Open Microscopy Environment

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345 repositories

upptime
Public
📈 Uptime monitor and status page for OME, powered by @upptime
uptime-monitor status-page upptime
Markdown
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MIT License
•1•1•1•1•Updated Dec 9, 2025Dec 9, 2025
status
Public
Status dashboard for the OME project
status dashboard gh-pages ome
HTML
•4•1•0•0•Updated Dec 9, 2025Dec 9, 2025
omero-rois
Public
OMERO python ROI utils
python omero
Python
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GNU General Public License v2.0
•5•3•2•3•Updated Dec 8, 2025Dec 8, 2025
omero-cli-server
Public
CLI plugin for managing an OMERO.server
Python
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GNU General Public License v2.0
•3•1•0•4•Updated Dec 8, 2025Dec 8, 2025
omero-ms-zarr
Public
Experimental micro-service for implementing the Zarr spec over HTTP
microservice io omero zarr
Java
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GNU General Public License v2.0
•12•20•17•1•Updated Dec 8, 2025Dec 8, 2025
omero-cli-zarr
Public
omero zarr ngff ome-zarr-converter
Python
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GNU General Public License v2.0
•10•18•20•12•Updated Dec 8, 2025Dec 8, 2025
bioimage-latency-benchmark
Public
Jupyter Notebook
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Other
•10•8•6•4•Updated Dec 8, 2025Dec 8, 2025
omero_search_engine
Public
App which is used to search metadata (key-value pairs)
Python
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GNU General Public License v2.0
•4•2•15•11•Updated Dec 8, 2025Dec 8, 2025
omero-web
Public
Django-based OMERO.web client
python client django web omero
Python
•38•23•131•14•Updated Dec 8, 2025Dec 8, 2025
omero-demo-cleanup
Public
A CLI plugin for managing the disk space on the OME demo server
Python
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GNU General Public License v2.0
•4•2•1•2•Updated Dec 8, 2025Dec 8, 2025
ome-zarr-py
Public
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
ome zarr ngff ome-zarr
Python
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Other
•65•217•74•12•Updated Dec 8, 2025Dec 8, 2025
omero-certificates
Public
OMERO server certificate management plugin
plugin cli deployment server certificates omero
Python
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GNU General Public License v2.0
•7•0•2•2•Updated Dec 8, 2025Dec 8, 2025
napari-ome-zarr
Public
A napari plugin for zarr backed OME-NGFF images
python napari-plugin zarr ngff
Python
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BSD 3-Clause "New" or "Revised" License
•24•42•28•6•Updated Dec 8, 2025Dec 8, 2025
ome_zarr_test_suite
Public
Test suite of reader and writer implementations
Python
•6•4•3•3•Updated Dec 8, 2025Dec 8, 2025
omero-cli-transfer
Public
An OMERO CLI plugin for creating transfer packets between OMERO servers.
omero omero-server omero-import
Python
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GNU General Public License v2.0
•17•19•5•0•Updated Dec 8, 2025Dec 8, 2025
docker-example-omero
Public
OMERO Docker compose example
docker deployment omero omero-server omero-web
Shell
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BSD 2-Clause "Simplified" License
•33•28•5•0•Updated Dec 6, 2025Dec 6, 2025
omero-scripts
Public
Core OMERO Scripts
python scripts omero
Python
•32•14•16•2•Updated Dec 5, 2025Dec 5, 2025
ngff
Public
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
data-science cloud spec bioimaging file-formats
Python
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Other
•59•146•114•22•Updated Dec 5, 2025Dec 5, 2025
omero-cli-render
Public
OMERO command-line tool for rendering
python plugin cli command omero
Python
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GNU General Public License v2.0
•10•2•6•6•Updated Dec 5, 2025Dec 5, 2025
omero-iviewer
Public
An OMERO.web app allowing to view images
webapp omero
JavaScript
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Other
•35•21•60•14•Updated Dec 4, 2025Dec 4, 2025
www.openmicroscopy.org
Public
OME main website
jekyll-site ome
HTML
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Creative Commons Attribution 4.0 International
•26•6•15•0•Updated Dec 4, 2025Dec 4, 2025
omero-build
Public
OMERO top-level build for all components
build omero meta-repo
Dockerfile
•7•1•3•3•Updated Dec 4, 2025Dec 4, 2025
ome-resources-monitor
Public archive
BSD 2-Clause "Simplified" License
•3•0•1•0•Updated Dec 4, 2025Dec 4, 2025
openmicroscopy
Public
OME (Open Microscopy Environment) develops open-source software and data format standards for the storage and manipulation of biological light microscopy data. A joint project between universities, research establishments and industry in Europe and the USA, OME has over 20 active researchers with strong links to the microscopy community. Funded …
python java image database server omero
Java
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GNU General Public License v2.0
•103•214•23•5•Updated Dec 4, 2025Dec 4, 2025
omero-gateway-java
Public
Gradle project containing OMERO Java Client Library
java api build sdk component gradle jar omero
Java
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GNU General Public License v2.0
•10•1•15•2•Updated Dec 3, 2025Dec 3, 2025
omero-web-docker
Public
OMERO.web production docker image
docker omero ome openmicroscopy omero-web
Makefile
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BSD 2-Clause "Simplified" License
•21•7•13•7•Updated Dec 3, 2025Dec 3, 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.
java metadata image format-reader format-converter bio-formats life-sciences-image whole-slide-imaging wsi lightsheet
Java
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GNU General Public License v2.0
•250•407•162•12•Updated Dec 3, 2025Dec 3, 2025
omero-web-zarr
Public
Implementation of OME-Zarr API with an omero-web app
Python
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GNU Affero General Public License v3.0
•5•5•5•3•Updated Dec 2, 2025Dec 2, 2025
ngff-spec
Public
(EXPERIMENTAL) Investigation of splitting NGFF specifications out of ome/ngff
Python
•4•9•2•3•Updated Dec 2, 2025Dec 2, 2025
presentations
Public
HTML-based presentations from the OME team.
html reveal-js presentations
HTML
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Creative Commons Zero v1.0 Universal
•19•0•0•0•Updated Dec 2, 2025Dec 2, 2025