The first Annual Meeting of the Infrastructures Nationales en Biologie Santé (INBS) was hold at CNRS, 9th December 2014. The aim of this meeting was to prepare the actualization of the Research Infrastructures road map defined in the National Strategy of the Research Infrastructures 2012-2020 by the DGRI (Direction Générale de la Recherche et de l’Innovation, National Ministry).


The general policy of the National Strategy of the Research Infrastructures 2012-2020 is to:

  • be leader in the construction of European Infrastructures
  • increase French participation in advanced international programs
  • assist the needs of research community in all activity domains
  • reinforce partnerships between economical suppliers and users


23 INBS are recognized:

  • ANAEE (Analyse et expérimentation sur les écosystèmes-Service)
  • CONSTANCES (Infrastructure épidémiologique ouverte pour la recherche et la surveillance)
  • CRB ANIM (Réseau de centres de ressources biologiques pour les animaux domestiques)
  • E-CELL France (Infrastructure nationale de médecine régénératrice basée sur les cellules souches mésenchymateuses)
  • EMBRC France (Centre national de ressources biologiques marines)
  • E-RECOLNAT (Valorisation de 350 ans de collections d’histoire naturelle : une plateforme numérique pour l’environnement et la société)
  • F-CRIN (French Clinical Research Infrastructure Network)
  • FLI (The French National Research Infrastructure for Medical Imaging)
  • France BIOIMAGING (The French National Research Infrastructure for Biological Imaging)
  • France GENOMIQUE
  • France HADRON (Hadronthérapie)
  • FRISBI (Infrastructure Française pour la biologie structurale intégrée)
  • HIDDEN (Infrastructure de recherche dédiée aux maladies hautement infectieuses)
  • IDMIT (Infrastructure nationale pour la modélisation des maladies infectieuses humaines et les thérapies innovantes)
  • IFB (Institut Français de bioinformatique)
  • INGESTEM (Infrastructure nationale d’ingénierie des cellules souches pluripotentes)
  • METABOHUB (Infrastructure nationale en métabolomique et fluxomique)
  • NEURATRIS (Infrastructure de recherche translationnelle pour les biothérapies en neurosciences)
  • PHENOME (Centre Français de phénomique végétale)
  • PHENOMIN (Infrastructure nationale en phénogénomique de la souris)
  • PROFI (Infrastructure Française de protéomique)
  • TEFOR (Transgenèse pour les études fonctionnelles sur les organismes modèles)

An analysis is conducted by AVIESAN ( and ARIIS ( about an outline of good practices of different types of service offer in the context of public-private partnership.

The C-CRAFT software for segmentation of particles and estimation of background fluorescence in 2D and 3D live cell imaging, was developed by the Serpico Team at Inria de Rennes, a member of the FBI-IPDM ( Bioimage informatics-Image Processing and Data Management) transversal node . See also

ICY is an open community platform for bioimage informatics developped at Institut Pasteur in the frame of “FBI-IPDM” projects. It gathers software ressources to visualize, annotate and quantify bioimaging data.

A team work, dear to the policies and objectives of France-BioImaging !


The 30th of January 2015, coordination staffs of 3 INBSs, laureates of the “Programme Investissement d’Avenir” in 2011 (FRISBI, Phenomin and FBI), get together for an informal meeting at IGBMC, Illkirch. The idea, that our INBSs could better interact, think of common projects or services and organize joint actions, was born during the INBSs meeting organized at the CNRS, in December 2014. Although at a very early stage, cooperation is definitively foreseen between FRISBI (Integrated Structural Biology), Phenomin (Mouse phenogenomics) and FBI (Bio-Imaging). Complementary or common technological approaches appear obvious. A shared session between the 3 Infrastructures will be organized during the next FBI Annual Meeting (17th- 18th of September, Institut Curie, Paris) with the goal to consider possible transverse activities.


Short presentation of these infrastructures


logo-frisbi The French Infrastructure for Integrated Structural Biology (FRISBI) provides an infrastructure for integrative structural biology approaches, from the molecular to the cellular level, integrating multi-resolution data from X-ray crystallography, small angle X-ray scattering, NMR, Cryo-EM and functional data including development for protein expression and crystallization. Opened to structural and molecular and cell biologists from both academia and industry from France and Europe FRISBI will reinforce technology transfer between national and international academics and industry for technological developments and therapeutically applications. FRISBI comprises strong component for training in integrative structural biology by the organization of congress, workshops & practical courses, and national and international master degree program.

phenomin-baseline PHENOMIN is devoted to serve the French community for the usage of mouse models. This National Infrastructure constitutes a unique distributed resource for the creation, the care, the phenotyping, the distribution and archiving of animal models for academics and private corporations. Its scientific goals are to improve the knowledge of the mammalian genome, identify and understand its variations and discover new opportunities for therapies and drugs. PHENOMIN will also participate to the International Mouse Phenotyping Consortium (IMPC) and plans to contribute to Infrafrontier and to ESFRI-identified pan-European infrastructure for functional genomics. PHENOMIN will be a key item of the the National Alliance for life sciences and health (AVIESAN).

FBI Grand France-BioImaging (FBI) gathers several biological Imaging Centers associated with R&D teams with the aim to cover recent advances in microscopy, spectroscopy, probe engineering, signal processing and BioImage Informatic. It is a pluridisciplinary project with participants in Biology, Physics, Chemistry, Computer science and engineering. The consortium brings together the efforts to overcome technological barriers persisting at different levels of Cellular Imaging and breaks the frontiers between research and innovation thanks to collaborative projects with industry. France Bioimaging is strongly involved in the strategy of the ITMOs BCDE of Aviesan through the French Networks of the CNRS (GDR-MIV) and directly linked to the “Euro-BioImaging” project of ESFRI.

International_Year_of_Light_2015_-_color_logo_2 The Year of Light is a global initiative voted by the United Nations (UN) which aims to raise awareness around the world about the importance, in daily life, of light and technologies associated as optics and photonics. By focusing on the light and its technologies, the UN recognizes their role in sustainable development by providing solutions to current and future global challenges such as energy, education, agriculture and health. Light plays an essential role in our daily lives and is a crucial cross-discipline of science in the 21st century. It revolutionized medicine, opened the international communication via the Internet, and continues to be an important factor in social, economic, and cultural policiess. A large consortium of scientific organizations in partnership with UNESCO brings together many stakeholders, including the scientific community, the world of education, technology platforms, non-profit organizations and private sector partners.

For France, the International Steering Committee set up by UNESCO, entrusted exclusively to the National Committee, led by the CNOP (National Committee for optics and photonics), coordination and animation of the event at the national level. “2015, Year of Light in France” will cover all of these topics by organizing various events: conferences, round tables, technical and scientific meetings, artistic events, development of educational tools, exhibitions, popular science operations, scientific site visits, industrial and cultural meetings with and for young people… They will highlight the various areas concerned by light and its applications: science, industry, daily life , nature, culture, history. The wide spectrum of these fields promises a major mobilization of all: scientists from mathematics to philosophy, communities, public and private institutions, cultural actors and artists, students, professors and researchers, schools and universities. Many local players are already mobilized and have requested the Executive Board obtaining the label and communicate their program.

logo The CNOP appointed an Executive Board which labelize the events, builds and manages communications tools, ensures a good distribution of events in terms of geography and audiences, handles the visibility of the Year from the various target audiences and the media. This committee brings together the main structures which work in the field of light: learned societies, associations and clubs, national organizations, scientific and cultural centers, museums, publishing houses, institutional, industrial…

National Committee
« 2015, Year of Light in France » With the sponsorship of the Nobel Prize in Physics Claude Cohen-Tanoudji and Serge HAROCHE

Executive Board

  • Costel SUBRAN – Chairman
  • Eric LAMBOUROUD – Communication
  • Ivan TESTART – Sponsorship and finance
  • Agnès HENRI – Secretary
  • Catherine HERCE – Webmaster


  • John DUDLEY – IYL2015-FEMTO-ST
  • Etienne KLEIN – CEA
  • Gérard MOUROU – Polytechnique

Institut Curie, Paris, January 5-6 2015


The second EUBIAS taggathon and showcase were both co-organized by FBI and were planned on separate dates , to allow the organization of EUBIAS showcase as a joint event to QBI in Institut Pasteur: about 50 attendees participated to both meetings. Since EUBIAS showcase is planned for communication between developers and analysts and QBI is for discussion among developers, co-organization seems to have facilitated more attendance in both meetings.

European Bioimage Analysis Symposium aims at increasing the accessibility of image analysis tools to biologists and also to facilitate feedbacks from biologists to software developers. Moreover, EUBIAS is the meeting organized by bioimage analysts to discuss about their roles in biology. The first EUBIAS was held in Barcelona in 2013. Efforts have been pursued for creating a community of image analyst, to bridge new algorithms, new microscopy methods and the users, and the same spirit continued to the 2nd EUBIAS held in Institut Curie, Paris in Dec. 2014 and Jan 2015 for Taggathon and showcase meeting.

The second EuBIAS showcase meeting gathered around 120 scientists from all over the world, 40 % from France, and around 50% working in microscopy facilities. During this 2 days meeting, 35 state-of-art quality talks including 3 keynote lectures were given on topics ranging from general purpose open image analysis software to more focused application packages for analyzing cells and particle. Two panel discussions were animated, with highly interactive exchange of opinions and views in lively atmosphere: one was on the open source licensing ecosystem and the coexistence between free and commercial software; the second one around the definition of the Bioimage Analysts community, its relationship and positioning with both life scientists and developpers. In addition as a new approach, the previous poster session was replaced by two ‘meet the developers’ sessions. Interactive live demos at individual presentation slots ignited fruitful and direct exchange of comments among participants and speakers and added further excitements to the meeting. The strong involvement of commercial companies in this event should also be noted here.

In a nutshell, the event was extremely successful in increasing the flow of information within the image analysis community. Many participants discovered themselves as being bioimage analyst and commented that “This is the meeting I was looking for”. The next EUBIAS is already planned for 2016, several locations are conceivable.

Institut Pasteur, Paris, January 7-9 2015

The 3rd QBI conference followed two previous sessions which were held in Albuqerque, New Mexico USA. QBI is meant to gather scientists concerned by bioimaging, from new microscopy technics especially single molecule nanoscopy and up to the statistical analysis and modeling, applied to life sciences issues, in a focused and interdisciplinary manner. The free of charge registration is another remarkable feature of QBI. The idea behind is to allow as many as possible PhD students and post-docs to attend.

This year, the third QBI conference was co-organized by FBI, in particular by elements of the “Bioimage Informatics-IPDM” WG (Institut Pasteur, Inria, Institut Curie). QBI was following the 2nd EUropean BoImage Analysis Symposium (Institut Curie, Paris, 5 and 6 January) in a joint Event fashion, making possible scientists to attend both meetings in a row quite successfully (about 50 attendees participated to both meetings). It gathered more than 180 scientists from all over the world. 66 talks were presented in 13 sessions, some from solicited speakers (19) but mostly selected from the 85 submitted abstracts. Lively poster sessions completed this scientific program. All in all, QBI 2015 was apparently a strong success and attendees look forward to the next QBI conference, which will be most probably held again in Europe, in Delft, Netherlands, Beginning of the next year.

Unfortunately, the conference was taking place at a very tragic time in Paris. The local organizers, wish to thank our foreigner colleagues for their support and their strong marks of solidarity with the French people.

We were all “Charlie” at QBI 2015 !

Serpico team makes some of its software applications available through a Mobyle web portal. This portal allows you to run image processing programs on your data. As the images are transfered across the internet, it is better used with small size data.


The aim of this portal is to show what Serpico team can offer to the France Bio Imaging community in terms of image processing and it is not designed to handle production usage. However, if you find the programs shown in the portal interesting, you can contact the team to get a copy in source or binary form.




In 2004 was launched the first edition of the MiFoBio CNRS Thematic School, created by the logo%20GDR2588 GDR(2588)-MIV (Microscopy and Imaging of Life) with the participation of the Technological Network, RTmfm. Yves Usson and Laurent Heliot, both former and actual directors of the GDR MIV, are back on the adventure. They answer a 7 points questionnaire on main goals and organization of MiFoBio, changes experienced over the years and assessment, vision for the next ten years.

Starting from biological questions and models up to data analysis, using up to date microscopy setup or even prototypes, to acquire data. During this school, we are all teachers and apprentices regardless of the rank or age.Yves Usson
MiFOBio is more than a thematic school. It allows to anticipate the next advances and to mobilize upstream new scientists of the communities, on technological aspects, thematic in biology or physic and image analysis. Laurent Héliot
  • What was your main goal in creating MiFoBio in 2004?

MiFOBio Microscopie Fonctionnelle en Biologie – functional microscopy in biology) is a summer school of the CNRS. Rapidly after the GDR-MIV (microscopy and imaging for life) was created in 2003, it emerged that we needed a recurrent scientific « rendez-vous » during which the scientific disciplines represented in the GDR could mix. Organizing a conference was rapidly discarded because this formula does not really encourage the mixing of diverse communities while our aim was to create real exchanges and to foster new approaches (trans-disciplinarity). The main tool, although not the only one, we chosen was the organization of real “hands-on” workshops, starting from biological questions and models up to data analysis, using up to date microscopy setup or even prototypes, to acquire data. Actually, this responded quite well to both the needs of a broad community and to our objective to favour the “get together” of scientists from biology, physics, chemistry, instrumentation, signal analysis. CNRS Being around a microscope makes these scientists accepting everyone to be ignorant of the knowledge of the others, but willing to share his own! During this school, we are all teachers and apprentices regardless of the rank or age. In 2004 with the MRCT (CNRS), we also created a technology network (RTmfm) that brought to the game, the microscopy core facility engineers. RTmfm was naturally associated to the organization of the thematic school and today it represents one of the main task force of MiFoBio.

  • How did you get the idea of a thematic school in biophotonic and biological imaging?

The program was soon a success with 150 participants for the first edition in 2004, on the island of Oléron. Since 2010, we passed more than 450 requests to participate.
The organization of MiFoBio was the main outcome of the first General Assembly of the GDR2588-MIV (microscopy and imaging for life). During this meeting we defined what would be the main scientific activities of our GDR. In 2003, with Bernard Vandenbunder we had organized an interdisciplinary school at Ambleuteuse (Pas de Calais) in connection with the creation of the Interdisciplinary Research Institute in Lille (IRI). This type of trainings is typically one week long and organized in an “out-of the-way place”, which facilitates interaction. However, most often these events do not have important practical sets. At that time, the ELMI meeting (European Light Microscopy Network) was running since 2 years and proposed in addition to conference sessions, workshops set up by private companies heading the microscopy field. A number of us were participating to the organization of the 2 first ELMI meetings (EMBL (funding meeting) and Italy 2001, France 2002). We took advantage of both experiences. But we wanted to foster interactivity and the use of real and live biological sample. In MiFoBio, workshops are realized by the academic scientists sometimes in collaboration with industrial representatives, on microscopy systems provided by manufacturers. It is always delightful to see how our colleagues from the private sector answer the demanding requirements of MiFoBio, over the years! We will never thank them all enough, for their fidelity and active commitment. The program was soon a success with 150 participants for the first edition in 2004, on the island of Oléron. Since 2010, we passed more than 450 requests to participate. In this respect, we feel very unfortunate to have started to limit the number of attendees.

  • Who is responsible for the thematic school?

MiFoBio is born from the collective will of the steering Committee of GDR2588-MIV. To be more precise MiFobio is organized as a modular triptych form: Courses-lectures, workshops, round tables. Its organization is coordinated since the beginning by Laurent Héliot, (IRI, Lille) with a committee constituted of 30 people. Some are members of the executive committees of the GDR and RTmfm, recently some are members of FBI. The thematic of courses-modules and organization of workshops are discussed in the organizing committee which then ensures the practical implementation of the school. Since 2012, Serge Monneret (Institut Fresnel, Marseille) is the co-coordinator of the school. In 2014, MiFoBio brought together over 440 people (participants, organizers, speakers, industrials). In total 58 courses and seminars, 80 distinct workshops, more than 20 advanced courses and round-tables RTmfm were organized in 2014, which make miFoBio a kind of “à la carte” School. During one full week, MiFoBio works daily as a buzzing beehive, from 8 am to midnight. Much later than bees, in fact !

  • What changes has experienced MiFoBio school?

The program has evolved in each edition to be adapted to the advanced in the field of biophotonics and bioimaging, the evolution of the community and its training needs. We can consider two phases since 2004. Until 2008 the first three editions created a real national interdisciplinary community in bioimaging by developing interdisciplinary knowledge based on the acquisition of common vocabulary and concepts. In the same period, microscopy has seen great progresses. Let’s just mention the two Nobel Prizes of chemistry 2008 and 2014. The number of participants dramatically and quickly increased. This led to new technical problems (electricity, size of the grow room, overall cost, …).

In the same period, microscopy has seen great progresses. Let’s just mention the two Nobel Prizes of chemistry 2008 and 2014.
Since 2010, MiFoBio has started a new phase on the basis of an interdisciplinary community that is now in place. This is marked by more scientists working on digital image processing and more home-made systems from physics laboratory during the workshops. Since 2010 the organizing committee was strengthened and structured to meet the new requirements around workshops. In addition we have inserted studies on new biological models, such as Xenopus and zebrafish. This second phase is also marked by the invitation of more and more foreign colleagues. Some who are now proposing to organize workshops, as well! Not to forget our special this year, with the presence of Eric Betzig the eve of his nomination for the Nobel Prize in Chemistry.

  • What finally brought the school Thematic?

It strongly contributed to recent advances in understanding life, and this is just the beginning.
MiFOBio school has created a dynamic interdisciplinary community of both researchers and engineers from different disciplines and technological areas around imaging life, beyond institutional structures. “Biophotonics” is not a clearly defined discipline but rather a thematic field exploring biology through other disciplines. It strongly contributed to recent advances in understanding life, and this is just the beginning. Specifically, the contributions of MiFoBio results in technological “premières”, fruitful, innovative and long term collaborations, in academic-industrials partnerships with both market indicators or pure scientific results (publications).
But above all, MiFoBio allows for anyone to advance in the understanding of how to apply technology to science. We can only hope that each participant becomes a little less ignorant after MiFoBio, but we are sure that each becomes more “interdisciplinary”.

  • What is your assessment after ten years of existence ?

This can be resumed in a few words: we did not anticipate its actual size and its notoriety.
This can be resumed in a few words: we did not anticipate its actual size and its notoriety. This is nice, but it can lead to some organization problems such as mobilization of resources, duration of the organizing phase. Until last session MiFoBio was an itinerant thematic school. This is motivating but logistically time consuming. This year we experienced to come back at the same place as in 2010, for the first time. MifoBio mobilizes a lot of voluntaries in the GDR and RTmfm. It will be insane to propose one MiFoBio every year, which however will better address the always growing demands. Work and pilot events are going on this matter. Together with FBI, we now have launched the FBI-AT (Advanced Training) in an alternate timing (year between two miFoBio sessions). This is a more focused training event, with fewer participants, but which should complete the overall activities of MiFoBio. To make it short, MiFoBio is a kind of “a la carte” school while FBI-AT is more designed as training “au menu”.

  • Are you proud of the success of MiFoBio ? How do you see the next ten years?

For sure, we are proud! image28_Overlay4++NT_2-Simmler It is a real success, the high quality of the lectures, the diversity and high technological grade of the proposed workshops makes it a unique scientific school in Europe and probably in the world. The friendly atmosphere, not forgetting some recreation sessions, is also an essential key of the MiFoBIo success. MiFOBio is more than a thematic school. It allows to anticipate the next advances and to mobilize upstream new scientists of the communities, on technological aspects, thematic in biology or physic and image analysis.

The input of signal processing and modeling is going to take an important position, in connection with “big data” approaches.
Naturally, we wish to pursue the adventure and we are thinking about MiFoBio 2016 for which it is necessary to put down the CNRS proposal next spring. This new editions of MiFoBio will be very different. We have to think about the microscopy within the next 5 to 10 years. MiFoBio has to help to create synergy between the actors of these future imaging approaches. Inclusion of Electronic, Ionic and Atomic force microscopy expertise is already a reality. The input of signal processing and modeling is going to take an important position, in connection with “big data” approaches. Besides, new chemical and bio-sensors start to be available. Optogenetics will be one main driver items of the next MiFoBio. Another issue which is not a new issue is how to export the MiFoBio concept, in order to answer an anticipated international demand? We do not have clear answer on that, although European Infrastructure (ESFRI projects), recent programs at the EU (Infra-Dev-Sup in H2020) or through other international organization could certainly help.

The Preparatory Phase of EuBI, (a pan‐European research infrastructure project on ESFRI Roadmap) lasted from Dec 2010 to May 2014. Euro-BioImaging entered now the Interim Phase, with representatives of 12 countries and EMBL (as an international organization) working together towards the future implementation of the infrastructure. France with Belgium, Czech Republic, Finland, Israel, Italy, Norway, Poland, Slovakia, Spain, The Netherlands, United Kingdom and EMBL is one of the signatories constituting the Euro-BioImaging Interim Board that governs the Interim Phase prior to operation.


FBI, part of the Game. In this phase, France-BioImaging represents the French Task force. In agreement with the Ministry (MESR) and the CNRS, FBI supports the French Financial Participation to this Interim Phase and participates to the Interim Board. Tasks of the Interim Board are to decide on the legal model and governance structure, finance plan and user access policy. IB will be also directly involved in the definition of criteria for the future Euro-BioImaging Hub, its choice and its missions.


Read more

Our contacts in the EuBI Interim Board : Daniel Choquet and Pierre François Lenne

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Stefan Hell, Eric Betzig and William Moerner have been honored with the highest scientific award, the Nobel Prize for Chemistry 2014, for the development of super-resolved fluorescence microscopy. Stefan Hell developed principles of Stimulated Emission Depletion (STED) microscopy while William Moerner and Eric Betzig laid the foundation for single molecule microscopy. Both methods allow scientists to visualize individual molecules in cells on nanometer range, a resolution that was until recently considered unreachable. Nobel Lectures will be held on Monday 8 December 2014, at the Aula Magna, Stockholm University. It was a rare honor and a real pride for the organizers of the CNRS summer school MiFoBio2014, one a the major training/teaching event of the GDR MIV and France-BioImaging community, to have welcomed among its distinguished speakers Eric Betzig who was awarded the day after his conference ! Next Focus on Microscopy conference meeting will be held in Gottingen, Stefan Hell’s city! Do not miss the registration date.