The BIC is setting up in a brand new space

In the last weeks of October 2016, the BIC has settled in a brand new building, constructed by the Regional Council of Aquitaine as part of the Neurocampus project. This building, of around 13 000 m2, is shared with the Interdisciplinary Institute for Neuroscience (IINS) and the Institute for Neurodegenerative Disorders (IMN). This building, constructed in two years, cost 47 M€ and is part of a large project to develop Neuroscience and imaging in Aquitaine. The new building is conveniently located and connected by footbridges between the Magendie Neuroscience center and the Center for functional genomics (CGFB) that hosts several core facilities.

buildingbic1

In total, the BIC will occupy 1000 m2, split between the CGFB and the new building. The major part in the new building is dedicated to photonic microscopy. Electron microscopy instruments, including two brand new ones coming in 2017, will be dispatched between the CGFB and Neurocampus building. In these new spaces, users have access to a culture room and also a room with analysis stations. Other rooms are dedicated to each kind of microscopy (one room for live cells imaging, one room for multiphoton, one room for confocal, one room for new scanning electron microscope etc…). Special rooms are dedicated to host R&D projects as well as confidential collaborations with industry.

Development of training capacities at the BIC – joint projects with the Cajal School of Neuroscience

buildingbic2

The BIC has engaged for many years in active training programs for imaging at all levels (beginners to advanced training) for local, national and transnational users. The BIC personnel also participates extensively to various theoretical and hands on training/showcase activities in France and abroad (MifoBio, NeuBias, etc…). Within the strategy to develop the BIC-FBI training, we are engaging a partnership with the Cajal Advanced Neuroscience Training Program to develop special ima ging training for Neuroscience. The Cajal school is a European FENS and IBRO initiative in partnership with Bordeaux Neurocampus and the Champalimaud Foundation, which offers state-of-the-art hands-on training courses in neuroscience.

Construction of a light sheet microscope for super resolution imaging inside living samples

Fast and non-damaging imaging of single molecules inside live organisms is essential to study physiologically relevant biochemical mechanisms occurring at the subcellular level. For example, the dynamic organization of transmitter receptors at the membrane of excitatory neurons should, ideally, be studied in vivo in the brain of animal models. Unfortunately super resolution techniques such as PALM1, STORM23 and uPAINT4 are mostly restricted to the sample external surfaces and are unable to image inside live samples.

For these reasons the Bordeaux Imaging Center is developing a new light sheet microscope specially dedicated to image single molecules into live samples. Light sheet fluorescence microscopy (LSFM) is recognized as the method of choice to image thick live samples. Compared to other fluorescence imaging modalities such as wide field, confocal, structured illumination, two-photon or STED, LSFM strongly reduces out of focus fluorescence, decreases photobleaching and phototoxicity, and improves temporal resolution. Among the numerous technical implementations of LSFM 5, we decided to build a lattice light sheet microscope (LLS) because it has been specifically designed to perform super resolution imaging in thick live samples 6. Indeed In LLS the illumination beam is shaped by a spatial light modulator (SLM) to produce a < 1 µm thick excitation plane over a length of  > 50 µm at the sample. A 1.1 NA detection objective ensures efficient light collection required for high localization precision. Illumination and detection objectives are both long working distance and water immersion, thus allowing observation of live samples up to 5 mm in diameter. (Fig 1 A)

Our LLS microscope is mostly based on the documentation freely and kindly shared by Eric Betzig’ group (HHMI Janelia Farms, USA).

fig1
Photo Credits: Mathieu Ducros

Fig 1. (A) The sample is placed at the intersection of the excitation and detection objective optic axes in a temperature controlled perfusion chamber. It is held at the tip of motorized arm on a 5 mm diameter cover slip (from 6). (B) The LLS microscope under construction in June 2016. (C) In blue and green the optical path of the excitation and detection beams respectively (from 6). A higher efficiency SLM, higher QE camera should improve the light budget compared to the original specifications. In addition, a targeted laser beam (red) will allow precise photo-conversion of light sensitive molecules.

We made a few modifications compared to the original specifications of the LLS as described in 6 : our microscope will be equipped with a laser combiner including 4 high power lasers at 405 nm (300mW), 488 nm (1 W), 560 nm (2 W), 642 nm (2W), a higher efficiency SLM (Fourth Dimension DD QXGA) and a sCMOS camera with improved quantum efficiency (Hamamatsu ORCA Flash V2). These improvements should mitigate the weak throughput of the LLS beam path, and, in turn, improve molecule localization precision and/or time resolution. In addition, a targeted photostimulation beam will be coupled through the detection objective to photo stimulate or photoconvert with a high spatial and temporal resolution photosensitive molecules.

STORM, PALM and PAINT imaging modalities will be fully compatible with the constructed LLS.

The microscope construction by Mathieu Ducros, INSERM research Engineer on the BIC, started in April (Fig 1B). First images are expected by the end of 2016. Once our LLS is fully operational and running, it will be accessible to all BIC users under the supervision of a local engineer.

For this project we are supported financially by the GIS IBiSA, LABEX brain and FBI.

References

  1. Betzig, E. et al. Imaging intracellular fluorescent proteins at nanometer resolution. Science 313, 1642–1645 (2006).
  2. Rust, M. J., Bates, M. & Zhuang, X. Sub-diffraction-limit imaging by stochastic optical reconstruction microscopy (STORM). Nat. Methods 3, 793–795 (2006).
  3. van de Linde, S. et al. Direct stochastic optical reconstruction microscopy with standard fluorescent probes. Nat. Protoc. 6, 991–1009 (2011).
  4. Giannone, G. et al. Dynamic superresolution imaging of endogenous proteins on living cells at ultra-high density. Biophys. J. 99, 1303–1310 (2010).
  5. Santi, P. a. Light sheet fluorescence microscopy: a review. J. Histochem. Cytochem. 59, 129–138 (2011).
  6. Chen, B.-C. et al. Lattice light-sheet microscopy: Imaging molecules to embryos at high spatiotemporal resolution. Science (80-. ). (2014). doi:10.1126/science.1257998

 

Bordeaux Imaging Center: http://www.bic.u-bordeaux.fr/

UMS 3420 CNRS-Université de Bordeaux, US4 INSERM

Contact: bic[at]u-bordeaux.fr

Photo Credits: www.bordeaux-neurocampus.fr

On September 22nd, 2016, a joint meeting took place between the FBI coordination, IPDM node and other partners, to discuss the implementation of data management services within FBI. Please find below the main points discussed during the meeting.

  1. Objective – Setting the required elements for public access to different types of Image Data within FBI.
  2. Purpose and expectations – to have, in one year’s time, a successful proof of concept for FBI. This topic is of particular importance for FBI, as it will soon be required of any project funded with public money to provide data management plans. In the very short term, infrastructures will likely be expected to guarantee the safe conservation and fast access to any data supporting a publication (see for example the Netherlands protocol).
  3. Audience – two different audiences were considered as targets of the project: users within the FBI perimeter, and the general public (fully public access); the former being more feasible in a year’s time than the latter.
  4. Proposals

    • WP1a Support
      • Support the work of WP1a in their benchmarking action (Contact: Orestis Faklaris);
      • Being workflow-oriented, so that the methods defined to support WP1a can be applied to other WPs.
    • Metrology-oriented database
      • Instrument-based metrology database: asking each site to share metrology benchmarking of microscopes from 2016, including software used when any;
      • At midterm: go to real biological object to associate metrology data as quality metrics;
      • Before the end of the project: include metrology oriented annotations to WP1a support;
      • Long term: include metrology-oriented annotations to open image data repositories.
    •  Open Image Data Repository:
      • Hosting 2016 publications acknowledging FBI, uploading raw data at least supporting published figures.
  5. Resources: Remaining funds from Pasteur IPDM could be mobilized to carry out the project (the funds would go towards financing the equipment and staff). Coordination funds will be allocated to the employment of an engineer for a period of approximately 9 months.

Meeting Participants:
Volker Baecker (Montpellier), Anatole Chessel (Paris Sud), Stéphane Dallongeville (IPDM Paris Centre), Anne Danckaert (Paris Centre), Elaine Del Nery (Paris Centre), Nimisha Gupta (OpenImadis Bengalore), Cédric Matthews (Marseille), Perrine Paul-Gilloteaux (IPDM), Jean Salamero (Coordination), Corinne Tessier (Coordination).

The Global BioImaging project entails an international job shadowing program that aims to give the opportunity to the project’s stakeholders to visit imaging facilities across the globe and learn from their peers.

The program will allow both the hosting facilities and their guests to exchange experiences and ideas, while working on innovative imaging technologies and the related technical aspects. It also has the added value to support networking and prepare possible future collaborations between imaging infrastructures.

The call for the first GBI international shadowing program is now open!

Deadline for submission of the applications is 31/10/2016.

NEUBIAS, the network of European BioImage Analysts funded by the EU framework COST, has opened a new activity that will run continuously for 4 years, and is centered on mobility grants, also called Short-Term Scientific Missions.

The first call deadline is the 10th of September, but several other call will be regularly published.

BioImage Analysts and Life Scientists, from Research Labs AND Core facilities, can apply for funds to cover their expenses when visiting a Host-Lab in a different country (Lab or industry) where they will perform a short scientific project strictly focused on BioImage Analysis, and that should enable:
1) collaborations on innovative image analysis methods,
2) access to big data analysis technology and/or image analysis tools for scientists lacking them locally,
3) knowledge transfer to support careers and regional development.

Please check all the information here: http://eubias.org/NEUBIAS/?page_id=707 and contact these people for any question: Julia Fernandez Rodriguez – NEUBIAS STSM Coordinator – juliafer@cci.sahlgrenska.gu.se Clara Prats – NEUBIAS WG7 Co-Leader – cprats@sund.ku.dk Julien Colombelli – NEUBIAS Action Chair – julien.colombelli@irbbarcelona.org

NEUBIAS: Network of BioImage Analysts Logo

 

 

Already before year 2016, FBI was involved in many teaching and training activities. With the care about “not reinventing the wheel”, FBI first brought its support to running activities in this domain at the national level. For this reason, it was decided to bring recurrent help to the MiFoBio school of the CNRS, organized by the GDR MIV since 2004. Moreover and similarly, FBI is co-organizing the FBI-Advanced Training sessions, also with the GDR MIV. These two 5-9 days events are highly valuable and are recognized as such by a large community, far beyond core facility staffs. They are largely focused on theory and hands-one training and on applying this knowledge to specific biological questions. In 2016, FBI was a pushing force to give an international visibility to both actions. Both concepts merit a stronger international impact as other workshops or training series do, like EMBL-EMBO or Woods Hall workshops and courses. Taking advantage on diverse opportunities at the European and International level together with other main international actors in this topic (H2020, EuBI, NEUBIAS, FENS CAJAL), FBI now drafted a strategy at an upper level, with the aim at defining a complete “train the trainers” portfolio.

 
Let us mention some almost achieved deliverables: organizing surveys on Training Activity and Training Sites for Core Facility Staff and User within the European landscape followed by the proposition of new and necessary “trainings” (H2020 WP7 EuBI PPII) which will be presented during the 1st EuBI Core Facility Staff meeting (30th of October beforehand the MiFobio 2016), including organizing virtual (e-training), soft and management skills courses, hands-on training.

 
In this respect, France BioImaging co-organizes and will also teach at the 1st International Training Courses for Imaging Core Facility Staff of the Global BioImaging project (deadline 18th September), next November 2016 in Heidelberg (GBI International Training Courses for Imaging Core Facility Staff) which will adress two specific issues:
-“Challenges in image data management and analysis”
-“Management and operation of imaging core facilities”

 
Our experience in international course activities, expertise, equipment of our Local-Nodes with state of the art imaging techniques, allow us to propose the largest and most advanced portfolio of “à la carte” trainings in BioImaging over Europe. As a future step, France-BioImaging is supporting the opening of a call for “EuBI Training Nodes” in which FBI will propose itself as a “Training Node”. FBI is in a very strong position to propose an integrated Training offer in bioimaging. The Marseille and Bordeaux Nodes are currently building Training Centers. In Paris Centre, an Imaging Training common program is part of the recent official partnership between Institut Pasteur and Institut Curie (February 2016). Joint ventures between Marseille and Montpellier nodes and inclusiveness between Paris Centre and IdF Sud nodes teaching programs are foreseen.

Nota Bene

Location: EMBL, Heidelberg, Germany
Registration: here
Registration deadline: 18th of September 2016

Dear All,

It is our pleasure to announce the first International Training Courses for Imaging Core Facility Staff organized by the Global BioImaging project consortium!

The two advanced courses address core facility staff working at Euro-BioImaging Node Candidates and at the international GBI partner institutions. The courses will take place back-to-back at the EMBL in Heidelberg (Germany) and will cover the topics of:

“Challenges in image data
management and analysis”
November 13-15th, 2016

 
The goal of the course on “Challenges in image data management and analysis” is to present the capabilities and technologies currently available to imaging facility staff in the field of image data management and analysis. The aim is to raise awareness on the current challenges in the field and to provide the course participants with a new set of tools (and references) that can be used tackle such challenges and improve their own facility’s working life.

Program

“Management and operation
of imaging core facilities”
November 16-18th, 2016

 
The course in “Management and operation of imaging core facilities” aims at providing an educational program for facility staff in the field of facility management and administration. It will entail a session on soft skills training, the presentation of case studies of imaging facilities in the fields of biological and biomedical imaging as well as visits to company-owned imaging centres.
 

Program

If you or your colleagues are interested in participating, please apply here: http://embl-web.ungerboeck.com/reg/reg_p1_form.aspx?oc=10&ct=NORMAL&eventid=5477 no later than Sunday, the 18th of September 2016.

The Global BioImaging project can provide a limited number of travel grants to successful applicants from Europe (up to € 750) and overseas (up to € 2.200).
However for administrative reasons we need to charge a registration fee of € 150 per course to all participants. A reduced fee of € 250 will be applied to those of you interested in attending both courses.

Since the number of places available for the courses is limited and in order to assign the travel grants, the applications will be evaluated and the successful applicants will receive an invitation to the course(s) within the end of September.

Do not hesitate to contact us if you have any question, and please spread the news also to your colleagues!

With best wishes and kindest regards,
Federica
federica.paina@embl.de

On behalf of Rainer Pepperkok and Jason Swedlow

Logos-GlobalBio-RGB

Dear colleague,
Dear FBI community,

Following the decision of the Executive Board of June 30, 2016, the National Coordination is proud to announce that the winners of the FBI Image Contest 2016 are:

1. Sébastien Mailfert – Centre d’immunologie de Marseille Luminy – Aix Marseille Université with “Dalton”

Dalton © Hugues Lelouard, Mailfert Sébastien & Mathieu Fallet CIML CNRS-INSERM-AMU
Dalton © Hugues Lelouard, Mailfert Sébastien & Mathieu Fallet CIML CNRS-INSERM-AMU
Confocal microscopy
Revealing sub-population of immune cells on small intestine by 10 colors spectral imaging

AND with “Le Saint Pierre Méditerranéen”

© Noushin Mossadegh & Mailfert Sébastien - CIML, CNRS-INSERM-AMU
Le St Pierre Mediterraneen © Noushin Mossadegh & Mailfert Sébastien – CIML, CNRS-INSERM-AMU
A l’aise comme un poisson dans l’eau, les spermatozoïdes se reposent dans leur habitat, qui ressemble à un œil, avant leur grande migration. Coupe d’un testicule de nouveau-né de souris. Marquage en immunofluorescence des noyaux cellulaires (DAPI) représentés ici en cyan. L’actine représentée ici en jaune, révèle le «squelette de la cellule» (phalloïdine marquée avec le fluorochrome Alexa-647). L’image représente 256×256µm sur 4096×4096 pixels. La coupe est d’une épaisseur de 20µm. Image de microscopie confocale sur Leica SP5 ; laser 405nm et laser blanc à 633nm ; objectif 40X, O.N. 1.25, immersion à huile.

 

2. Michael Lang – Institut Jacques Monod – ImagoSeine with “Fly Monster”

Fly monster © Orestis Falklaris & Michael Lang – Institute Jacques Monod, CNRS UMR7592 - ImagoSeine
Fly monster © Orestis Faklaris & Michael Lang – Institut Jacques Monod, CNRS UMR7592 – ImagoSeine
Multifocal confocal microscopy (spinning disk, Spinning CSU W1)
Drosophila third instar larval head, nuclear-RFP, neronal-GFP and green autofluorescence, 25x magnification, scale bar is 100 μm.

Thank you to the participants for their great contribution:

  • Sébastien Mailfert – Centre d’immunologie de Marseille Luminy – Aix Marseille Université
  • Ariane Peyret – Laboratoire de Chimie des Polymères Organiques – Bordeaux Imaging Center
  • Melina Petrel – Bordeaux Imaging Center – Université Bordeaux Segalen
  • Patrice Mascalchi – Interdisciplinary Institut of Neuroscience – University of Bordeaux – Bordeaux Imaging Center
  • Michael Lang – Institut Jacques Monod – ImagoSeine
  • Olga Nagy – Institut Jacques Monod, Drosophila Evolution Group – ImagoSeine
  • Théophile Déjardin – Institut Jacques Monod – ImagoSeine
  • Liu Zeng Zhen – Institut Jacques Monod – ImagoSeine
  • Melina Heuze – Institut Jacques Monod – ImagoSeine
  • Orestis Faklaris – Institut Jacques Monod – ImagoSeine
  • David Pereira – Laboratoire Matière et Systèmes Complexes – ImagoSeine

Thank you also to the core facilities staff and heads for having forwarded the contest to their users and for providing them state of the art Bioimaging.

The next edition of our Image Contest will open early 2017. Get ready!

The National Coordination

Dear colleagues from the BioImaging community,

NEUBIAS, the “Network of European BioImage Analysts”, a recently created network funded by the COST framework, is very glad to communicate the start of its activities which will evolve over the next 4 years and that might trigger interest in your research environment.

Mission : strengthening the bridge between life science, computer science and digital image processing by:

    1) Establishing the role and identity of bioimage analysts in the life science community
    2) Sharing bioimage analysis knowledge and techniques
    3) Improving image analysis technology, foster innovations and collaborations
About NEUBIAS

NEUBIAS aims to promote the mutual communication between Life Scientists, Instrumentalists, Developers and BioImage Analysts and to establish and promote the role of Bioimage Analysts in Life Science. Gathering, as of June 2016, more than 100 members in 33 European countries, the network will implement:

  • A training programme with 3 levels (Early Career, Facility, Analysts), 15 Training Schools for about 400 trainees.
  • An events series (yearly NEUBIAS conference, workshops, Taggathons)
  • Online Resources: Repository of tools and workflows, Benchmarking and Sample datasets, Training material and Open Textbook.
  • A Short Term Scientific Mission mobility programme for Scientists to visit Host Labs and get in depth insights into cutting edge Image Analysis technology.
  • Outreach material and other stuff.

More Information on our preliminary web: http://eubias.org/NEUBIAS/

Training School
The 1st of a series of 15 courses in 2016-2020

The first Activity is a Training School in BioImage Analysis for Facility Staff, to enable Imaging Core Specialists to become more proficient at custom Image Analysis and Workflows construction (theory and applications, hands-on, scientific programming, ImageJ- and Matlab- based primarily).

The Training School will be held in Barcelona on 13-16th of September 2016, hosted and co-organized by the University Pompeu Fabra (Dr. Chong Zhang), and by the Training Workgroup within NEUBIAS (Dr. Gaby Martins and Dr. Fabrice Cordelières + co-workers)

  • Registration is open as of today (selection based).
  • Within the COST framework, a few travel grants are available to applicants.
  • Registration deadline: 15th of July, 2016.
  • Selection and Travel Grants notification: 19th of July, 2016.

More information on our preliminary web: http://eubias.org/NEUBIAS/Training_Schools

On behalf of all NEUBIAS members,

Julien Colombelli, Chair
Kota Miura, Vice-Chair

Sébastian Munck & Arne Seitz, Strategy & Events WG1 Leaders
Gaby Martins & Fabrice Cordelières, Training WG2 Leaders
Jean Salamero & Paula Sampaio, Outreach and Inreach WG3 Leaders
Perrine Paul-Gilloteaux & Chong Zhang, Webtool WG4 Leaders
Sébastien Tosi & Graeme Ball, Benchmarking & Sample Datasets WG5 Leaders
Juergen Reymann and Natasa Sladoje, Open Publications WG6 Leaders
Julia Fernandez-Rodriguez and Clara Prats, Short Term Scientific Missions and Career Path WG7 Leaders

The R&D division of FBI-Montpellier is focused on the development of super-resolution and fluctuation microscopy methods. On the super-resolution front, we have recently developed a new instrument for the rapid acquisition of single-molecule localization microscopy (SMLM) images of thick intracellular structures (>5µ) at nanometer resolutions without scanning.
In conventional SMLM, the gain in resolution arises from the precise localization of single emitters labeling the structure of interest, thus enabling the reconstruction of images in 2D with a resolution of ~10-20 nm. Most of the biological structures are, however, three-dimensional. To increase the axial depth while conserving spatial resolution, we combined two ingredients. First, we used multi-focus microscopy (MFM) (Abrahamsson, 2013), a technology that allows for the simultaneous acquisition of several image planes on the same camera chip. We combined MFM with point-spread function (PSF) engineering, a method that relies on the use of asymmetric PSFs to enable axial localization. For this development, we designed and built binary multifocus gratings with ~ 400 nm spacing, ideal for SMLM intracellular imaging of eukaryotic cells using organic dyes or photo-activatable proteins. Our method requires only the detection and localization of emitters in a single imaging plane, thus allowing for an increase in the distance between MFM planes to reach thicker axial imaging depths. Importantly, our method also allows for a considerable increase in image reconstruction speed without sacrificing localization precision, as it requires the fitting of the emitter PSF in a single plane to yield a 3D localization. This development led to a Patent application filing (European Patent EP15305787.2 filed on May 26, 2015) and a publication (Oudjedi, 2016) (Figure 1).

Figure 1 Figure 1: (A) Multi-focus microscopy (MFM) allows for the instantaneous acquisition of whole nuclei in a single camera frame. (B) Reconstruction of the nuclear envelope of a S2 Drosophila cell with >4µm depth of field at nanometer resolutions can be achieved with our microscope, 10-100 times faster than conventional 3D-SMLM.

On the fluctuation microscopy front, we have developed a method to measure protein concentration, diffusion coefficient and brightness for low photon flux fluorophores and eliminating cross-talk between channels. Fluorescence correlation spectroscopy (FCS) techniques allow for the determination of the concentration (N), the diffusion coefficient (D), and the brightness (B) of fluorescent molecules of interest, and thus report on their oligomerization properties and interactions with cellular components (Figure 2). However, FCS measurements are traditionally disturbed by a low photon flux (especially under two-photon excitation), strong photobleaching, and cross-talk between spectrally distinct detection channels. Recently, thanks to a CNRS “Instrumentation aux limites” funding, we have developed a homemade microscope that will overcome all these limitations (Hendrix, 2014), by combining : (1) A pulsed supercontinuum source allowing great versatility of choice of colors of excitation, and therefore of fluorophores used, and an increase in the photon flux, thus improving the signal / noise ratio; (2) An alternating laser excitation scheme (Olofsson, 2013) coupled to a dual-channel TCSPC detection card, to eliminate cross-talk effects; and (3) A laser scanning galvanometric system to reduce photobleaching, and obtained spatially resolved Number, Brightness, and Cross-interaction maps in living cells.

Figure 2

References
Abrahamsson, S., Chen, J., Hajj, B., Stallinga, S., Katsov, A. Y., Wisniewski, J., … Gustafsson, M. G. L. (2013). Fast multicolor 3D imaging using aberration-corrected multifocus microscopy. Nature Methods, 10(1), 60–63.
Hendrix J., Lamb D.C. Implementation and Application of Pulsed Interleaved Excitation for Dual-Color FCS and RICS (2014). In Fluorescence Spectroscopy and Microscopy: Methods and Protocols, Methods in Molecular Biology. 1076, 371-417
Olofsson L., Margeat E. Pulsed interleaved excitation fluorescence spectroscopy with a supercontinuum source (2013). Optics Express, 21(3), 3370-8
Oudjedi, L., Fiche, J.-B., Abrahamsson, S., Mazenq, L., Lecestre, A., Calmon, P.-F., … Nöllmann, M. (2016). Astigmatic multifocus microscopy enables deep 3D super-resolved imaging. Biomedical Optics Express, 7(6), 2163.

“User Access” and “Technological and Methodology Transfer” projects

After only 6 months of opening, FBI calls for projects are quite successfull and very promising. If the call “Support to events” has already funded more than 40 events since 2012, the two new calls launched in January are also quite successfull; both are available on our Web Access Portal (https://france-bioimaging.org/service-offering/). The first call is meant to enable “User Access” to highly advanced and rare technologies available in FBI infrastructure. Geo_origin The second one is devoted to “Technological and Methodology Transfer” projects and aims to disseminate emerging approaches and know-how. As a start, on average, France BioImaging has selected and funded two projects of 10 weeks duration per month.

Among the eleven selected projects, 60% were submitted by foreigner colleagues and 40% by French scientists, external to FBI perimeter. Among international projects, two came from North America, two from South America and two from European countries. France BioImaging is proud to attract users from diverse backgrounds and different countries.

The Paris-Center FBI node drains a large number of projects (50%). PICT of the Institut Curie reaches 3 projects submitted by scientists from three different countries. Distribution The Institute Jacques Monod hosted one project and the Photonics lab (Paris-Descarte University) will soon host the last project approved by the Executive Board. Bordeaux Node with the Interdisciplinary Institute of NeuroSciences hosted two projects and the Bordeaux Imaging Center, Jorge Toledo, University of Chile. Until now, other FBI-Nodes were serving external Users at the national level.

Dissemination of our service offering at the European level, beyond the FBI-Web, through the EuroBioImaging WAP should soon allow a wider promotion of imaging technologies and expertise available on France BioImaging Core Facilities and associated R&D labs.

In conclusion after the first six months of opening calls, we are more than ever motivated to continue on this path of opening state of the art imaging technologies to a broad scientific community in France and worldwide. There is still much to do, but the progress already made and the FBI impact beyond our expectation, encourage us to pursue our work for the future of Biological Imaging.

“Access” application
“Tech Transfer” application
Support to Event
Other applications
RIA Global BioImaging (GBI) &
ESFRI EuroBioImaging Preparatory Phase II (EuBI PPII)

A series of workshops and meetings on H2020 BioImaging projects, in which France BioImaging is involved, held at EMBL, Heidelberg, from 8 to 10 June. The first Exchange of Experience Workshop (EoE1) of GBI gathered colleagues from Australia, USA, India, Japan, Argentina and Europe. A large number of topics were discussed, including professional training for imaging core facility staff, e-tools for training/teaching.
General Organization at various levels were presented and compared (AIC at Janelia Campus, USA; the Australian program for national infrastructure, ELIXIR, BioImaging France, Czech Republic, Argentina, Indian- BioImaging Bangalore …). Breaking sessions were also held in order to organize the 1st GBI Course in November (at EMBL) on image data management and training services in imaging research infrastructures, two topics in which France BioImaging is heavily involved.

GBI was followed on Friday afternoon for the first meeting of representatives of node candidates for EuBI. The meeting brought together representatives of more than half of EuBI node candidates. Among the many elements showing that EuBI entered a phase of operation ad interim, the Access Web Portal is now operational in its first version (presentation by J. Eriksson), image data management model was proposed (Jason Swedlow), preliminary results of the survey on training activities within EuBI, launched by the FBI, were presented by D. Choquet. Budget templates for user access appear to be particularly heterogeneous and harmonization of access prices, beyond the scope of the project. However, all agreed that an improved model for cost calculation, approved by all of us, would be of great value. The next step is the meeting of platforms personnel, the day before the Mifobio school at Seignosse (30 September), during which a proposal for teaching / training program at EuBI, will be proposed and discussed.

From September 2015 to January 2016, the National Coordination had been leading a pilot survey aiming at listing the actual resources, equipment (including IT dedicated one), tools and expertise in the fields of image data management and bioimage informatics existing in the different FBI sites. It also aimed at identifying bottlenecks in order to recover needs and foresee potential projects. Perrine Paul-Gilloteaux from the IPDM FBI node had been assigned to collect this information by visiting on-site FBI platforms and R&D laboratories, and interviewing staff in charge, mainly engineers and researchers. The overall view and the main proposals for action resulting from this survey are presented below.

 

When it comes to IT infrastructure for image data, most FBI nodes are disconnected and even sites of the same node do not share IT infrastructures, have different data repositories when they exist, and have access to different network levels.
However, Core Facilities are facing a deluge of data resulting from the novel imaging technologies (see below) , notably acquired in the Frame of the FBI program, and Associated Research & Development teams would consider sharing their data, through dedicated tools ( Image Data Repository) to facilitate development of image processing tools or validation/cross comparisons of data, or exchange in the frame of new collaborations.

As mentioned by multiple sites/nodes, a big jump in data production and inherent difficulties, are expected with innovative approaches (SPIM, Serial Block Face …) but, up to now, no clear and even less commonly approved solutions are proposed for accurate storage and analysis. Image-Data storage requires a dedicated infrastructure and software in use are inadequate for processing and visualization of large data sets (3D). OMERO seems to be the most current centralized system of storage/ Data Base, but others coexist. In any case, there are no bridges between them within FBI. Yet, centralized storage is underused in most of the places.

A data management plan may be needed in order to break practical drag and improve the service in a national process of a qualitative approach involving to:

  • Get a data structure in terms of common semantic
  • Develop interoperable software & tools adapted to big data human assimilation
  • Organize meetings between IT proximity engineers or technician to exchange on current hardware infrastructure for data storage and transfer.
  • Define a common policy of FBI nodes regarding data responsibility
  • Set up a centralized repository to publish FBI working groups data and users gold standard data to facilitate the exchange between users of multiple nodes and present new data modalities to image processing teams

It will be also important to communicate and teach how to use data management systems so as to erase behavioral barriers and involve the research community towards a better understanding of the challenge ahead:

  • Big data valorization (diffusion with correct curation, exploitation, convenient visualization)
  • Training for facility people for data curation and annotation
  • Metrology/facility monitoring from image data base
  • Coding parties/Tagging on tools to facilitate access to software, development and diffusion of user friendly tools, interfacing software tools with data base. Use of Grid computing
  • On-demand focalized training on thematic image processing notions or to more general software platform (Icy or others)
Digest “On Site” Visits IPDM