Open Microscopy Environment

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339 repositories

prod-playbooks
Public
Playbooks used by the OME team for deploying production services including OMERO
ansible deployment production playbooks omero
Jinja
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BSD 2-Clause "Simplified" License
•18•4•11•1•Updated Jan 10, 2025Jan 10, 2025
omero-python-superbuild
Public
OMERO build for Python server components
python build omero meta-repo
4•0•1•0•Updated Jan 10, 2025Jan 10, 2025
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•0•Updated Jan 10, 2025Jan 10, 2025
omero-plugins
Public
Collection of OMERO extensions (plugins, apps)
ecosystem build plugins omero meta-repo
7•0•1•2•Updated Jan 10, 2025Jan 10, 2025
omero-documentation
Public
Sphinx-based documentation for the Open Microscopy Environment
documentation omero ome
Python
•
BSD 2-Clause "Simplified" License
•51•22•27•6•Updated Jan 10, 2025Jan 10, 2025
bio-formats-build
Public
Bio-Formats top-level build for all components
build bio-formats meta-repo
Shell
•10•0•1•5•Updated Jan 9, 2025Jan 9, 2025
omero-py
Public
Python project containing Ice remoting code for OMERO
python component lib omero
Python
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GNU General Public License v2.0
•33•24•73•14•Updated Jan 9, 2025Jan 9, 2025
omero-figure
Public
An OMERO.web app for creating Figures from images in OMERO
webapp omero
JavaScript
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GNU Affero General Public License v3.0
•31•16•65•3•Updated Jan 9, 2025Jan 9, 2025
ome-model
Public
OME model (specification, code generator, implementation)
image schema data-model specification code-generation ome-model
XSLT
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Other
•27•14•14•1•Updated Jan 9, 2025Jan 9, 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
•54•169•54•12•Updated Jan 8, 2025Jan 8, 2025
omero-server-docker
Public
OMERO.server production docker image
docker ome openmicroscopy omero-server omero
Shell
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BSD 2-Clause "Simplified" License
•28•14•11•8•Updated Jan 8, 2025Jan 8, 2025
www.openmicroscopy.org
Public
OME main website
jekyll-site ome
HTML
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Creative Commons Attribution 4.0 International
•22•5•10•2•Updated Jan 8, 2025Jan 8, 2025
ome-metakit
Public
Library for reading Metakit database files
metakit
Java
•
GNU General Public License v2.0
•7•2•0•0•Updated Jan 8, 2025Jan 8, 2025
bio-formats-documentation
Public
Bio-Formats documentation
documentation bio-formats
Java
•
BSD 2-Clause "Simplified" License
•17•8•1•1•Updated Jan 7, 2025Jan 7, 2025
ome-common-java
Public
Java library providing common functionality for all OME Java components
Java
•
Other
•19•2•1•1•Updated Jan 7, 2025Jan 7, 2025
napari-ome-zarr
Public
A napari plugin for zarr backed OME-NGFF images
napari-plugin zarr ngff python
Python
•
BSD 3-Clause "New" or "Revised" License
•21•32•23•7•Updated Jan 6, 2025Jan 6, 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 Jan 6, 2025Jan 6, 2025
ome_zarr_test_suite
Public
Test suite of reader and writer implementations
Python
•6•4•3•3•Updated Jan 6, 2025Jan 6, 2025
omero-cli-zarr
Public
omero zarr ngff ome-zarr-converter
Python
•
GNU General Public License v2.0
•10•16•17•4•Updated Jan 6, 2025Jan 6, 2025
bioimage-latency-benchmark
Public
Jupyter Notebook
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Other
•10•7•6•4•Updated Dec 23, 2024Dec 23, 2024
ome2024-ngff-challenge
Public
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
ome-ngff ome-zarr-converter
Python
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BSD 3-Clause "New" or "Revised" License
•14•17•7•3•Updated Dec 23, 2024Dec 23, 2024
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 whole-slide-imaging wsi lightsheet bio-formats life-sciences-image
Java
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GNU General Public License v2.0
•243•384•198•12•Updated Dec 20, 2024Dec 20, 2024
omero-rois
Public
OMERO python ROI utils
python omero
Python
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GNU General Public License v2.0
•4•2•2•1•Updated Dec 19, 2024Dec 19, 2024
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 image database server omero java
Java
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GNU General Public License v2.0
•101•202•26•6•Updated Dec 18, 2024Dec 18, 2024
omero-scripts
Public
Core OMERO Scripts
scripts python omero
Python
•32•12•16•4•Updated Dec 17, 2024Dec 17, 2024
omero-guides
Public
Guides for using OMERO
docs help omero guides manuals omero-training
Python
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BSD 2-Clause "Simplified" License
•5•1•15•1•Updated Dec 17, 2024Dec 17, 2024
ngff
Public
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
data-science cloud spec bioimaging file-formats
Bikeshed
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Other
•43•123•91•19•Updated Dec 17, 2024Dec 17, 2024
omero-cli-server
Public
CLI plugin for managing an OMERO.server
Python
•
GNU General Public License v2.0
•3•1•0•3•Updated Dec 16, 2024Dec 16, 2024
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
•14•17•6•0•Updated Dec 16, 2024Dec 16, 2024
omero-guide-scripts
Public
BSD 2-Clause "Simplified" License
•3•0•0•0•Updated Dec 16, 2024Dec 16, 2024