Publications
Publications by the group and by people using our work
Melissa Linkert, Curtis T. Rueden, Chris Allan, Jean-Marie Burel, Will Moore, Andrew Patterson, Brian Loranger, Josh Moore, Carlos Neves, Donald MacDonald, Aleksandra Tarkowska, Caitlin Sticco, Emma Hill, Mike Rossner, Kevin W. Eliceiri, and Jason R. Swedlow (2010) Metadata matters: access to image data in the real world. The Journal of Cell Biology, Vol. 189no. 5777-782
doi: 10.1083/jcb.201004104
An article outlining the importance of metadata and introducing the OME Compliant Specification.
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Alexander M. Thomson, Peter J. Gillespie, and J. Julian Blow. (2010) Replication factory activation can be decoupled from the replication timing program by modulating Cdk levels. The Journal of Cell Biology, Vol. 188, No. 2, 209-221
doi:10.1083/jcb.200911037
A paper that uses OME Server and OMERO for image to analyse how CDK activity regulates replication factories.
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Jason R. Swedlow and Kevin W. Eliceiri. (2009) Open source bioimage informatics for cell biology. Trends Cell Biol. 2009 November; 19(11-3): 656–660.
doi: 10.1016/j.tcb.2009.08.007
Jason R. Swedlow, Ilya G. Goldberg, Kevin W. Eliceiri, and the OME Consortium. (2009) Bioimage Informatics for Experimental Biology. Annual Review of Biophysics. Vol. 38: 327-346 (Volume publication date June 2009)
Dikovskaya D, Schiffmann D, Newton IP, Oakley A, Kroboth K, Sansom O, Jamieson TJ, Meniel V, Clarke A, Näthke IS. (2007) Loss of APC induces polyploidy as a result of a combination of defects in mitosis and apoptosis. PMID: 17227893
Another example of using OME software (the OME server and FindSpots) for image visualisation, analysis, and management.
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Porter IM, McClelland SE, Khoudoli GA, Hunter CJ, Andersen JS, McAinsh AD, Blow JJ, Swedlow JR. (2007) Bod1, a novel kinetochore protein required for chromosome biorientation. PMID: 17938248
Another example of using OME software (the OMERO software suite) for image visualization, analysis, and management.
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Swedlow, J. R., Lewis, S. E., Goldberg, I. G. (2006) Modelling data across labs, genomes, space and time. Nat Cell Biol. 8:1190-1194.
An opinion piece discussing the use of data models in quantitative biology.
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Schiffmann, D. A, Dikovskaya, D., Appleton P. L., Newton, I. P., Creager, D. A., Allan, C., Nathke, I. S., Goldberg, I. G. (2006) Open Microscopy Environment and FindSpots: integrating image informatics with quantitative multidimensional image analysis. Biotechniques 41:199-208.
A methods paper showing how to use the OME Server, FindSpots and OME-Excel for quantitative analysis of mitotic kinetochores.
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Hochheiser, H. and Goldberg, I. G. (2006) Quasi-Hierarchical, Interactive Navigation of Images and Meta-Data in the Open Microscopy Environment. 2006 IEEE International Symposium on Biomedical Imaging.
Describes a Java user interface for browsing the OME Data Model.
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Johnston, J., Nagaraja, A., Hochheiser, H., and Goldberg, I. G. (2006) A Flexible Framework for Web Interfaces to Image Databases: Supporting User-Defined Ontologies and Links to External Databases. 2006 IEEE International Symposium on Biomedical Imaging.
Describes OME's extensible web-based user interfaces.
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T. J. Macura, J. N. Johnston, D. A. Creager, P. K. Sorger, and I. G. Goldberg. (2005) The Open Microscopy Environment Matlab Handler: Combining a Bioinformatics Data & Image Repository with a Quantitative Analysis Environment
A white paper describing integration of OME and MATLAB.
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Eliceiri, K. W. and C. Rueden. (2005) Tools for Visualizing Multidimensional Images from Living Specimens. Photochemistry and Photobiology 81(5), 1116-1122.
A survey of visualisation tools, including
Visbio.
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Goldberg, I., C. Allan, J.-M. Burel, D. Creager, A. Falconi, H. Hochheiser, J. Johnston, J. Mellen, P.K. Sorger, and J.R. Swedlow. (2005) The Open Microscopy Environment (OME) Data Model and XML File: Open Tools for Informatics and Quantitative Analysis in Biological Imaging. Genome Biol. 6:R47.
Describes the OME Data Model and XML File.
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Swedlow, J.R., I. Goldberg, E. Brauner, and P.K. Sorger. (2003) Informatics and quantitative analysis in biological imaging. Science. 300:100-2.
Our first position paper on image informatics.
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Platani, M., I. Goldberg, A.I. Lamond, and J.R. Swedlow. (2002) Cajal body dynamics and association with chromatin are ATP-dependent. Nature Cell Biol. 4:502-508.
The first use of OME for large-scale image analysis.
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