporting open science data sharing (like AWS Open Data, Google Cloud Public Datasets, Microsoft Azure Open Datasets, etc).
Extended metadata frameworks#
While these projects do not adopt OME-Zarr, they are resources studied in the context of extending the metadata capabilities of OME-Zarr.
They are all projects which users of OME-Zarr may find useful to be aware of for workflows that require more complex metadata management, or for integration with other ecosystems.
Name |
Link |
Description |
Status |
|---|---|---|---|
Thumbnails convention |
|
A convention for storing thumbnail images in PNG or JPEG format alongside OME-Zarr datasets. |
|
RO-Crate |
|
An approach to packaging research data with metadata with pilots for OME-Zarr integration. |
work in progress (see also the ome2024-ngff-challenge) |
BioCroissant |
|
A community effort to extend the Croissant standard for packaging and sharing machine learning datasets in biology. |