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

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.

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

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/

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

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. 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. 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.

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)

On 1st and 2d February 2016 representatives from the sites of FBI Paris-Centre node met in the Eden Park Hotel of Pont l’Eveque (Normandy, France) to exchange about the implementation of their projects, identify local difficulties and needs, define a strategy and start to work on an action plan for the FBI Paris-Centre node.
For their first global meeting dedicated to the node, engineers and researchers from its different sites (Imagopole-Ultrapole, ImagoSeine, PICT-Curie, IBENS, Institut Curie, Institut Pasteur, ENS, Lab. de Neurophotonique – Univ. Paris Descartes, etc.) were joined by the IPDM team from Pasteur and the FBI national coordination team.

The retreat was organized in two main parts.
The first consisted of scientific and technical presentations of the various projects undertaken by the associated platforms and laboratories FBI, the progress of these projects and their integration into the general schema missions and program of the national distributed infrastructure. Charles Kervrann from INRIA Rennes and one of the responsible of the IPDM Node, was also invited to the retreat and presented the IPDM node (missions and goals of the node, overview of the results of the IPDM survey on-site led by Perrine Paul-Gilloteaux). These various sessions were then followed by informal and fruitful discussions.
The second part of the retreat was organized in workshops and parallel working groups (lead facilitators indicated); the themes were proposed in advance and the reviews were presented “on-the-spot” at the end of the meeting.

Below are some elements of reflections, proposals for action, scientific and technical projects undertaken or proposed during the workshops

WORKSHOP 1: CORE FACILITIES RUNNING (OLIVIER RENAUD)

• Organization of an annual meeting about Core Facilities management in order to optimize equipment management, overcome the saturation of technology, standardize administrative procedures, develop the quality of materials to the new standards (NF-X50-900)
• Creation of a form for tracking collaborations within and between FBI nodes
• Creation of a Data Base “experts”
• Proposals to be transmitted to WP “training”: develop and disseminate e-learning modules for users, development of training certificate room for personal Core Facilities

WORKSHOP 2: TECHNOLOGY TRANSFER (VALENTINA EMILIANI)

• To identify, pool and facilitate the access to existing resources (workshops, 3D printers…)
• To give priority to universal software solutions, develop software for private companies, use appropriate personal and dedicated
• To conduction an “FBI” action with the CS CNRS so as to develop technologies to make it a source of funding (patents)
• Develop training tools and tutorials to make time for platform engineers. Setting priorities with% time between service and R & D
• Solicit bids for systems duplication.

WORKSHOP 3: PARTNERSHIPS, JOINT ACTIVITIES AND OUTLOOK (LUDOVIC JULLIEN)

Action involving developers
• Metrology and benchmarking: reference samples, comparative studies protocols, image analysis procedures
• Thematic Appetizers for scientific foresight (educated biologists, newspaper publishers, guardianship)
• Drafting of collective reviews, comments on articles

Developers and platforms

• Action inventory and good collaborative practices for resource optimization
• Establishment of a generic alias
• Some readability rates platforms
• Inventory sensors and actuators optogenetic. Workshops back experience and foresight (CLEM bimodal probes for example)

Dissemination to non-specialists

• Core facilities: rather a place of advice than a place of technicians
• Short Videos (3 min) for the dissemination of new systems and instruments explaining what biologists could make users

WORKSHOP 4: DATA MANAGEMENT (STEPHANE DALLONGEVILLE & JEAN SALAMERO)

Proposals
• Establishment of a national portal with a Bio-Imaging database. This database will be used first to store data publications from FBI (projects funded or co-financed by FBI). In addition to giving visibility to the FBI inflows, this base is also intended to serve as a “gold standard” for the FBI users, both images themselves and the associated metadata. A reflection should be made on the choice and structure of metadata (OME model?) And the ontology to be used (see http://bioportal.bioontology.org/) to provide a model for the whole community.
• Implementation of the common API interoperability (as a web service) enabling communication between image analysis software and databases (among others). The portal will provide documentation and all necessary details for the implementation of this API for any center or institute may put in place on its own data management system (organization hackatons in this sense).
• Setting up a benchmarking platform for image processing algorithms by exploiting both the hardware “gold standard” of the database and API for accessing it (idea to dig).
• Reflection on storage strategies, choices, sorting, but also the visualization and analysis of its large images.

Training

• Train users to image analysis tools such stand-alone (Icy, Fiji, ImageJ …)
• Train users of analysis tools distributed cluster-type / grid computing (OpenMole, Galaxy / Mobile)
• Educate users to databases, provide a vision of the possibilities offered by these systems