Work Packages

France-BioImaging operational level relies on five main Work Packages (WPs) described below. They gather trans-node and external experts in the corresponding domains. Depending on the complexity of their respective domains of interest, some WPs are managed by multiple “Working Groups” (or sub WPs). Their aims are to define new technological and methodological developments, to solve eventual barriers in sharing methods and techniques and to organize training, transfer and communication for user access to emerging technologies and methods.
All WGs stand at least once a year and report their results and proposals to the Executive Board and to the National Advisory Committee during France-BioImaging annual meeting.

Optical methods have emerged recently for the visualization of single molecules and biological structures at multiscale (nano, micro and mesoscopic) levels, their dynamics and interactions. Moreover, the integration of different scale imaging is certainly at the forefront of cell biology imaging because this provides structural information (obtained with electron microscopy) of the microenvironment of the macromolecules visualized in living cells by fluorescence microscopy. New technological and methodological developments are proposed to overcome technological barriers in the field of four sub Work Packages:

After years of transcriptomics approaches aiming at defining signature and targets, which have been quite frustrating despite prestigious publications, functional validation on a large scale appears a required step to annotate genes forming the signature. Large-scale imaging screening has been a major challenge due to the logistics of imaging and lack of automated image acquisition and analysis software. During the last years, technological advances in automated cell manipulation, microscopy and software, together with an ever-growing pool of commercially available collections of genetic tools (knock-out, over-expression, histone point mutations, fluorescent-tagged, etc.) have allowed the development of high throughput functional genomics and high-content imaging systems that exploit the power of genetics in a systematic way.

Methods for remote control of cell signaling have seen explosive growth. In addition to caged compounds and reversibly caged photochromic ligands, efforts have led to the engineering of light-sensitivity into proteins by the attachment of photoswitched tethered ligands that turn the function of the protein on and off in response to light. Associated with optical methods of excitation beam shaping, these approaches to the control of protein function provide an outstanding alternative to standard methods of controlling proteins through genetic or pharmacological means by providing the control of protein function at high temporal and spatial resolutions.

Bioimage Informatics address the questions related to the computerized analysis and handling of image data. New Imaging technologies as they are presented above are very greedy in terms of image processing and data management. New methodological approaches to extract information from massive amounts of image data are definitively required. If not developed concomitantly, the lack of accurate methods in this field can become the real bottleneck of innovative bioimaging approaches. Several lines of research and development can be delineated:
1. image processing and analysis solutions for bioimaging data quantification and modeling;
2. intelligent image data archival and retrieval;
3. high performance computing infrastructures dedicated to massive computational demands.

Because these tasks require the gathering of expertise from each Nodes, WP4 is supported by the only transversal node of FBI (BioImage Informatics/IPDM node).

Considering Dissemination & Training a lot has already been achieved over the years, through technological and research networks (RTmfm, “Mission pour l’Interdisciplinarité CNRS”, GDR-IMABIO) and research organizations (CNRS & INSERM trainings) at the FBI nodes and inter-nodes levels. Extension and support for existing Core Facility management tutoring (metrology, quality etc.) are still mandatory. Specific trainings have been now implemented such as tutoring in “Managing image data”. Since advanced technologies are obviously growing fast in imaging, new types of interdisciplinary training actions with strong theoretical and practical parts have been organized (FBI-AT). They concern PhD candidates, research fellows, engineers and permanent researchers at the national and European levels. Facing the deluge of Massive Data produced by new technologies as described in WP1 also requires intelligent image data management, archival and retrieval. Consequently the use of high performance computing infrastructures dedicated to massive computation is mandatory. The WG5b is a strategic WG at this stage. Knowing the nodes and sites needs in this matter and making a precise survey of strength and weaknesses inside FBI, is its first mission. Then, integration to a common and dedicated infrastructure or association to existing ones in other national INBS or International Networks will be decided.