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.






The abstract submission site for QBI 2019, Rennes, France, is now open. The conference will be held 9-11 January 2019, with pre-conference workshops on 8 January, 2019.

We seek contributions in any area of quantitative microscopy. Presentations that demonstrate new approaches in detail are particularly welcome, including but not limited to algorithmic and software developments, physical modeling approaches, etc. The use of quantitative imaging techniques in biological applications is also of great interest. For submission details, please see the conference website (www.quantitativebioimaging.com).

Submission deadline: September 15th, 2018

Registration fees for academics: None (supported by external funding)
Local accommodation: Dinners and lunches are offered to all participants

In addition to contributed talks we will feature special sessions on:

  • Machine learning and microscopy image analysis
  • New developments in single molecule microscopy
  • Subcellular trafficking in cell biology
  • Microscopy software development
  • Microscopy in biopharma
  • Structured illumination: a review of the state of the art

The pre-conference workshops are:

  • Machine and deep learning in bioimaging and microscopy
  • Adaptive optics
  • 3D single molecule microscopy

Confirmed Speakers

  • Yann LeCun [AI Research – Facebook / NYU Center for Data Science] – Paris, France (Tentative)
  • Pierre Bon [Laboratoire Photonique Numérique et Nanosciences] – Talence, France
  • Edward Cohen [Imperial College] – London, UK
  • Hans-Ulrich Dodt [Medical University of Vienna and Vienna University of Technology] – Vienna, Austria
  • Michael Elad [Technion Israel Institute of Technology] – Haifa, Israel
  • Kevin Elicieri [University of Wisconsin at Madison] – Madison, Wisconsin
  • Seth Flaxman [Imperial College London] – London, UK
  • Spencer Freeman [University of Toronto] – Toronto, Canada
  • Rainer Heintzmann [Institute of Photonic Technology / Friedrich Schiller University] – Jena, Germany
  • Thomas Huser [Biomolecular Photonics Group] – Bielefeld, Germany
  • Khuloud Jaqaman [UT Southwestern Medical Center] – Dallas, Texas
  • Ludger Johannes [Curie Institut] –  Paris, France
  • Florian Jug [Max Planck Institute of Molecular Cell Biology and Genetics] – Dresden, Germany
  • Yannis Kalaidzidis [Max Planck Institute of Molecular Cell Biology and Genetics] – Dresden, Germany
  • Friedemann Kiefer [Max Planck Institute for Molecular Biomedicine] – Muenster, Germany.
  • Judith Klumperman [University Medical Center Utrecht] – Utrecht, The Netherlands
  • Julien Mairal [Inria] – Grenoble, France
  • Molly Maleckar [Allen Institute of Cell Science] –  Seattle, Washington
  • Fred Maxfield [Weill Cornell Medical College] – New York, New York
  • Jean-Christophe Olivo-Marin [Institut Pasteur] – Paris, France
  • Steve Presse [University of Arizona] –  Tucson, Arizona
  • Bernd Rieger [Delft University of Technology] – Delft, Netherlands
  • Jonas Ries [European Molecular Biology Library] – Heidelberg, Germany
  • Daniel Sage [EPFL] – Lausanne, Switzerland
  • Anne Sentenac [Institut Fresnel] – Marseille, France
  • Ernst Stelzer, [Buchmann Institute for Molecular Life Sciences] – Frankfurt, Germany
  • Per Uhlén [Karolinska Institutet] – Stokholm, Sweden
  • Geert van den Bogaart [Groningen Biomolecular Sciences and Biotechnology Institute] – Groningen, Netherlands
  • Simon Walker-Samuel [University College] – London, UK
  • Daniel Wüstner [Syddansk Universitet] – Odense, Denmark
  • Marino Zerial [Max Planck Institute of Molecular Cell Biology and Genetics] – Dresden, Germany
  • Christophe Zimmer [Institut Pasteur] – Paris, France

As in prior years, assuming that our fundraising is again successful, we plan on not having a registration fee for academic attendees.

To obtain email updates, please sign up for membership of the QBI Society at www.quantitativebioimaging.com. Membership is free of charge.

NEUBIAS is a COST Action which brings together life-scientists, microscopists, bioimage analysts and image analysis developers from 36 European, three neighboring countries + Australia, Singapore and the USA (www.neubias.org).

NEUBIAS is a forum to exchange the newest findings, applications, and cutting-edge developments in Bioimage Analysis, machine learning, data mining, and storage. European Bioimage Analysts, an emergent group within the bioimaging analysis community, organize this event, bringing together an international, interdisciplinary community of scientists in life and computer sciences.

Andreas Girod and Aymeric Fouquier d’Hérouël will be hosting the conference in Luxembourg, which will include a Training School for Early Career Investigators, a Training School for Bioimage Analysts, a Taggathon to continue building the NEUBIAS online resources for the Bioimage Analysis Community. Moreover, the Bioimage Analysis Symposium will be organized from the 6th to the 8th of February, 2018, which will include a new Satellite workshop open for bioimage analysts on the 5th of February (afternoon).

The symposium will highlight Keynote lectures from Susan Cox, Kevin Eliceiri, and Ivo Sbalzarini and will include talks from other 14 exciting invited speakers. Also, contributed talks will be selected from abstracts. The NEUBIAS symposium will feature signature sessions: the Call for Help or “image clinics” session (C4H), the Open source Software Lounge (OsSL), the Panel Discussions as well as company Workshops and Digital Posters.

The second edition of the Workshop on High-Resolution Light Microscopy will cover recent advances in fluorescence microscopy, enabling measurement and computational analysis of a wide range of cellular activities. It consists of both lectures and hands-on sessions, giving the necessary theoretical background and practical insight into the application fluorescence microscopy to study cell migration and cellular processes at high spatial and temporal resolution.

The main topics that will be covered are:

– Principles of microscopy;
– Fluorescent probes;
– Live imaging;
– FRAP, FRET and photo-activation;
– Image processing and analysis.

Speakers and Workshop tutors:
– Anna Pezzarossa | iMM, Portugal
– Jean Salamero | Institut Curie, France
– José Rino | iMM, Portugal
– Rainer Pepperkok I EMBL, Germany

Target audience:
15 participants from iMM, Institut Curie, DKFZ will be selected to attend this Workshop. A selection committee will be responsible for selecting the participants. This imaging workshop is aimed at Master and PhD students, post-doctoral fellows and senior faculty members either with or without previous working experience in using light microscopy.

To apply for the Workshop on High-Resolution Light Microscopy – 2nd Edition please submit the Workshop Application Form

Preference will be given to applications from ReTuBi partner institutions (iMM, Institut Curie and DKFZ).

Applications should be sent to: imm-tumourbiology@medicina.ulisboa.pt

Application deadline is September 15, 2018 and the selected participants will be communicated by September 20, 2018

Please note there is no registration fee. Travel and accommodation expenses for participants from iMM, Institut Curie and DKFZ will be covered by the ReTuBi project.

More information: ReTuBi Website

The CytoData Symposium brings together the image-based morphological profiling community to exchange new developments in the field. We will kick things off with full-day symposium on Sep 21, featuring speakers from industry and academia. We will factor in enough time so you connect with each other during and after the event. The 2-day hackathon (Sep 24-25) will have you fully immersed in the techniques underlying profiling! We will form teams and tackle some exciting problems in the field. So pack your laptops and prepare to hack!

Cette journée, ImabioTED, se déroulera de 10h30 à 16h à l’institut de Biologie du Développement de Marseille Luminy. Chaque industriel présentera deux innovations technologiques sur une durée de 10 min maximum. La communication sera pleinement ouverte et à destination des chercheurs ingénieurs intéressés par l’imagerie et de ses dernières innovations.

CORBEL, EMBL, German BioImaging and NEUBIAS are delighted to announce a joint blended learning course on Machine Learning for Image Analysis.

The course will be a great mix of intensive learning, extensive hands-on and community networking. Participants will review the fundamentals of machine learning in three up-front webinars complemented by online tutorials.

The webinars will take place on 2nd, 9th and 16th October 2018, 12:00 – 14:00 CEST but a recorded alternative can be provided.
Next, they will apply their knowledge on-site (EMBL Heidelberg, 29-31st October), in small interactive groups (the workshop has 16 available seats and ~8 trainer/lecturer), to both reference datasets and their own data.

After the on-site workshop, two optional advanced training webinar, complemented by online tutorials, will be given on 9th and 16th November 2018. These will focus on simulation of data, transfer learning and boosting.

NEUBIAS (COST Action CA15124) is providing up to four travel grants for eligible applicants.

Application deadline: June 15th, 2018.

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.
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.

The CMI Imaging in the Life Sciences (ILS) Meeting 2018 is organized by BioImaging Austria-CMI and will take place on September 20th & 21st at the Vienna BioCenter Campus, Research Institute of Molecular Pathology, IMP Lecture Hall.

You will find the program below, which features top-class keynote speakers.

Follow the link for registration for the ILS Meeting, Lunch Seminars or poster submissions: http://www.bioimaging-austria.at/web/pages/cmi-imaging-meeting.php

Seats are limited; don’t hesitate to register or submit a poster abstract by July 15th.

Invited speakers cover a wide range of state-of-the-art imaging technologies and their unprecedented application in the life sciences: Werner Kühlbrandt, Willy Suppato, Monika Ritsch-Marte, Martina Marchetti-Deschmann, Rainer Kaufmann, Florian Schur, Eva Pereiro, Birgit Plochberger, Marcus Hacker, Ulrich Dodt, Wolfgang Graier, Jacky Goetz, Wolfgang Drexler, Thomas Beyer and Ivan Viola.

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

Registration Deadline: April 11, 2018

This EMBO Practical Course is aimed at junior researchers in developmental biology, struggling with imaging of cell movement and tissue morphogenesis in vivo using conventional microscopy techniques. Exploring techniques such as confocal, two-photon, light-sheet, and optical tomography with different samples is a major feature of the course. Several commercial partners contribute with state-of-the-art equipment for students to use during the course.

This year we will have:

Six keynote lectures
Four labs for eight different projects (selected from applications)
One multi-photon microscope
Three laser scanning and three spinning disk confocals
Four light-sheet (commercial & custom built) and two optical tomography systems
Seven workstations for 3D image analysis
More equipments being confirmed…

Les 29 Mai au 31 Mai prochain, nous organisons à Bordeaux une formation en Super Résolution qui traitera de la microscopie STED et des techniques basées sur la détection des molécules uniques (STORM, PALM, U-PAINT..). Elle se déroule avec une alternance entre cours théoriques (de la base vers les nouvelles techniques en développement), analyse d’images et ateliers pratiques devant les machines commerciales ou développées maison. Cette formation pourra se faire en anglais.