github.com/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.

Stars: 405 - Last synced: 15 May 2026

github.com/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.

Stars: 214 - Last synced: 15 May 2026

github.com/ome/ome-zarr-py

Implementation of next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

Stars: 200 - Last synced: 04 Jun 2026

github.com/ome/ngff

Next-generation file format (NGFF) specifications for storing bioimaging data in the cloud.

Stars: 136 - Last synced: 04 Jun 2026

github.com/ome/napari-ome-zarr

A napari plugin for zarr backed OME-NGFF images

Stars: 37 - Last synced: 04 Jun 2026

github.com/ome/ansible-role-prometheus-postgres

Prometheus Postgres exporter

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github.com/ome/omero-py

Python project containing Ice remoting code for OMERO

Stars: 27 - Last synced: 15 May 2026

github.com/ome/docker-example-omero

OMERO Docker compose example

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github.com/ome/ansible-role-cadvisor

cAdvisor container monitoring

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github.com/ome/omero-documentation

Sphinx-based documentation for the Open Microscopy Environment

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github.com/ome/omero-web

Django-based OMERO.web client

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github.com/ome/ome2024-ngff-challenge

Project planning and material repository for the 2024 challenge to generate 1 PB of OME-Zarr data

Stars: 19 - Last synced: 14 May 2026

github.com/ome/omero-iviewer

An OMERO.web app allowing to view images

Stars: 19 - Last synced: 06 Jun 2026

github.com/ome/omero-cli-transfer

An OMERO CLI plugin for creating transfer packets between OMERO servers.

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github.com/ome/devspace

Continuous integration tool for OME projects

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github.com/ome/omero-ms-zarr

Experimental micro-service for implementing the Zarr spec over HTTP

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github.com/ome/ansible-role-nfs-mount

Manage NFS4 mounts

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github.com/ome/omero-figure

An OMERO.web app for creating Figures from images in OMERO

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github.com/ome/omero-cli-zarr

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github.com/ome/ansible-role-prometheus

Prometheus monitoring server

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github.com/ome/omero-scripts

Core OMERO Scripts

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github.com/ome/ome-model

OME model (specification, code generator, implementation)

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github.com/ome/omero-server-docker

OMERO.server production docker image

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github.com/ome/bio-formats-examples

Examples of usage of the Bio-Formats API

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github.com/ome/awstats-docker

Run Awstats in Docker

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github.com/ome/ansible-role-ssl-certificate

Generate SSL certificates

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github.com/ome/ansible-role-nginx-proxy

Install Nginx for use as a front-end proxy.

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github.com/ome/octave-docker

Dockerfile to build an Octave container

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github.com/ome/ansible-role-postgresql

Install upstream PostgreSQL server. Optionally creates users and databases.

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github.com/ome/omero-deployment-examples

Examples playbooks for installing OMERO with Ansible and Docker

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github.com/ome/omero-guide-python

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github.com/ome/shape-editor

Javascript library based on Raphael.js for editing shapes

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github.com/ome/ome-ngff-validator

Web page for validating OME-NGFF files

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github.com/ome/ome-docker

Docker files for http://github.com/openmicroscopy

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github.com/ome/EMBL-EBI-imaging-course-05-2022

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github.com/ome/ZarrReader

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github.com/ome/omero-insight

Gradle project containing insight java client for OMERO

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github.com/ome/bio-formats-documentation

Bio-Formats documentation

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github.com/ome/omero-metadata

OMERO plugin for metadata manipulation https://www.openmicroscopy.org/omero/

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github.com/ome/ome-ngff-prototypes

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github.com/ome/training-scripts

A set of scripts to access, analyse image and metadata from OMERO

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github.com/ome/bioimage-latency-benchmark

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github.com/ome/omero-server

Gradle project containing main server logic for OMERO

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github.com/ome/vsftpd-anonymous-upload-docker

Vsftpd Docker image for anonymous FTP uploads only

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github.com/ome/conda-bioformats2raw

Bio-Formats image file format to raw format converter

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github.com/ome/omero-web-docker

OMERO.web production docker image

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github.com/ome/openmicroscopy.org

OME main website

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github.com/ome/EMBL-EBI-imaging-course-04-2025

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github.com/ome/ansible-role-network

Set up network interfaces with Ansible

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github.com/ome/aspera-client-docker

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github.com/ome/rOMERO-gateway

OMERO R Gateway

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github.com/ome/omego

OME, Go! Installation and administration tool for OME applications.

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github.com/ome/EMBO-Practical-Course-2023

Advanced methods in bioimage analysis

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github.com/ome/omero-guide-ilastik

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github.com/ome/ansible-role-fluentd

Install Fluentd log collector with Ansible

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github.com/ome/ansible-role-mysql-backup

Setup a cron job for regular full Mysql/Mariadb database dumps.

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github.com/ome/ansible-role-postgresql-backup

Backup PostgreSQL database servers

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github.com/ome/spatial-omics-hackathon-2021

See https://forum.image.sc/t/ome-ngff-spatial-omics-hackathon/57337

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github.com/ome/omero-mapr

An OMERO.web app allowing to browse the data through attributes linked to the image

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github.com/ome/omero-gallery

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github.com/ome/rsync-ssh-docker

Docker image to allow SSH and rsync access to volumes using github keys

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github.com/ome/ansible-role-docker

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github.com/ome/omero-downloader

An OMERO client for downloading data in bulk from the server.

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github.com/ome/ansible-roles

Collection of OME Ansible roles

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github.com/ome/ome_zarr_test_suite

Test suite of reader and writer implementations

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github.com/ome/ome-codecs

OME image compression (coder-decoder implementations)

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github.com/ome/omero-install

OMERO installation scripts

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github.com/ome/training-docker

Software carpentry lesson about Docker

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github.com/ome/ome-mdbtools

Java API to handle Microsoft MDB format (Access). Used by Bio-Formats for Zeiss LSM metadata in MDB files.

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github.com/ome/omero-test-infra

Test infrastructure for decoupled repositories

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github.com/ome/omero-cpp

Multiple OMERO libraries in C++

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github.com/ome/omero-guide-cellprofiler

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github.com/ome/omero-marshal

OMERO marshalling infrastructure

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github.com/ome/ansible-role-minio-s3-gateway

Minio S3 gateway with additional restricted users

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github.com/ome/ansible-role-iptables-raw

Ansible module to import iptables_raw library

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github.com/ome/EMBL-EBI-imaging-course-04-2024

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github.com/ome/prod-playbooks

Playbooks used by the OME team for deploying production services including OMERO

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github.com/ome/ansible-role-omero-server

Installs and configures OMERO.server

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github.com/ome/EMBL-EBI-imaging-course-05-2023

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github.com/ome/omero-ms-queue

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github.com/ome/omero-web-zarr

Implementation of OME-Zarr API with an omero-web app

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github.com/ome/ansible-role-postgresql-client

Install PostgreSQL clients from the upstream distribution

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github.com/ome/ansible-role-python3-virtualenv

Install Python3 virtualenv dependencies and a wrapper script for the Ansible pip module

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github.com/ome/ome-zarr-metadata

ome-zarr extension for parsing metadata

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github.com/ome/omero-rois

OMERO python ROI utils

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github.com/ome/omero-cli-render

OMERO command-line tool for rendering

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github.com/ome/omero-fpbioimage

FPBioImage as an OMERO.web app

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github.com/ome/ome-common-java

Java library providing common functionality for all OME Java components

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github.com/ome/docker-example-omero-grid

Multi-container OMERO

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github.com/ome/cookiecutter-omero-webapp

Cookiecutter to create OMERO.web apps

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github.com/ome/omero-guide-fiji

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github.com/ome/.github

Community health files for the @OME organization

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github.com/ome/ome-ngff-tools

Document available viewers and other tools for the OME-NGFF image format

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github.com/ome/omero-prometheus-tools

Utilities for monitoring OMERO with Prometheus

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github.com/ome/ansible-role-local-accounts

Create or remove local user accounts.

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github.com/ome/cookiecutter-omero-cli-plugin

Cookiecutter for OMERO.cli plugins

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github.com/ome/docker-example-omero-microservices

Example of running OMERO.server microservices

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github.com/ome/ome-ngff-java

Metadata stubs of the NGFF specification in Java

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github.com/ome/ansible-role-selinux-utils

Install utilities for interactions with SELinux

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github.com/ome/ecdp2019-publication

Supplementary information associated with Besson et al. (2019) ECDP 2019

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