Dr Spencer Shorte, Institut Pasteur
The Imagopole (ISO9001-2008; IBiSA) founded in 2006 regrouped campus-wide expertise into 4 technological platform teams comprising around 35 research and engineering staff, including a translational research group (CIH- Centre for Human Immunology). We have currently more than 40 light and electron imaging systems including advanced dynamic (in vivo and intra-vital) fluorescence imaging; confocal LSM & spinningdisk (Amino et al., 2007; Amino et al., 2006; Arhel et al., 2006); FRET (Hoppe et al., 2008), and HCA (Mostowy et al., 2009); in vivo molecular imaging, including: bioluminescence in whole animals (e.g. (Logeart-Avramoglou et al., 2010), fluorescence and 3D-FMT (collaboration with CEA-Leti); and electron microscopy (TEM, SEM, Cryo-EM, CLEM e.g. (Marteyn et al., 2010; Pais-Correia et al., 2010). In addition, we have received significant support for developing flow-, 2D-scanning-, and image-in-flow cytometry, and digital histopathology. In turn, the expertise of these experienced personnel covers the gamut of microscopic, ultrastructural and cytometry based imaging technologies.
The Imagopole has over 700 registered users including 10 percent external to the institute, from France, Europe and beyond; and at any given moment is handling 100 active research projects. Among these we have had, and continue to harbor, an active history of research collaborations (Arhel et al., 2007; Hoppe et al., 2008; Ramsden et al., 2007), partnerships and publications (Frischknecht et al., 2009) with UK-based laboratories working on infectious disease, and/or imaging sciences; and have had trained PhD’s whom have go on to successful research in UK labs (Boeda et al., 2007; Boeda et al., 2002); or simply maintained long-standing, regular scientific and technical exchange (e.g. Debbie Smith and Peter O’Toole, York University; Jason Swedlow, Dundee University).
Three key projects are envisaged for articulating OME/OMERO to:
- High-content commercial analysis tools & advanced bio-statistics, e.g. Colombus and R (Anne Danckaert, 15%).
- Functional genomics, ontologies, annotation and chemical genomic screening (open source) software tools e.g. HC-DC/KNIME/Taverna (Bernd Jagla, 15%).
- Multi-modal (open source) image data analysis tools e.g. ImageJ/Fiji (Jean-Yves Tinevez, 15%)
However, none of these individuals is expert in OME/OMERO nor its toolkit component parts (e.g. Python, Apache, Tomcat, Hibernate, ICE, etc.). Rather they are experts at the applications interface and thus perfectly positioned to benefit as the relay between user and high-end developer. With the input of these individuals we can propose to ensure a Pasteur- Imagopole OME/OMERO user-application-developer resource aiming to refine the functionality and implementation of OMERO tools from file-system to API. With the singular aim to assure the promotion of OME/OMERO as the standard for image data management across the board within Pasteur, this team will nurture the local and international community of users grouped around the Imagopole on a two-way street between applications and development; a project-driven mission fed by a breadth of application pipelines listed above.
We hope that OMERO will provide therein a standard for image database architecture compatible with other areas of in silico analysis in life sciences research. Ultimately, we wish to put in place a network of image-data handling pipelines allowing to triage, annotate and share our data in a manner that will provide the model for thematic data structuring across a medium-sized site. Ultimately this tool will be focused mainly on pre-clinical, and clinical image datasets derived from infectious paradigms, and we hope that this will provide a hub for sharing with third-parties along the lines of this same thematic wherein an open resource will be naturally fueled by a community effort. While we fully understand the complexities, and enormity of this work, we are optimistic that the OME project’s ongoing efforts do go in the right direction, and will be reinforced by other compatible and like-minded open source imaging db software projects.
Further information is available on the Imagopole website