Repositories list

• bio-formats-build

  Public
  Bio-Formats top-level build for all components

  buildbio-formatsmeta-repo

  Shell

  •10•0•1•4•Updated Feb 5, 2025Feb 5, 2025

• upptime

  Public
  📈 Uptime monitor and status page for OME, powered by @upptime

  uptime-monitorstatus-pageupptime

  Markdown

  •

  MIT License

  •1•1•1•0•Updated Feb 5, 2025Feb 5, 2025

• action-workflows

  Public
  2•0•0•1•Updated Feb 5, 2025Feb 5, 2025

• action-ice

  Public
  1•0•0•1•Updated Feb 5, 2025Feb 5, 2025

• www.openmicroscopy.org

  Public
  OME main website

  jekyll-siteome

  HTML

  •

  Creative Commons Attribution 4.0 International

  •22•5•11•3•Updated Feb 5, 2025Feb 5, 2025

• bio-formats-documentation

  Public
  Bio-Formats documentation

  documentationbio-formats

  Java

  •

  BSD 2-Clause "Simplified" License

  •17•8•1•0•Updated Feb 5, 2025Feb 5, 2025

• bio-formats-examples

  Public
  Examples of usage of the Bio-Formats API

  apimavenexamples+ 2gradlebio-formats

  Java

  •

  Other

  •19•13•1•0•Updated Feb 5, 2025Feb 5, 2025

• bio-formats-fiji

  Public
  A simple POM to update Bio-Formats on a Fiji distribution

  fijibio-formats

  Shell

  •7•0•1•1•Updated Feb 5, 2025Feb 5, 2025

• bioformats

  Public
  Bio-Formats is a Java library for reading and writing data in life sciences image file formats. It is developed by the Open Microscopy Environment. Bio-Formats is released under the GNU General Public License (GPL); commercial licenses are available from Glencoe Software.

  javametadataimage+ 7format-readerformat-converterwhole-slide-imagingwsilightsheetbio-formatslife-sciences-image

  Java

  •

  GNU General Public License v2.0

  •245•388•200•10•Updated Feb 5, 2025Feb 5, 2025

• meeting-minutes

  Public
  Minutes from the weekly OME community meetings

  Creative Commons Attribution 4.0 International

  •6•0•1•0•Updated Feb 5, 2025Feb 5, 2025

• ome-model

  Public
  OME model (specification, code generator, implementation)

  imageschemadata-model+ 3specificationcode-generationome-model

  XSLT

  •

  Other

  •27•14•13•2•Updated Feb 5, 2025Feb 5, 2025

• omero-rois

  Public
  OMERO python ROI utils

  pythonomero

  Python

  •

  GNU General Public License v2.0

  •4•2•2•1•Updated Feb 3, 2025Feb 3, 2025

• omero-web

  Public
  Django-based OMERO.web client

  pythonclientdjango+ 2webomero

  Python

  •31•17•127•14•Updated Feb 3, 2025Feb 3, 2025

• bioimage-latency-benchmark

  Public
  Jupyter Notebook

  •

  Other

  •10•7•6•4•Updated Feb 3, 2025Feb 3, 2025

• omero-cli-server

  Public
  CLI plugin for managing an OMERO.server

  Python

  •

  GNU General Public License v2.0

  •3•1•0•3•Updated Feb 3, 2025Feb 3, 2025

• omero-cli-zarr

  Public
  omerozarrngff+ 1ome-zarr-converter

  Python

  •

  GNU General Public License v2.0

  •10•16•17•5•Updated Feb 3, 2025Feb 3, 2025

• ome-zarr-py

  Public
  Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

  omezarrngff+ 1ome-zarr

  Python

  •

  Other

  •55•171•54•24•Updated Feb 3, 2025Feb 3, 2025

• omero-demo-cleanup

  Public
  A CLI plugin for managing the disk space on the OME demo server

  Python

  •

  GNU General Public License v2.0

  •4•2•1•2•Updated Feb 3, 2025Feb 3, 2025

• omero_search_engine

  Public
  App which is used to search metadata (key-value pairs)

  Python

  •

  GNU General Public License v2.0

  •4•1•13•10•Updated Feb 3, 2025Feb 3, 2025

• omero-ms-zarr

  Public
  Experimental micro-service for implementing the Zarr spec over HTTP

  microserviceioomero+ 1zarr

  Java

  •

  GNU General Public License v2.0

  •12•18•17•1•Updated Feb 3, 2025Feb 3, 2025

• napari-ome-zarr

  Public
  A napari plugin for zarr backed OME-NGFF images

  napari-pluginzarrngff+ 1python

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •21•32•23•7•Updated Feb 3, 2025Feb 3, 2025

• ome_zarr_test_suite

  Public
  Test suite of reader and writer implementations

  Python

  •6•4•3•3•Updated Feb 3, 2025Feb 3, 2025

• omero-certificates

  Public
  OMERO server certificate management plugin

  pluginclideployment+ 3servercertificatesomero

  Python

  •

  GNU General Public License v2.0

  •7•0•2•3•Updated Feb 3, 2025Feb 3, 2025

• omero-plugins

  Public
  Collection of OMERO extensions (plugins, apps)

  ecosystembuildplugins+ 2omerometa-repo

  7•0•1•3•Updated Jan 31, 2025Jan 31, 2025

• ngff

  Public
  Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

  data-sciencecloudspec+ 2bioimagingfile-formats

  Bikeshed

  •

  Other

  •45•127•91•16•Updated Jan 30, 2025Jan 30, 2025

• omero-figure

  Public
  An OMERO.web app for creating Figures from images in OMERO

  webappomero

  JavaScript

  •

  GNU Affero General Public License v3.0

  •31•16•63•6•Updated Jan 30, 2025Jan 30, 2025

• ZarrReader

  Public
  Java

  •

  Other

  •11•7•23•1•Updated Jan 27, 2025Jan 27, 2025

• omero-iviewer

  Public
  An OMERO.web app allowing to view images

  webappomero

  JavaScript

  •

  Other

  •30•19•57•8•Updated Jan 27, 2025Jan 27, 2025

• ome2024-ngff-challenge

  Public
  Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data

  ome-ngffome-zarr-converter

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •14•19•8•4•Updated Jan 27, 2025Jan 27, 2025

• omero-documentation

  Public
  Sphinx-based documentation for the Open Microscopy Environment

  documentationomeroome

  Python

  •

  BSD 2-Clause "Simplified" License

  •51•22•27•7•Updated Jan 24, 2025Jan 24, 2025