Discover ome/webemdb Open Source project

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.

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openmicroscopy

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

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ngff

Bikeshed

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ome-zarr-py

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

cAdvisor container monitoring

ansible-role-cadvisor

DEPRECATED FORK - use https://github.com/zeroc-ice/ice instead.

zeroc-ice

omero-documentation

Sphinx-based documentation for the Open Microscopy Environment

A repository containing scripts for managing infrastructure

infrastructure

Continuous integration tool for OME projects

devspace

OMERO Docker compose example

docker-example-omero

An OMERO.web app allowing to view images

omero-iviewer

A napari plugin for zarr backed OME-NGFF images

napari-ome-zarr

Prometheus Postgres exporter

ansible-role-prometheus-postgres

omero-cli-zarr

A mirror of the Java Application Bundler fork

appbundler

Prometheus monitoring server

ansible-role-prometheus

Examples of usage of the Bio-Formats API

bio-formats-examples

OME model (specification, code generator, implementation)

ome-model

XSLT

omero-ms-zarr

Experimental micro-service for implementing the Zarr spec over HTTP

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

omero-cli-transfer

Django-based OMERO.web client

omero-web

ansible-role-nfs-mount

Manage NFS4 mounts

Python project containing Ice remoting code for OMERO

omero-py

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

omero-figure

Dockerfile to build an Octave container

awstats-docker

Run Awstats in Docker

Perl

octave-docker

Dockerfile

omero-scripts

Core OMERO Scripts

Javascript library based on Raphael.js for editing shapes

shape-editor

Install upstream PostgreSQL server. Optionally creates users and databases.

ansible-role-postgresql

omero-guide-python

Generate SSL certificates

ansible-role-ssl-certificate

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

ome2024-ngff-challenge

EMBL-EBI-imaging-course-05-2022

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

ome-docker

Dockerfile

bioimage-latency-benchmark

Examples playbooks for installing OMERO with Ansible and Docker

omero-deployment-examples

omero-server-docker

OMERO.server production docker image

Install Nginx for use as a front-end proxy.

ansible-role-nginx-proxy

ome-ngff-prototypes

Gradle project containing insight java client for OMERO

omero-insight

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

training-scripts

OMERO.web production docker image

omero-web-docker

Makefile

bio-formats-documentation

Bio-Formats documentation

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

omego

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

omero-metadata

Vsftpd Docker image for anonymous FTP uploads only

vsftpd-anonymous-upload-docker

Advanced methods in bioimage analysis

EMBO-Practical-Course-2023

OME Files is a C++ library for reading and writing data using the open and standard OME-TIFF file format using the OME data model

ome-files-cpp

Dump all variables to a file on the remote host.

ansible-role-debug-dumpallvars

omero-mapr

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

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

ansible-role-mysql-backup

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

spatial-omics-hackathon-2021

ZarrReader

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

rsync-ssh-docker

Set up network interfaces with Ansible

aspera-client-docker

Dockerfile

ansible-role-network

www.openmicroscopy.org

OME main website

EMBL-EBI-imaging-course-05-2023

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

prod-playbooks

Multiple OMERO libraries in C++

omero-cpp

OME image compression (coder-decoder implementations)

ome-codecs

pydoop-features

Software carpentry lesson about Docker

training-docker

Install Fluentd log collector with Ansible

ansible-role-fluentd

Test suite of reader and writer implementations

ome_zarr_test_suite

omero-gallery

OMERO installation scripts

rOMERO-gateway

OMERO R Gateway

omero-install

Web page for validating OME-NGFF files

ome-ngff-validator

Svelte

ome-common-cpp

C++ library providing common and portability functionality for all OME C++ components

omero-guide-ilastik

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

ome-mdbtools

ansible-role-docker

Installs and configures OMERO.server

ansible-role-omero-server

Test infrastructure for decoupled repositories

omero-test-infra

omero-ms-queue

Python bindings for OME Files

ome-files-py

An OMERO.web app for prototypes and examples

omero-webtest

Ansible module to import iptables_raw library

ansible-role-iptables-raw

Minio S3 gateway with additional restricted users

ansible-role-minio-s3-gateway

CMake super-build for the OME C++ libraries

ome-cmake-superbuild

CMake

ansible-roles

Collection of OME Ansible roles

Backup PostgreSQL database servers

ansible-role-postgresql-backup

ome-zarr extension for parsing metadata

ome-zarr-metadata

Bio-Formats JACE C++ bindings

bio-formats-jace

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

ansible-role-python3-virtualenv

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

omero-downloader

omero-guide-fiji

omeroweb-install

OMERO command-line tool for rendering

omero-cli-render

Cookiecutter for OMERO.cli plugins

cookiecutter-omero-cli-plugin

Utilities for monitoring OMERO with Prometheus

omero-prometheus-tools

OMERO command-line tool for duplicating database objects

omero-cli-duplicate

ansible-role-logrotate

Customise log-rotation.

Java library providing common functionality for all OME Java components

ome-common-java

Metadata stubs of the NGFF specification in Java

ome-ngff-java

omero-guide-cellprofiler

omero-guides

Guides for using OMERO

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

ome-ngff-tools

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omero-web-zarr

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