Open Microscopy Environment

Software and data format standards for management of microscopy image data. Joint project between international private and public research

Pinned Repositories

apacheds-docker
Dockerfile to build an ApacheDS container providing an LDAP and optionally a Kerberos service.
Language:Python42 8 1560
bio-formats-examples
Examples of usage of the Bio-Formats API
Language:Java15 10 519
bioformats
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.
Language:Java370 30 474241
napari-ome-zarr
A napari plugin for zarr backed OME-NGFF images
Language:Python26 10 5321
ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Language:Bikeshed110 23 12638
ome-zarr-py
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Language:Python144 20 13952
omero-deployment-examples
Examples playbooks for installing OMERO with Ansible and Docker
10 13 412
omero-figure
An OMERO.web app for creating Figures from images in OMERO
Language:JavaScript15 12 15830
omero-insight
Gradle project containing insight java client for OMERO
Language:Java7 10 21414
openmicroscopy
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 by private and public research grants, OME has been a major force on the international microscopy stage since 2000.
Language:Java189 26 82100

Open Microscopy Environment's Repositories

ome/bioformats
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.
Language:Java370 30 474241
ome/openmicroscopy
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 by private and public research grants, OME has been a major force on the international microscopy stage since 2000.
Language:Java189 26 82100
ome/ome-zarr-py
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Language:Python144 20 13952
ome/napari-ome-zarr
A napari plugin for zarr backed OME-NGFF images
Language:Python26 10 5321
ome/omero-documentation
Sphinx-based documentation for the Open Microscopy Environment
Language:Shell20 13 6250
ome/omero-py
Python project containing Ice remoting code for OMERO
Language:Python19 11 11032
ome/omero-iviewer
An OMERO.web app allowing to view images
Language:JavaScript18 15 8528
ome/omero-ms-zarr
Experimental micro-service for implementing the Zarr spec over HTTP
Language:Java16 15 3412
ome/omero-web
Django-based OMERO.web client
Language:Python16 12 20028
ome/omero-cli-zarr
Language:Python15 8 2310
ome/omero-figure
An OMERO.web app for creating Figures from images in OMERO
Language:JavaScript15 12 15830
ome/omero-scripts
Core OMERO Scripts
Language:Python11 10 2332
ome/bioimage-latency-benchmark
Language:Jupyter Notebook8 9 910
ome/ome2024-ngff-challenge
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
Language:Python7 17 02
ome/www.openmicroscopy.org
OME main website
Language:HTML5 14 1822
ome/ome_zarr_test_suite
Test suite of reader and writer implementations
Language:Python4 12 46
ome/ome-ngff-validator
Web page for validating OME-NGFF files
Language:Svelte3 6 73
ome/omero-rois
OMERO python ROI utils
Language:Python2 8 44
ome/bio-formats-build
Bio-Formats top-level build for all components
Language:Shell1 7 210
ome/omero-build
OMERO top-level build for all components
Language:Dockerfile1 9 57
ome/omero-cli-server
CLI plugin for managing an OMERO.server
Language:Python1 4 03
ome/omero-common
Gradle project containing common utilities for OMERO
Language:Java1 9 111
ome/omero-demo-cleanup
A CLI plugin for managing the disk space on the OME demo server
Language:Python1 11 24
ome/omero-plugins
Collection of OMERO extensions (plugins, apps)
1 10 37
ome/omero_search_engine
App which is used to search metadata (key-value pairs)
Language:Python1 4 314
ome/upptime
📈 Uptime monitor and status page for OME, powered by @upptime
Language:Markdown1 8 2.1k1
ome/ansible-role-omero-ms-image-region
Language:Jinja2 02
ome/omero-ms-image-region
OMERO image region Vert.x asynchronous microservice server
Language:Java0 02
ome/omero-python-superbuild
OMERO build for Python server components
8 14
ome/scc
OME tools for managing the Git(Hub) workflow
Language:Python8 5615