The FBI Marseille node is composed of the PICsL light and electron microscopy core facility and three associated research and development (R&D) labs. The FBI-PICsL facility is located on the Marseille Luminy campus and hosted by two institutes: the Centre d’Immunologie de Marseille Luminy (CIML) and the Institut de Biologie du Développement de Marseille (IBDM). The R&D labs comprise two labs of these institutes (Lenne lab at IBDM and Marguet lab at CIML) and the biophotonics lab of the Fresnel institute (Mosaic group led by H. Rigneault).  The FBI-PICsL facility via its microscopy resources is dedicated to help its users deciphering cellular mechanisms in the fields of cell biology, immunology and developmental biology.

PICsL Staff
The PICsL staff. From left to right : Fabrice RICHARD, Aïcha AOUANE, Nicolas BROUILLY, Sébastien MAILFERT, Cédric MATTHEWS, Rémi FLORES-FLORES, Elsa CASTELLANI, Mathieu FALLET, Claire CHARDES, Brice DETAILLEUR, Roxane FABRE.

In 2017, the FBI-PICsL facility comprises 40 setups. Altogether, these microscopes cover a wide range of temporal and spatial scales from the second to milliseconds and from single molecules to entire organisms. This repertoire of microscopes is composed of cutting-edge light microscopes (FCS, FCCS, STED 3D, PALM/dSTORM, Fast polarization-resolved spinning disk, Light sheet microscopes) among which 8 are homemade and 3 electron microscopes (two TEMs and one SBF-SEM). Ten staff members manage the facility under the scientific supervision of Pierre-François Lenne (IBDM) and Didier Marguet (CIML). The FBI-PICsL facility staff is also involved in teaching microscopy techniques to the facility users and within courses open to external academic and industrial users.

New set-ups on the FBI-PICsL facility
LSM 880 Fast-Airyscan
Carl Zeiss Microscopy GmbH
Photo credits: Carl Zeiss Microscopy GmbH

A new confocal microscope using the technology Airyscan (LSM 880 Fast-Airyscan, Zeiss) has been purchased through a co-funding FBI/Inserm/CNRS/Region PACA. The Airyscan improves spatial resolution (1.7 x) by imaging the Airy disk onto a concentrically arranged hexagonal detector array. Its detection area consists of 32 single detector elements, each of which acts like a very small pinhole. The confocal pinhole itself remains open and doesn’t block light – thus all photons of the whole Airy disk are collected. The signals from all detector elements are then reassigned to their correct position, producing an image with increased signal-to-noise ratio and resolution.

Photo credits: Roxane Fabre
Zeiss-workshop-AiryScan
Photo credits: Sébastien Mailfert
FEI Teneo VS

The FBI-PICsL facility also recently homed an electron microscope dedicated to automated 3D imaging.

Revealing the complex 3D architecture of cells and tissues is crucial for the structure-function correlation in biological systems. However, in most of the electron microscopy experiments, only a small portion of the sample is imaged. For instance, one 70nm-section of an average vertebrate cell only represents 0.4-1.0% of its volume. Beyond the fact that this tiny volume might not be representative to account for the entire cell ultrastructure, the sectioning also avoids a definite visualization of the cellular organization.

Until recently, the imaging of big volumes (tens to hundreds of cubic micrometres) by electron microscopy was tedious because it involved manual serial sectioning. Beyond the need of super-skilled people, manual serial sectioning has a limited z resolution of 70nm and is a time-consuming process at the sectioning, imaging and post-processing steps. Within the last 10 years, the Serial Block-Face Scanning Electron Microscopy (SBF-SEM) has emerged as the method of choice for the imaging of big volumes by electron microscopy.

FEI Teneo VS
Photo credits: FEI

The concept behind SBF-SEM is to have a microtome within the chamber of a scanning electron microscope (see Figure). This set-up enables the iterative sectioning and imaging of the sample block-face for hundreds of microns in a fully automated way (Figure). When an electron beam hits a sample, it interacts with it and yields several signals that can be detected and assigned back to the scanned positions on the sample surface. Among these signals, the backscattered electrons can be collected to retrieve information on the sample electron density at a given point. Routinely, a working pixel size in SBF-SEM datasets is ±5nm and the slicing can be as thin as 20-30 nm.

In addition to be an excellent microscope in classical SEM mode, the Teneo VS microscope by FEI is currently the most advanced microscope to carry out SBF-SEM. It does not only allow you to cut and image the sample in a fully automated way but it also gives the possibility to avoid charging artefacts during imaging by putting the sample in low vacuum conditions. By limiting the charging, the microscope gives you the opportunity to retrieve more information from the sample. For instance, the sample can be scanned with different acceleration voltages in order to retrieve ultrastructural information at different depths (10nm – 20nm – 30nm – 40nm). When this multi-energy imaging is combined to a 40nm mechanical slicing, it gives rise to previously inconceivable datasets of hundreds of cubic microns of tissue with a voxel size of 5x5x10nm !

Since the delivery of the FEI Teneo VS microscope at the FBI-PICsL facility in December 2016, we tested the microscope on a broad range of biological samples in classical SEM mode (fly egg-laying apparatus, Xenope embryo, mouse face…) and in SBF-SEM mode (cell pellets, Drosophila muscle, mouse brain, marine sponges, Xenope embryo…). In particular, the group of Laurent Kodjabachian (IBDM), working on multiciliated cells, wanted to image the same cell type in both classical SEM mode and in SBF-SEM. We could 1. assess the penetrance of a mutant phenotype in classical SEM mode and 2. localize the basal bodies of these multi-ciliated cells in SBF-SEM (see Figure below).
SBF-SEM Multicliée
Photo credits: Virginie Thome and Nicolas Brouilly

Major implications of the FBI-PICsL facility
Spot variation fluorescence correlation spectroscopy (svFCS) (Hai-Tao He and Didier Marguet’s team)

In collaboration with Nicolas Bertaux (Institut Fresnel, AMU, Centrale Marseille), members of the Hai-Tao He and Didier Marguet team published a user guide for characterizing plasma membranes subdomains in living cells by sv-FCS2. This book chapter aims to serve as a guide for setting and applying the svFCS methodology to study the plasma membrane of both adherent and nonadherent cell types.

Optical setup for svFCS and fluorescence
recovery after photobleaching (FRAP).
SvFCS
svFCS recording and data analysis workflow.
(Click to view the image in full size)

 

This technique has been used to understand a genetic disease by studying molecular diffusion at the plasma membrane. In collaboration with Christophe Lamaze (Institut Curie) and Céline Galès (Institut des Maladies Métaboliques et Cardiovasculaires de Toulouse), Hai-Tao He and Didier Marguet’s team worked on decoding the dysfunction of molecular mechanisms involving interferon-γ (IFN-γ), key protein for immune defense. This protein is not able to fulfil its natural function as a protective cytokine when its receptor is “blocked” in the wrong place on the cell membrane: a modification to the immune response causing severe infections sometimes even life-threatening for young children.

Glycosylation-Dependent IFN-γR Partitioning in
Lipid and Actin Nanodomains Is Critical for JAK
Activation

IFN-γ receptor is composed of two protein chains to which are generally associated six sugars. However, some patients diagnosed with Mendelian susceptibility to mycobacterial diseases syndrome (MSMD) have seven sugars. This simple gain of glycosylation affects greatly the immune response against mycobacteria.

Using their expertise in biophysics and more particularly in svFCS, this CIML team showed the existence of nanodomains and their fundamental role in signaling activity. “It was completely unexpected that only one additional sugar could modify the way the receptor is localized on the surface of the cells, affecting greatly the later signaling events”, explained Hai-Tao He. “IFN-γ receptor is then delocalized towards another membrane nanodomain populated by galectin proteins, that bind to this additional sugar” added Yannick Hamon2 (cf Figure)

As therapeutic target, galectins are an appealing perspective, particularly as turning off their expression canceled in vitro the pathologic effect linked to the glycosylation gain of the IFN-γ receptor. However, therapeutic programs towards patients requires the exploration and understanding of molecular mechanisms by uniting expertise of biologists and physicians but also mathematicians and physicists as it was the case in this discovery4.

News

In March 2017, a workshop on super-resolution is organized in Marseille by Sébastien Mailfert, Jean-Bernard Fiche and Orestis Faklaris on multicolor STORM an dSPT-pointillism data analysis, this workshop is dedicated to advanced researchers in this field. This event is supported by FBI.

The FBI-PICsL facility is also homing the 14th RTmfm convention from the 20th to the 22nd of March 2017. This convention is a great opportunity for imaging facilities staff to share their experiences and ideas on the past, present and future of their work (technical development, big data issues and solutions, link with industry).

Our facility also yearly organizes the following course: Scientific platform, instrumental sharing, how to build up and develop a service. The aim of the course is to acquire, by alternating courses, exercises and practical conditions, methods and constraints to the development of a provision of scientific equipment service. We insist on how to develop a contributory model for managing a scientific platform.

References
  1. Mailfert, S., Hamon, Y., Bertaux, N., He, H-T. & Marguet, D. Methods in Cell Biology, 139, 1-22 (2017)
  2. Blouin, C., Hamon, Y. et al. Cell, 166, 920-934 (2016)
  3. http://www.cell.com/cell/fulltext/S0092-8674(16)30909-6
Reporting on the 1st international training course on “Management and Operation of Imaging Core Facilities”, Global BioImaging H2020 Project November 16-18, EMBL, Heidelberg

20 participants attended this first course, representing European and international facilities (Argentina, Australia, India, South Africa). The course was organized around 4 sessions (Soft Skills for Core Facility Staff; Administrative Skills, Quality Management, Metrology; How to set-up an Imaging Core Facility (exchange workshop); E-learning/hands-on in virtual training platform) with a strong participation of the French Community members as speakers. All sessions were overall well received, as suggested by the feedback collected via survey. Some adjustments were however proposed that should frame the next GBI Training Course (planned in Australia, summer 2018). In the meantime, GBI will also organize the 2nd workshop “Exchange of Experience” for core facility managers, 15-16 September 2017 in Bangalore, India and will continue to develop its “shadowing” program (personal exchanges between imaging facilities worldwide; second session March  – September 2017). Stay tuned! For details, read more on the Euro BioImaging website.

France BioImaging was present at the ASCB 2016 meeting in San Francisco (December 3-7).  It was a great occasion to present our infrastructure on our booth and to draw future strategies in BioImaging for Cell and Development Biology.

The France BioImaging booth at ASCB 2016
(Click the image to view)

We also interacted with scientific organizations and funders, such as the Howard Hughes Medical Institute,  the National Science Foundation and the Gordon and Betty Moore Foundation to whom we presented our R&D programs as well as the overall FBI organization. Most of them were amazed by what we could propose and surely other meetings and new programs could emerge from those informal although in depth discussions.

Beyond the above type of contacts, young scientists were attracted by FBI possibilities in terms of training capacity, accessibility to the most emerging technologies, software platform and lots of them were asking about FBI PhD and Post-doc programs. Certainly a prospect we could mine in the future.

As a general feedback on what were the active new fields of interest in the scientific area of the congress, let us mention the obvious developments in the Biology of Induced Pluripotent stem Cell (IPCs), CRISPR/Cas genome editing techniques, cell mechanics approaches and structure/function of macromolecular complexes in living cell and organisms. It is clear that FBI anticipation in developing super-resolution, optogenetics, multi-scale and highly sensitive imaging techniques will best serve our research teams focusing their interest in these diverse fields.

Finally, as many of our foreigner colleagues mentioned, attendance of French researchers was quite remarkable at ASCB this year. A number of them gave talks that were highly appreciated. A majority of them were coming from the direct perimeter of the FBI Nodes and clearly benefited from or even participated to the development of advanced technologies in imaging provided by France BioImaging.

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.