standards > model/format > DOI:10.25504/FAIRsharing.zk8p4g


ready Open Microscopy Environment eXtensible Markup Language

Abbreviation: OME-XML


General Information
OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community. The purpose of OME-XML is to provide a rich, extensible way to save information concerning microscopy experiments and the images acquired therein.

Homepage http://www.openmicroscopy.org/site/support/ome-model/ome-xml/index.html

Developed in France , Italy , United Kingdom , United States

Created in 2005

Taxonomic range




How to cite this record FAIRsharing.org: OME-XML; Open Microscopy Environment eXtensible Markup Language; DOI: https://doi.org/10.25504/FAIRsharing.zk8p4g; Last edited: Nov. 23, 2018, 11:27 a.m.; Last accessed: Dec 12 2018 1:10 a.m.


This record is maintained by hflynn  ORCID , joshmoore  ORCID  and sbesson  ORCID

Record updated: Oct. 1, 2018, 3:02 p.m. by The FAIRsharing Team.

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In Collections
OME
FAIRDOM Community Standards


Support

General

blog Open Microscopy Blog
forum Issue Tracker
Mailing List OME-XML Mailing List
online documentation OME-XML Specification (html)
online documentation OME Data Model and File Formats Document ...
online documentation Schema information

Additional Information

Contact Jason Swedlow   ORCID

Tools

    No tools defined


Schemas

No XSD schemas defined




Publications

Metadata matters: access to image data in the real world

Linkert M,Rueden CT,Allan C,Burel JM,Moore W,Patterson A,Loranger B,Moore J,Neves C,Macdonald D,Tarkowska A,Sticco C,Hill E,Rossner M,Eliceiri KW,Swedlow JR
J Cell Biol 2010

View Paper (PubMed) View Publication

The Open Microscopy Environment (OME) Data Model and XML file: open tools for informatics and quantitative analysis in biological imaging.

Goldberg IG,Allan C,Burel JM,Creager D,Falconi A,Hochheiser H,Johnston J,Mellen J,Sorger PK,Swedlow JR
Genome Biol 2005

View Paper (PubMed) View Publication

Related Standards

Reporting Guidelines

No guidelines defined

Terminology Artifacts

No semantic standards defined

Models and Formats

Identifier Schemas

No identifier schema standards defined


Implementing Databases (4)
OMERO
OMERO is client-server software for visualization, management and analysis of biological microscope images.
Image Data Resource
IDR is a prototype platform for publishing, mining and integrating bioimaging data at scale, following the Euro-BioImaging/ELIXIR imaging strategy using the OMERO and Bio-Formats open source software built by the Open Microscopy Environment. Deployed on an OpenStack cloud running on the EMBL-EBI’s Embassy resource, it includes image data linked to independent studies from genetic, RNAi, chemical, localisation and geographic high content screens, super-resolution microscopy, and digital pathology.
SSBD: Systems Science of Biological Dynamics
SSBD is a database that collects and shares quantitative biological dynamics data, microscopy images, and software tools. SSBD provides a rich set of resources for analyzing quantitative biological data, such as single-molecule, cell, and gene expression nuclei. Quantitative biological data are collected from a variety of species, sources and methods. These include data obtained from both experiment and computational simulation.
Microenvironment Perturbagen LINCS Center image server
The MEP LINCS project contributes to the development of the NIH Library of Integrated Network-based Cellular Signatures (LINCS) program by developing a dataset and computational strategy to elucidate how microenvironment (ME) signals affect cell intrinsic intracellular transcriptional- and protein-defined molecular networks to generate experimentally observable cellular phenotypes measured by high-content imaging.

Implementing Policies

This record is not implemented by any policy.


Credit

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Grant Number(s)