France-BioImaging

A National Research Infrastructure for Biological Imaging

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.

Index

 

WP1 – Instrumentation and Methods

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:

WP 1aWP 1bWP 1cWP 1d
Super Resolution & Single Molecule Tracking

Each super-resolution imaging modality comes with benefits and limitations in terms of resolution, sensitivity, speed. FBI aims at pushing further the spatial and temporal resolution of these approaches (SMLM, STED, SIM…) by combining them and at extending their applicability beyond single cells. Essential for this will be the development of new probes (see WP2) and advanced computational approaches (see WP5) allowing processing of “big-image data”.

Multimodal & Quantitative Fluorescence Microscopies

FBI aims at implementing tools to measure molecular interactions and dynamics in complex environments, from cells to organisms. A number of high-end technologies have been already developed and made accessible. We will focus on FCS-related methods (svFCCS, SPIM-FCCS, scF(L)C(C)S, in vivo-endoscopic-FCS (see 4-), on merging bioluminescence with 2-photon/LSM, on polarimetry with multicolor fast polar imaging, on new techniques based on photothermal effects or photonic crystals.

Multiscale and Correlative Microscopy

Methods to achieve a workflow of integrated observations from data obtained on cells and tissues by light and electron microscopy are mandatory if one want to integrate the contextual environment of bio-molecular processes. Such methods (CLEM, SuperCLEM when High Res Light microscopy (see WP 1a) is used or FullCLEM when including space-time imaging) are applied to biological material in health or pathological conditions (cancer, lysosomal and neurodegenerative diseases, host-pathogen phytopathology).

New Contrast & In-Depth Imaging

We developed innovative photonics tools dedicated to in depth imaging and endoscopy (SHG, THG, CARS…). Two axes are explored, the first one focuses on new contrast generation, that do not rely on conventional refractive, absorption or fluorescence contrast mechanisms; the second aims at building methodologies and instruments that can extend the imaging depth of conventional microscopes (LSM, OPO, AdOp …), in order to study living organisms or small animals.

 

WP2 – High Throughput & High Content Screening

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.

 

WP3 – Probe development, Optomanipulation & Optogenetics

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.

 

WP4 – BioImage Informatics, Image Processing & Data Management

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).

WP 4aWP 4b
Quantitative Bioimage Informatics – Image Processing

All technologies offered or developed inside FBI generate BIG DATA, comparable to the volume produced by NGS. This sub WP focuses on their processing and analysis and perform intensive development of innovative algorithms, software and automation of image treatment workflows.

BioImage Analysis and Data Management

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 WG4b 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.

 

WP5 – Training, Dissemination & Technological Transfer

Considering Dissemination & Training a lot has already been achieved over the years, through technological and research networks (RTmfm, “Mission pour l’Interdisciplinarité CNRS”, GDR-MIV 2588) 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 WG4b 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.

WP 5aWP 5bWP 5c
Training & Education

A sub WP5a has been delineated beginning of 2015, in order to better answer the needs of both the users and FBI internal communities. The WP5a missions are two parts. Significantly support and innovate in training activities for both new and experienced users in imaging approaches and to organize or co-organize important events (vocational training and exchange dedicated workshops) for the internal community (e.g. engineers working in core facilities and R&D labs). Members of the WG5a are involved in the organization of FBI-AT and participate to the organizing and scientific committees of the MiFoBio CNRS School. Two members of this WG5a are also members of the GDR MIV pilot committee. WG5a also corresponds to a group particularly but not exclusively involved in H2020 projects (Infra Dev Sup II EuroBioImaging; Global bioImaging RIA; COST on image analysis…). More to come!

Dissemination & Communication

Since end of 2014, FBI entered its operational phase. Strong efforts must be done to expand its visibility within the broadest scientific community. This sub-WP aims at increasing FBI notoriety, with the goal to allow the infrastructure to fully take its locomotive role in Biological Imaging at both national and international levels. To do so, the infrastructure has to work out the awareness of the might of the French community in bioimaging.
The following tools are deployed:
– Events planning and support, outreach efforts
– Communication via the newsletter and the website
– A clear service offering
– Dissemination of calls for scientific projects
– Highlighting and communication on FBI publications
– Strategic involvement in H2020 and international programs

Technological transfer & industrial relationship

While tech transfer and industrial contractual partnership is a common feature of all nodes and sites of FBI, a common strategy remains to be clarified in this matter. No way to start a productive strategy in this domain without having a “Consortium Agreement” between all parties of the infrastructure. This has been finally achieved by the coordination team and the CNRS services, middle of 2015. At this stage however, this mission remains under the control of the diverse and more or less local business teams and other organizations (SATT, Carnot Institutes…). We plan to organize a “call for projects” for tech transfer beginning of 2016.