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:Python41 8 1560
bio-formats-examples
Examples of usage of the Bio-Formats API
Language:Java13 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:Java382 29 506242
napari-ome-zarr
A napari plugin for zarr backed OME-NGFF images
Language:Python31 10 5821
ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Language:Bikeshed123 23 13642
ome-zarr-py
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Language:Python168 21 14954
omero-deployment-examples
Examples playbooks for installing OMERO with Ansible and Docker
11 13 512
omero-figure
An OMERO.web app for creating Figures from images in OMERO
Language:JavaScript16 11 16231
omero-insight
Gradle project containing insight java client for OMERO
Language:Java7 11 21914
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:Java202 31 84101

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:Java382 29 506242
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:Java202 31 84101
ome/ome-zarr-py
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Language:Python168 21 14954
ome/ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
Language:Bikeshed123 23 13642
ome/napari-ome-zarr
A napari plugin for zarr backed OME-NGFF images
Language:Python31 10 5821
ome/omero-cli-transfer
An OMERO CLI plugin for creating transfer packets between OMERO servers.
Language:Python17 6 4414
ome/omero-web
Django-based OMERO.web client
Language:Python17 12 21031
ome/ome2024-ngff-challenge
Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data
Language:Python16 16 2214
ome/omero-cli-zarr
Language:Python16 9 2510
ome/ome-model
OME model (specification, code generator, implementation)
Language:XSLT14 10 2626
ome/omero-scripts
Core OMERO Scripts
Language:Python12 10 2332
ome/bio-formats-documentation
Bio-Formats documentation
Language:Java8 11 1317
ome/bioimage-latency-benchmark
Language:Jupyter Notebook7 9 910
ome/www.openmicroscopy.org
OME main website
Language:HTML5 14 1922
ome/ome_zarr_test_suite
Test suite of reader and writer implementations
Language:Python4 11 46
ome/prod-playbooks
Playbooks used by the OME team for deploying production services including OMERO
Language:Jinja4 10 3118
ome/omero-web-zarr
Implementation of OME-Zarr API with an omero-web app
Language:Python3 6 33
ome/ome-common-java
Java library providing common functionality for all OME Java components
Language:Java2 8 619
ome/ome-metakit
Library for reading Metakit database files
Language:Java2 7 07
ome/omero-prometheus-tools
Utilities for monitoring OMERO with Prometheus
Language:Python2 5 49
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-cli-server
CLI plugin for managing an OMERO.server
Language:Python1 4 03
ome/omero-demo-cleanup
A CLI plugin for managing the disk space on the OME demo server
Language:Python1 11 24
ome/omero-guides
Guides for using OMERO
Language:Python1 11 245
ome/omero-plugins
Collection of OMERO extensions (plugins, apps)
1 10 37
ome/omero-signup
OMERO.web app to allow anyone to signup for an OMERO account
Language:Python1 11 57
ome/upptime
📈 Uptime monitor and status page for OME, powered by @upptime
Language:Markdown1 9 2.7k1
ome/omero-guide-scripts
5 03
ome/omero-python-superbuild
OMERO build for Python server components
8 14