Literature DB >> 15892875

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

Ilya G Goldberg1, Chris Allan, Jean-Marie Burel, Doug Creager, Andrea Falconi, Harry Hochheiser, Josiah Johnston, Jeff Mellen, Peter K Sorger, Jason R Swedlow.   

Abstract

The Open Microscopy Environment (OME) defines a data model and a software implementation to serve as an informatics framework for imaging in biological microscopy experiments, including representation of acquisition parameters, annotations and image analysis results. OME is designed to support high-content cell-based screening as well as traditional image analysis applications. The OME Data Model, expressed in Extensible Markup Language (XML) and realized in a traditional database, is both extensible and self-describing, allowing it to meet emerging imaging and analysis needs.

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Year:  2005        PMID: 15892875      PMCID: PMC1175959          DOI: 10.1186/gb-2005-6-5-r47

Source DB:  PubMed          Journal:  Genome Biol        ISSN: 1474-7596            Impact factor:   13.583


  16 in total

1.  Systematic subcellular localization of novel proteins identified by large-scale cDNA sequencing.

Authors:  J C Simpson; R Wellenreuther; A Poustka; R Pepperkok; S Wiemann
Journal:  EMBO Rep       Date:  2000-09       Impact factor: 8.807

2.  Minimum information about a microarray experiment (MIAME)-toward standards for microarray data.

Authors:  A Brazma; P Hingamp; J Quackenbush; G Sherlock; P Spellman; C Stoeckert; J Aach; W Ansorge; C A Ball; H C Causton; T Gaasterland; P Glenisson; F C Holstege; I F Kim; V Markowitz; J C Matese; H Parkinson; A Robinson; U Sarkans; S Schulze-Kremer; J Stewart; R Taylor; J Vilo; M Vingron
Journal:  Nat Genet       Date:  2001-12       Impact factor: 38.330

Review 3.  Kinetic modelling approaches to in vivo imaging.

Authors:  R D Phair; T Misteli
Journal:  Nat Rev Mol Cell Biol       Date:  2001-12       Impact factor: 94.444

Review 4.  To 5D and beyond: quantitative fluorescence microscopy in the postgenomic era.

Authors:  Paul D Andrews; Ian S Harper; Jason R Swedlow
Journal:  Traffic       Date:  2002-01       Impact factor: 6.215

Review 5.  Studying protein dynamics in living cells.

Authors:  J Lippincott-Schwartz; E Snapp; A Kenworthy
Journal:  Nat Rev Mol Cell Biol       Date:  2001-06       Impact factor: 94.444

6.  Informatics and quantitative analysis in biological imaging.

Authors:  Jason R Swedlow; Ilya Goldberg; Erik Brauner; Peter K Sorger
Journal:  Science       Date:  2003-04-04       Impact factor: 47.728

7.  Phenotypic screening of small molecule libraries by high throughput cell imaging.

Authors:  J C Yarrow; Y Feng; Z E Perlman; T Kirchhausen; T J Mitchison
Journal:  Comb Chem High Throughput Screen       Date:  2003-06       Impact factor: 1.339

8.  Automatic identification of subcellular phenotypes on human cell arrays.

Authors:  Christian Conrad; Holger Erfle; Patrick Warnat; Nathalie Daigle; Thomas Lörch; Jan Ellenberg; Rainer Pepperkok; Roland Eils
Journal:  Genome Res       Date:  2004-06       Impact factor: 9.043

9.  Organising multi-dimensional biological image information: the BioImage Database.

Authors:  J M Carazo; E H Stelzer; A Engel; I Fita; C Henn; J Machtynger; P McNeil; D M Shotton; M Chagoyen; P A de Alarcón; R Fritsch; J B Heymann; S Kalko; J J Pittet; P Rodriguez-Tomé; T Boudier
Journal:  Nucleic Acids Res       Date:  1999-01-01       Impact factor: 16.971

Review 10.  Computational imaging in cell biology.

Authors:  Roland Eils; Chaitanya Athale
Journal:  J Cell Biol       Date:  2003-05-12       Impact factor: 10.539

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  97 in total

1.  BioImageXD: an open, general-purpose and high-throughput image-processing platform.

Authors:  Pasi Kankaanpää; Lassi Paavolainen; Silja Tiitta; Mikko Karjalainen; Joacim Päivärinne; Jonna Nieminen; Varpu Marjomäki; Jyrki Heino; Daniel J White
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

2.  A call for bioimaging software usability.

Authors:  Anne E Carpenter; Lee Kamentsky; Kevin W Eliceiri
Journal:  Nat Methods       Date:  2012-06-28       Impact factor: 28.547

3.  Whole-body tissue stabilization and selective extractions via tissue-hydrogel hybrids for high-resolution intact circuit mapping and phenotyping.

Authors:  Ken Y Chan; Nicholas C Flytzanis; Bin Yang; Jennifer B Treweek; Benjamin E Deverman; Alon Greenbaum; Antti Lignell; Cheng Xiao; Long Cai; Mark S Ladinsky; Pamela J Bjorkman; Charless C Fowlkes; Viviana Gradinaru
Journal:  Nat Protoc       Date:  2015-10-22       Impact factor: 13.491

4.  The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.

Authors:  Maryann E Martone; Joshua Tran; Willy W Wong; Joy Sargis; Lisa Fong; Stephen Larson; Stephan P Lamont; Amarnath Gupta; Mark H Ellisman
Journal:  J Struct Biol       Date:  2007-10-16       Impact factor: 2.867

5.  Evaluation of Face Datasets as Tools for Assessing the Performance of Face Recognition Methods.

Authors:  Lior Shamir
Journal:  Int J Comput Vis       Date:  2008       Impact factor: 7.410

6.  Channeling the data deluge.

Authors:  Jason R Swedlow; Gianluigi Zanetti; Christoph Best
Journal:  Nat Methods       Date:  2011-06       Impact factor: 28.547

7.  Intelligent Interfaces for Mining Large-Scale RNAi-HCS Image Databases.

Authors:  Chen Lin; Wayne Mak; Pengyu Hong; Katharine Sepp; Norbert Perrimon
Journal:  Proc IEEE Int Symp Bioinformatics Bioeng       Date:  2007-11-05

8.  IICBU 2008: a proposed benchmark suite for biological image analysis.

Authors:  Lior Shamir; Nikita Orlov; David Mark Eckley; Tomasz J Macura; Ilya G Goldberg
Journal:  Med Biol Eng Comput       Date:  2008-07-31       Impact factor: 2.602

9.  Managing and Querying Whole Slide Images.

Authors:  Fusheng Wang; Tae W Oh; Cristobal Vergara-Niedermayr; Tahsin Kurc; Joel Saltz
Journal:  Proc SPIE Int Soc Opt Eng       Date:  2012-02-16

10.  Nonlinear optical imaging of cellular processes in breast cancer.

Authors:  Paolo P Provenzano; Kevin W Eliceiri; Long Yan; Aude Ada-Nguema; Matthew W Conklin; David R Inman; Patricia J Keely
Journal:  Microsc Microanal       Date:  2008-12       Impact factor: 4.127

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