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Publications

Publications by the group and by people using our work

  • Dikovskaya D, Schiffmann D, Newton IP, Oakley A, Kroboth K, Sansom O, Jamieson TJ, Meniel V, Clarke A, Näthke IS. 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. Download.

  • 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. Download.

  • 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. Download.

  • 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. Download.

  • 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. Download

  • 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. Download

  • T. J. Macura, J. N. Johnston, D. A. Creager, P. K. Sorger, and I. G. Goldberg 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. Download

  • 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. Download

  • 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. Download

  • 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. Download.

  • 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. Download.

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