NEUBIAS, the Network of European BioImage Analysts (www.neubias.org), is delighted to announce that the 4th NEUBIAS Conference will take place in Bordeaux, France on February 29 – March 6, 2020.
The conference will include two Training Schools, a Taggathon and will culminate with the Bioimage Analysis Symposium (March 4-6, 2020).

Highlights of the Symposium

Keynote Speakers:

Dr. Suliana Manley
Dr. Emma Lundberg
Dr. Kristin Branson

Discussion topics:

BioImage Analysis & Workflows in Life Science, Current Developments & Applications, Machine Learning, Deep Learning, BioImage Data-Mining, Formats, Management, Object segmentation, Tracking, Atlases, Reconstruction, Visualization, Registration, Correlation, Fusion, Automation, Open Science, and many more.

Interactive sessions:
Open source Software Lounge, Call4Help, Industry Workshops/Techbites/Digital posters, Panel Discussion, and more

For more information please see: http://eubias.org/NEUBIAS/neubias2020-conference/bordeaux-2020/

Registration opening soon!

Après le succès de Bordeaux en 2017 et à l’occasion de son soixantième anniversaire, la Société Française des Microscopies (Sfµ) a choisi la ville de Poitiers pour accueillir la seizième édition de son colloque. Suite aux traditionnels ateliers de formation qui se dérouleront le lundi 1er juillet 2019, le colloque se tiendra du 2 au 5 juillet 2019 dans les locaux de l’Ecole Nationale Supérieure d’Ingénieurs de Poitiers (ENSIP).

Le colloque de la Sfµ a vocation à rassembler la plus large communauté autour des études développant ou faisant usage des microscopies (électronique, optique, à champ proche, sonde atomique tomographique, …). Le programme scientifique s’articulera autour de douze symposia : quatre orientés Sciences du Vivant (SDV), quatre dédiés aux Sciences des Matériaux (SDV) et quatre symposia communs (SDV/SDM) à l’image de l’interdisciplinarité qui caractérise notre société. Les thèmes abordés dans plusieurs symposia seront l’occasion de pérenniser notre partenariat avec le GN-MEBA qui tiendra ses journées semestrielles à la même période à Poitiers. Le programme scientifique du colloque et la liste des conférenciers et conférencières invités sont consultables ici.

Il est encore temps….. N’hésitez pas à déposer vos résumés !!!!
Après avoir créé un compte dans l’espace Sfμ, vous pourrez soumettre vos contributions: https://colloque.sfmu.fr/fr/inscription/soumission/

Les inscriptions au colloque sont ouvertes à un tarif préférentiel jusqu’au 15 mai 2019: https://colloque.sfmu.fr/fr/inscription/frais/

Le 25 mai 2019, l’Institut Cochin vous invite à découvrir ses outils innovants d’imagerie biologique et leurs applications en recherche biomédicale.

 

 

  FBI opens a call for the recruitment of its next Scientific Director

(2020-2025)

(Deadline is 1st of May)

France BioImaging-FBI (laureate of the INBS program of the PIA in 2011) is the National Research Infrastructure in Biological Imaging.  FBI is built on five geographical Nodes identified on the basis of strong relationship between developers of new imaging approaches (R&D labs) and large imaging Core Facilities, answering the IBiSA criteria. Each Node shows a specialization of a local expertise in main biological topics. This crossover between imaging technologies and expertise in scientific topics is a characteristic of the complementarity between FBI Nodes. A 6th Transversal Node gathers FBI strengths and resources in Image Analysis and DATA management. The Operating Coordination is insured by the UMS 3714.

Our motto is “Innovation-Training-Access”

(i) Disseminate and invent new imaging technologies
(ii) Expand the portfolio of training courses for users and staff in charge of these approaches
(iii) Make them accessible to as many people as possible.

 Role of the Scientific Director of FBI

-He/She is the Strategic Manager of the Infrastructure

He/She leads the National Coordination (NC) in continuous interaction with the Executive Committee (EC). With the Help of its international Scientific Advisory Board (SAB), he/she reports the overall Infrastructure policy and strategy to the Institutional Committee (Steering Committee, SC) which is the “decision maker”

He/She is responsible, for the arbitration of recruitment proposals (in interaction with the other governance bodies), equipment investments (PIA, TGIR, other National and International common actions…) and new service opening, in relation to the development objectives (R&D, service offers…) and the overall infrastructure strategy at national and international levels

He/She is responsible, with the staff concerned (NC), for the inventory of the different activities/tasks of the infrastructure: links with Europe and International, work with the different committees, web site/communication, trainings, animation of the “FBI-community”, scientific and financial reports…

He/She is responsible, in interaction with the EC, for managing interactions/collaborations (R&D, service providing, partnerships, technology watch…) with other PIA Research Infrastructures.
More details and information in the pdf below 

Entry into function is planned for the 1st of January 2020,

If you are interested, please send a short CV and a motivation letter (2 pages) indicating your vision and strategy at FIVE years and beyond at  node-access@france-bioimaging.org
BEFORE the 1st of May

 

 

 

 

 

 

In February 2019, France officially became a founding member of the “Euro-Bioimaging” research infrastructure (EuBI ERIC), and the national infrastructure France BioImaging (FBI) will host the EuBI French Node, open to all European scientists applying for access.

The EuBI ERIC (https://www.eurobioimaging-interim.eu) is the European Research Infrastructure for Imaging Technologies in Biological and Biomedical Sciences and provides open physical user access to a broad range of state-of-the-art technologies in biological and biomedical imaging for life scientists. In addition, EuBI will offer image data support and training for infrastructure users and providers.

As a former “Node Candidate” of the Euro BioImaging ESFRI project and leader of the EuBI Working Group dedicated to training during the preparatory phase II of the project (See WP7 deliverables), France Bioimaging is now the only French node validated as a single entity in this new European research infrastructure. FBI core facilities will thus be participating directly in the activities carried out by the EuBI ERIC, opening their premises to EuBI user access and training activities.

A cette occasion, les plateformes d’imagerie France BioImaging participantes organiseront des activités grand public lors d’une journée “portes ouvertes” le weekend du 25-26 Mai 2019.
Ces activités s’articuleront autour:
– de l’histoire de « l’Imagerie Biologique au CNRS », présentée conjointement par les différents sites de l’infrastructure FBI;
– de diverses animations avec l’objectif de montrer l’éventail impressionnant des outils de l’Imagerie Biologique aujourd’hui et leur fonctionnement,
– des découvertes/applications fantastiques que l’Imagerie Biologique peut apporter en Biologie.

 

 

 

 

 

We are very pleased to announce the 2019 Inserm Workshop "Intracellular dynamics of molecules: analysis and models" (poster attached).

The objective of this workshop is to introduce the main experimental methods for quantifying the mobility and trajectories of biomolecules in living cells, with an emphasis on methods for quantifying individual trajectories and the application of computer simulations and models for their analysis and interpretation.

Phase I (theoretical) will take place in Bordeaux, France, from 24 to 26 June 2019, and Phase II (practical) from 1 to 4 July 2019 in Lyon, France.

All information and (open) registrations are available on the workshop website:

Feel free to register now, as the number of places is limited!

The organizers of the Workshop
Hugues Berry
Cyril Favard
Jean-Baptiste Masson

Symposium Electron Microscopy in Bordeaux

 

[:en]France BioImaging is organising an “BioImage Analysis OpenDesk” session on November the 29th from 9:00 to 12:30, in its different nodes and online.

What is an OpenDesk ?

During the event, users in search for answers to image processing-related questions come to a dedicated spot, within the Facility. Individual questions are processed by BioImage Analysts, on a “first come-first served basis”.

Will I really get my image processing questions answered ?

We will work on that ! Depending on the topic, local BioImage Analyst may choose from one of those three options:
1-The problem might be solved locally, quickly: you will leave the Facility with either a procedure/advices on how to analyse your data.
2-The problem might be solved locally, but requires additional time to be processed: your Facility staff will propose an appointment so that a proper solution is found.
3-The problem might not be solved locally: we will take benefit of the France BioImaging infrastructure, through its dedicated transversal node (FBI-IPDM). Your local Facility staff will introduce you to specialists in the field, using remote communication means.

I’m in ! Where and when is it taking place ?

November the 29th, from 9:00 to 12:30.
Bordeaux — Bordeaux Imaging Centre, Photonic Unit, 1st floor, Centre Broca Nouvelle-Aquitaine
Montpellier
Paris Centre
Marseille — IBDM ground Floor  Luminy
Paris Sud
Nantes — Room 2 , ground floor IRS UN 8 quai Moncousu

If you can not join physically, join on https://rendez-vous.renater.fr/ipdm

By the way, what is FBI-IPDM ?

The objective of the BioImage Informatics – Image Processing & Data Management transversal node is to create a general framework and a complete and integrated image analysis and IT (Information Technology) solution to address a number of challenges in biological imaging and microscopy, as well as setting up a high performance grid-computing infrastructure dedicated to massive computational and data storage demands. The FBI-IPDM node proposes different IT frameworks to deal with the data flow from the different imaging nodes. FBI-IPDM node is thus transverse, by definition.[:fr]France BioImaging is organizing a “BioImage Analysis OpenDesk” session on November the 29th from 9:00 to 12:30, in its different nodes and online.

What is an OpenDesk ?

During the event, users in search for answers to image processing-related questions come to a dedicated spot, within the Facility. Individual questions are processed by BioImage Analysts, on a “first come-first served basis”.

Will I really get my image processing questions answered ?

We will work on that! Depending on the topic, local BioImage Analyst may choose from one of those three options:
1-The problem might be solved locally, quickly: you will leave the Facility with either a procedure/ advice on how to analyze your data.
2-The problem might be solved locally, but requires additional time to be processed: your Facility staff will propose an appointment so that a proper solution is found.
3-The problem might not be solved locally: we will take benefit of the France BioImaging infrastructure, through its dedicated transversal node (FBI-IPDM). Your local Facility staff will introduce you to specialists in the field, using remote communication means.

I’m in ! Where and when is it taking place ?

November the 29th, from 9:00 to 12:30.
Bordeaux — Bordeaux Imaging Centre, Photonic Unit, 1st floor, Centre Broca Nouvelle-Aquitaine
Montpellier
Paris Centre
Marseille — IBDM ground Floor Luminy
Paris Sud
Nantes — Room 2, ground floor IRS UN 8 Quai Moncousu

If you can not join physically, join on https://rendez-vous.renater.fr/ipdm

By the way, what is FBI-IPDM ?

The objective of the BioImage Informatics – Image Processing & Data Management transversal node is to create a general framework and a complete and integrated image analysis and IT (Information Technology) solution to address a number of challenges in biological imaging and microscopy, as well as setting up a high performance grid-computing infrastructure dedicated to massive computational and data storage demands. The FBI-IPDM node proposes different IT frameworks to deal with the data flow from the different imaging nodes. FBI-IPDM node is thus transverse, by definition.[:]

Image processing and data analysis are crucial steps in biological research. Gathering usable data presents challenges; exploiting the data efficiently also has its own issues. While every lab has its way of dealing with that matter, it became clear over the last years that there is a lack of local and transversal expertise on the topic. As such, there is a growing need for reliable solutions for data analysis.

These observations call for the creation of integrated solutions in image data processing and analysis (pipeline, workflow, etc.), at the crossroads between innovation and end-user needs.

To this end, the France BioImaging Image Processing and Data Management team created a questionnaire which aims to gather information about your current practices and your needs. It takes less than 3 minutes to fill out. We will use the responses to elaborate new image analysis services catered to the requirements of the biological imaging community.

Thank you in advance for your contribution!

Image Analysis Questionnaire
Please answer the questions below to allow us to evaluate your needs for image analysis. We will use the responses to elaborate new image analysis services catered to the needs of the French biological imaging community.
6
Hourly rate in Euros.
Hourly rate in Euros.

General information

If you are not located in France, please indicate the country and state/city in the "Other" field.
The information collected in this questionnaire is entirely anonymous, and will not be used outside of France BioImaging's activities.

La petite Venise de la biologie © Carine Rossé, Emilie Lagoutte & Marie Irondelle, Institut Curie
La petite Venise de la biologie © Carine Rossé, Emilie Lagoutte & Marie Irondelle, Institut Curie

Researchers and imaging engineers know better than anyone that an image is always more than meets the eye. Let us honor the winning image of our 2017 Image Contest by delving a little deeper into what lies behind these Venice canals.

The image represents a large part of mice mammary gland. The canals spreading out like branches, are composed of two layers of cells: the epithelial epithelial cells – stained by anti-keratin 8 (in pink) – are surrounded by myoepithetial cells (in blue) stained by an anti-Smooth Muscle Actin. These cells, thanks to their contractile properties, participate in the? secretions from the gland. The yellow cells are modified cells, overexpressing tomato protein. The adipocytes of the mammary gland can be seen in the background.

The image was made by Marie Irondelle (PICT-IBiSA Biomaging Cell and Tissue Core Facility, Curie Institute), using a confocal microscope. It is a mosaic reconstruction – using the tile scan technique -from several depths of field with a range of 110 µm. The lighter areas are higher up in the sample, while the darker areas correspond to zones deeper in the tissue. The final projection measures 1.2 by 0.78 mm. The ducts shown in the picture have a diameter of 50 to 60 microns.

Carine Rossé and Emilie Lagoutte in the lab of Philippe Chavrier (membrane & Actin dynamics lab), from the Curie Institute, set out to study the behavior and movement of few cancerous cells inside the mammary gland. However, such a study required the development of alternative methods of observation, from the traditional methods of analysis, in order to observe the localization of the cells in the whole gland. The solution came from a 2016 Nature Methods paper entitled “Shrinkage-mediated imaging of entire organs and organisms using uDISCO”[1]. In this method, the researchers described the advantages of the uDISCO tissue-clearing protocol for the analysis of large samples, compared to other well-known methods. After adapting the protocol, Emilie Lagoutte was able to clear entire mice. She obtained and stained mammary glands that were shrunk by about 70% compared to their original size, cleared. The advantages of this technique are numerous; in particular, there is no more tissue loss due to slicing samples, the fluorescence can be maintained for a few weeks, and the reduced size of the sample allows to visualize the whole organ, leading to a higher chance to detect the zone of interest.

Imaging facilities and researchers have to work hand-in-hand to produce the best results possible. Marie Irondelle stressed the necessity for researchers to be educated about imaging technologies and their limitations; a state-of-the-art microscope will never be able to compensate for a low-quality sample. In the case of The Little Venice, the PICT-IBiSA Biomaging Cell and Tissue Core Facility collaboration with the Chavrier lab is undoubtedly a winning one.

[1] https://www.nature.com/articles/nmeth.3964

Dear colleagues, dear FBI community,

The National Coordination and Industry Board are proud to announce that the winners of the FBI Image Contest 2017 are:

1. Marie Irondelle – PiCT Institut Curie with “Biology’s Little Venice”

La petite Venise de la biologie © Carine Rossé, Emilie Lagoutte & Marie Irondelle, Institut Curie


La petite Venise de la biologie © Carine Rossé, Emilie Lagoutte & Marie Irondelle – Institut Curie
Confocal microscopy

Transparisation par U DISCO d’une glande mammaire murine régénérée à partir d’un transplant d’organoides mammaire murin.

2. Orestis Faklaris – Institut Jacques Monod – ImagoSeine with “The Tree of Life”


The Tree of Life © Orestis Faklaris, Nicolas Chevalier – Institut Jacques Monod
Ultramicroscope – light sheet microscopy

3D z-stack projection of transparised chicken embryo stomach. Label betaIII-tubulin – Alexa488.

3. Clémence Simon – UMR 8576 CNRS/Université Lille 1 with “When Chemistry Transcends Lignin”


Quand la chimie transcende la lignine ! 1 © Clémence Simon, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576
Microscopie confocale, MIP, BLISS

Application de la stratégie de double réaction chimique BLISS aux unités p-hydroxyphényle et guaïaicyle de la lignine sur coupe de racine de lin. Observation du double marquage (+ autofluorescence) par microscopie confocale et représentation par projection maximale d’intensité. Taille de l’image : 510 x 510 microns.

FBI Industry Committee Special Prize: Nathanaël Prunet – California Institute of Technology with “Arabidopsis Inflorescence”


Arabidopsis inflorescence 1 © Nathanaël Prunet, Caltech, Meyerowitz lab
Confocal microscopy

This is a live Arabidopsis inflorescence with young flower buds developing at the periphery. Cell walls have been stained with propidium iodide (grey). Fluorescent reporters were used to monitor the expression of the APETALA3 (AP3, green) and SUPERMAN (SUP, red) genes. AP3 is required for the development of stamens (the male organs), while SUP establishes the boundary between the male and female part of the flower. This picture was acquired using live confocal imaging, which allows us to describe the expression of several genes in both space and time, in the same live biological samples, with a precise cellular resolution. It finally allows us to understand a question that has been elusive for 25 years: how the male/female boundary is established during the formation of the flower. My research aims at understanding how flower buds are patterned as they form.

Thank you to all the participants for their great contributions:

  • Dario Donnarumma, Laboratoire Charles Coulomb UMR 5221 CNRS-UM
  • Filippo Piccinini, IRST
  • Aude Nommick, IBDM – Marseille University
  • Sébastien Marais, Bordeaux Imaging Center
  • Marie Held, Biochemistry, University of Liverpool, Levy Lab
  • Patrice Mascalchi, Bordeaux Imaging Center and Frédéric Saltel, INSERM U-1053, University of Bordeaux
  • Corrado Viotti, Institut de Biologie Moléculaire des Plantes, CNRS, Strasbourg – P. Genschik Lab
  • Marcello Delfini & Mathieu Fallet, CIML CNRS-INSERM-AMU
  •  Jonathan Daniel, Institut des Sciences Moléculaires
  • Laurence Dubreil, APEX-UMR703 PAnTher INRA Oniris
  • Pierre-Olivier Strale, Interdisciplinary Institute for Neuroscience
  • Clémence Simon, Unité de Glycobiologie Structurale et Fonctionnelle, UMR8576
  • Jérémie Teillon, INSERM U1034
  • Morgane Rabineau, Inserm
  • Eve Gazave & Nicolas Rabet, Institut Jacques Monod-CNRS
  • Nathanaël Prunet, Caltech, Meyerowitz lab
  • Françoise Geffroy, CEA-DRF-NeuroSpin-UNIRS, Midas Team
  • Valeria Davi, ImagoSeine – Institut Jacques Monod – CNRS
  • Anna Smirnova, University of Strasbourg – GMGM
  • Debora Olivier, Institut Pasteur
  • Orestis Faklaris, Institut Jacques Monod
  • Xavier Baudin, Institut Jacques Monod
  • Mathieu P. Dailly, CMAS
  • Lucie Sengmanivong, UMR 144, Institut Curie, Paris
  • Marie Irondelle, Institut Curie

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 National Coordination