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.
bio-formats-examples
Examples of usage of the Bio-Formats API
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.
napari-ome-zarr
A napari plugin for zarr backed OME-NGFF images
ngff
Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
ome-zarr-py
Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.
omero-deployment-examples
Examples playbooks for installing OMERO with Ansible and Docker
omero-figure
An OMERO.web app for creating Figures from images in OMERO
omero-insight
Gradle project containing insight java client for OMERO
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.
Open Microscopy Environment's Repositories
ome/apacheds-docker
Dockerfile to build an ApacheDS container providing an LDAP and optionally a Kerberos service.
ome/devspace
Continuous integration tool for OME projects
ome/ansible-role-prometheus
Prometheus monitoring server
ome/ome-model
OME model (specification, code generator, implementation)
ome/omero-cli-transfer
An OMERO CLI plugin for creating transfer packets between OMERO servers.
ome/ansible-role-nginx-proxy
Install Nginx for use as a front-end proxy.
ome/omero-guide-python
ome/ansible-role-minio-s3-gateway
Minio S3 gateway with additional restricted users
ome/ansible-role-omero-server
Installs and configures OMERO.server
ome/EMBL-EBI-imaging-course-04-2024
ome/ome-mdbtools
Java API to handle Microsoft MDB format (Access). Used by Bio-Formats for Zeiss LSM metadata in MDB files.
ome/omero-guide-cellprofiler
ome/omero-test-infra
Test infrastructure for decoupled repositories
ome/.github
Community health files for the @OME organization
ome/ansible-role-selinux-utils
Install utilities for interactions with SELinux
ome/conda-bftools
Bio-Formats command line tools
ome/cookiecutter-omero-cli-plugin
Cookiecutter for OMERO.cli plugins
ome/ome-metakit
Library for reading Metakit database files
ome/ansible-role-anonymous-ftp
Anonymous FTP uploads with Docker
ome/ansible-role-omero-web
Installs and configures OMERO.web and Nginx
ome/omero-dropbox
OMERO.dropbox server for watching directories
ome/action-ansible-molecule-list-scenarios
ome/action-gradle
ome/action-workflows
ome/ansible-role-cli-utils
Useful command-line utilities for administering a server.
ome/bioformats2raw-docker
Bio-Formats image file format to raw format converter
ome/ome-jai
OME Java ImageIO fork (deprecated)
ome/ome-poi
OME fork of Apache Jakarta POI
ome/ome-stubs
Stubs for optional third-party components
ome/presentations
HTML-based presentations from the OME team.