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Publications by the group and by people using our work

If you wish to cite our work choose from the publications below, or see our citation page.


Tjelvar S. G. Olsson​, Matthew Hartley (2016) jicbioimage: a tool for automated and reproducible bioimage analysis. PeerJ - doi:10.7717/peerj.2674

Tool making use of Bio-Formats

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Luca Lianas, Marco Enrico Piras, Elodia Musu, Simona Podda, Francesca Frexia, Emanuela Ovcin, Giovanni Bussolati, Gianluigi Zanetti (2016) Cy-TEST - A new platform for training and testing in cytopathology. Diagnostic Pathology - doi:10.17629/www.diagnosticpathology.eu-2016-2:208

Combining an OMERO-based repository with an e-learning platform

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S. E. Taylor, J. Bagnall, D. Mason, R. Levy, D. G. Fernig, V. See (2016) Differential sub-nuclear distribution of hypoxia-inducible factors (HIF)-1 and -2 alpha impacts on their stability and mobility. Open Biology - doi:10.1098/rsob.160195

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View data in OMERO


Colin Blackburn, Chris Allan, Sébastien Besson, Jean-Marie Burel, Mark Carroll, Richard K. Ferguson, Helen Flynn, David Gault, Kenneth Gillen, Roger Leigh, Simone Leo, Simon Li, Dominik Lindner, Melissa Linkert, Josh Moore, William J. Moore, Balaji Ramalingam, Emil Rozbicki, Gabriella Rustici, Aleksandra Tarkowska, Petr Walczysko, Eleanor Williams, Jason R. Swedlow (2016) The Open Microscopy Environment: open image informatics for the biological sciences. Proc. SPIE 9913, Software and Cyberinfrastructure for Astronomy III - doi:10.1117/12.2232291

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José Salavert-Torres, Andrii Iudin, Ingvar Lagerstedt, Eduardo Sanz-García, Gerard J. Kleywegt, Ardan Patwardhan (2016) Web-based volume slicer for 3D electron-microscopy data from EMDB. Journal of Structural Biology - doi:10.1016/j.jsb.2016.02.012

OMERO-based web tool

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Simon Li, Sébastien Besson, Colin Blackburn, Mark Carroll, Richard K. Ferguson, Helen Flynn, Kenneth Gillen, Roger Leigh, Dominik Lindner, Melissa Linkert, William J. Moore, Balaji Ramalingam, Emil Rozbicki, Gabriella Rustici, Aleksandra Tarkowska, Petr Walczysko, Eleanor Williams, Chris Allan, Jean-Marie Burel, Josh Moore, Jason R. Swedlow (2016) Metadata management for high content screening in OMERO. Methods - doi:10.1016/j.ymeth.2015.10.006

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Amy J. Gerc, Andreas Diepold, Katharina Trunk, Michael Porter, Colin Rickman, Judith P. Armitage, Nicola R. Stanley-Wall, Sarah J. Coulthurst (2015) Visualization of the Serratia Type VI Secretion System Reveals Unprovoked Attacks and Dynamic Assembly. Cell Reports - doi:10.1016/j.celrep.2015.08.053

Use of OMERO.mtools

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Sara Carvalhal, Susana Abreu Ribeiro, Miguel Arocena, Taciana Kasciukovic, Achim Temme, Katrin Koehler, Angela Huebner, and Eric R. Griffis (2015) The nucleoporin ALADIN regulates Aurora A localization to ensure robust mitotic spindle formation. Molecular Biology of the Cell - doi:10.1091/mbc.E15-02-0113

Use of OMERO, OMERO.mtools and OMERO.figure

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Jean-Marie Burel, Sébastien Besson, Colin Blackburn, Mark Carroll, Richard K. Ferguson, Helen Flynn, Kenneth Gillen, Roger Leigh, Simon Li, Dominik Lindner, Melissa Linkert, William J. Moore, Balaji Ramalingam, Emil Rozbicki, Aleksandra Tarkowska, Petr Walczysko, Chris Allan, Josh Moore, Jason R. Swedlow (2015) Publishing and sharing multi-dimensional image data with OMERO. Mammalian Genome - doi:10.1007/s00335-015-9587-6

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Ellen T. Arena, Francois-Xavier Campbell-Valois, Jean-Yves Tinevez, Giulia Nigro, Martin Sachse, Maryse Moya-Nilges, Katharina Nothelfer, Benoit Marteyn, Spencer L. Shorte, and Philippe J. Sansonetti (2015) Bioimage analysis of Shigella infection reveals targeting of colonic crypts. Proceedings of the National Academy of Sciences - doi:10.1073/pnas.1509091112

Images stored in OMERO.

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Josh Moore, Melissa Linkert, Colin Blackburn, Mark Carroll, Richard K. Ferguson, Helen Flynn, Kenneth Gillen, Roger Leigh, Simon Li, Dominik Lindner, William J. Moore, Andrew J. Patterson, Blazej Pindelski, Balaji Ramalingam, Emil Rozbicki, Aleksandra Tarkowska, Petr Walczysko, Chris Allan, Jean-Marie Burel, Jason Swedlow (2015) OMERO and Bio-Formats 5: flexible access to large bioimaging datasets at scale. SPIE Proceedings 9413 - doi:10.1117/12.2086370

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Sarah Young, Sebastien Besson, Julie P.I. Welburn (2014) Length-dependent anisotrophic scaling of spindle shape. Biology Open - doi:10.1242/bio.201410363

Analysis using OMERO.matlab.

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Veronika Graml, Xenia Studera, Jonathan L.D. Lawson, Anatole Chessel, Marco Geymonat, Miriam Bortfeld-Miller, Thomas Walter, Laura Wagstaff, Eugenia Piddini, Rafael E. Carazo-Salas (2014) A Genomic Multiprocess Survey of Machineries that Control and Link Cell Shape, Microtubule Organization, and Cell-Cycle Progression. Developmental Cell - doi:10.1016/j.devcel.2014.09.005

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OMERO database


Gianmauro Cuccuru, Massimiliano Orsini, Andrea Pinna, Andrea Sbardellati, Nicola Soranzo, Antonella Travaglione, Paolo Uva, Gianluigi Zanetti and Giorgio Fotia (2014) Orione, a web-based framework for NGS analysis in microbiology. Bioinformatics - doi:10.1093/bioinformatics/btu135

Part of an on-going project to integrate Galaxy with tools such as OMERO.biobank.

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Aleksandras Gutmanas, Younes Alhroub, Gary M. Battle, John M. Berrisford, Estelle Bochet, Matthew J. Conroy, Jose M. Dana, Manuel A. Fernandez Montecelo, Glen van Ginkel, Swanand P. Gore, et al (2014) PDBe: Protein Data Bank in Europe. Nucleic Acids Research 42(D1): D285-D291 - doi:10.1093/nar/gkt1180

A Protein data bank using OMERO technology to allow storage and browsing of image data.

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Harald Stachelscheid, Stefanie Seltmann, Fritz Lekschas, Jean-Fred Fontaine, Nancy Mah, Mariana Neves, Miguel A. Andrade-Navarro, Ulf Leser, Andreas Kurtz (2014) CellFinder: a cell data respository. Nucleic Acids Research 42(D1): D950-D958 - doi:10.1093/nar/gkt1264

A cell data repository using OMERO technology to allow storage and browsing of image data.

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Paul Antony, Christophe Trefois, Aleksandar Stojanovic, Aidos Sagatovich Baumuratov, Karol Kozak (2013) Light microscopy applications in systems biology: opportunities and challenges. Cell Communication and Signaling: 11:24 - doi:10.1186/1478-811X-11-24

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Jamie S.J. Wilson, Agueda M. Tejera, Dennis Castor, Rachel Toth, Maria A. Blasco, John Rouse (2013) Localization-dependent and -independent roles of SLX4 in regulating telomeres. Cell Reports 4(5): 853-860 - doi:10.1016/j.celrep.2013.07.033

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David A. Ball, Neil R. Adams, Nadine Reischmann, Debashis Barik, Christopher T. Franck, John J. Tyson and Jean Peccoud (2013) Measurement and modeling of transcriptional noise in the cell cycle regulatory network. Cell Cycle 12(19): 32-3-3218 - doi:10.4161/cc.26257

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Sean C. Warren, Anca Margineanu, Dominic Alibhai, Douglas J. Kelly, Clifford Talbot, Yuriy Alexandrov, Ian Munro, Matilda Katan, Chris Dunsby and Paul M. W. French (2013) Rapid Global Fitting of Large Fluorescence Lifetime Imaging Microscopy Datasets. PLoS ONE 8(8): e70687 - doi:10.1371/journal.pone.0070687

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Data in OMERO


Mark Woodbridge, Christopher D. Tomlinson, Sarah A. Butcher (2013) ADAM: automated data management for research datasets Bioinformatics (2013) 29 (1): 146-147 doi: 10.1093/bioinformatics/bts644 View


Baek Hwan Cho, Ivan Cao-Berg, Jennifer Ann Bakal and Robert F Murphy (2012) OMERO.searcher: content-based image search for microscope images. Nature Methods 9, 633–634 - doi:10.1038/nmeth.2086

A tool for finding images in OMERO that are similar to a given search image.
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Chris Allan, Jean-Marie Burel, Josh Moore, Colin Blackburn, Melissa Linkert, Scott Loynton, Donald MacDonald, William J Moore, Carlos Neves, Andrew Patterson, Michael Porter, Aleksandra Tarkowska, Brian Loranger, Jerome Avondo, Ingvar Lagerstedt, Luca Lianas, Simone Leo, Katherine Hands, Ron T Hay, Ardan Patwardhan, Christoph Best, Gerard J Kleywegt, Gianluigi Zanetti & Jason R Swedlow (2012) OMERO: flexible, model-driven data management for experimental biology. Nature Methods 9, 245–253. Published: 28 February 2012 - doi:10.1038/nmeth.1896
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Christian Loyek, Nasir M Rajpoot, Michael Khan, Tim W Nattkemper (2011) BioIMAX: A Web 2.0 approach for easy exploratory and collaborative access to multivariate bioimage data BMC Bioinformatics 2011 12:297. Published 21 July 2011 - doi:10.1186/1471-2105-12-297
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Oliver Müller, Peter Lipp & Lars Kaestner (2011) ATOM - an OMERO add-on for automated import of image data. BMC Research Notes 4:382. Published 6 October 2011 - doi:10.1186/1756-0500-4-382
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Jason R. Swedlow (2011) Finding an image in a haystack: the case for public image repositories. Nature Cell Biology 13, 183. Published: 01 March 2011 - doi:10.1038/ncb0311-183
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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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David Sloan, Catriona Macaulay, Scott Loynton, Paula Forbes
User research in a scientific software development project. Proceeding BCS-HCI '09 - View


Scott Loynton, Jean-Marie Burel, David Sloan, Catriona Macaulay
Towards a project community approach to academic scientific software development. E-Science Workshops, 2009 5th IEEE International Conference (2009) -doi:10.1109/ESCIW.2009.5407962 View


Catriona Macaulay, David Sloan, Xinyi Jang, Paula Forbes, Scott Loynton, Swedlow Jason, Peter Gregor Usability and User-Centered Design in Scientific Software Development. Software, IEEE (2009) doi:10.1109/MS.2009.27 View


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

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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) - doi:10.1146/annurev.biophys.050708.133641

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Moore J, Allan C, Burel JM, Loranger B, MacDonald D, Monk J, Swedlow JR. (2007) Open tools for storage and management of quantitative image data. Methods Cell Biol. 85:555-70. - doi:10.1016/S0091-679X(08)85024-8

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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 - doi:10.1083/jcb.200610099

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. - 10.1562/2004-11-22-IR-377

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. - doi:10.1186/gb-2005-6-5-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. - doi:10.1126/science.1082602

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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