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)
• BIOBANQUES
• 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 (http://www.aviesan.fr/) and ARIIS (http://www.ariis.fr/) 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 http://mobyle-serpico.rennes.inria.fr/

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.

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 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).

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.

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.

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…

Webiste
Institut Curie, Paris, January 5-6 2015

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.

Webiste
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.

http://mobyle-serpico.rennes.inria.fr