standards > model/format > DOI:10.25504/FAIRsharing.zk8p4g
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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. OME-XML as a file format is superseded by OME-TIFF, which is the preferred container format for image data making use of the OME Data Model.



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: Feb. 7, 2021, 7:56 p.m.; Last accessed: Jul 29 2021 10:48 a.m.


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

Record updated: Feb. 6, 2021, 9:59 a.m. by The FAIRsharing Team.

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Support

General

Additional Information


Tools

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

Identifier Schemas

No identifier schema standards defined

Metrics

No metrics standards defined


Related Databases (2)
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.

Implementing Policies

This record is not implemented by any policy.


Credit

Record Maintainer

Funds

Maintains

Grant Number(s)

  • 095931/Z/11/Z (The Wellcome Trust, UK)

  • BB/G022585/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)

  • BB/L024233/1 (Biotechnology and Biological Sciences Research Council (BBSRC), UK)