France BioImaging and all the French community aims to develop and promote innovative imaging technologies and methods. But microscopy images can also take an artistic, creative look and make the invisible world beautiful, allowing people to see the visual appeal of the life sciences.
We enjoyed the diversity of the images submitted with many different microscopy techniques, models and applications represented. A big thank you to all the participants!
The National Coordination Team and the Executive Board are proud to announce the winners of the FBI Image Contest 2021:
1st Place: Léna Meneux, Eye Team, Institut des Neurosciences de Montpellier
“The eye of the storm”
Sensory fibers of a mouse cornea imaged with a confocal microscope. The corneal nervesconverge toward the centre forming a vortex. This particular transgenic mouse model allows stochastic expression of fluorescent proteins, unravelling the heterogeneity of the fiber origines inside the corneal epithelium. Acknowledgements to Karine Loulier for the mouse model and Laetitia Hudececk for her help during the acquisition.
Confocal microscopy
2nd Place:Eunice HoYee Chan, Muscle Dynamics Team, Developmental Biology Institute of Marseille (IBDM)
“Sarcomeric bouquet”
Myofibrils isolated from Drosophila indirect flight muscle labelled with titin (yellow) and actin (blue). Image captured from confocal microscope. We are studying the role of titin protein in muscle mechanics and organisation during development.
Confocal LSM880
3rd Place:Camille Boutin, Biology of multiciliated cells Team, Developmental Biology Institute of Marseille (IBDM) &Nicolas Brouilly, PICsL Imaging facility, Electron Microscopy department
“Clown”
Lamellar structure in a differentiating multiciliated cell observed by transmission electron microscopy with a Tecnai G2 200kV FEI.
Transmission Electron Microscopy, Tecnai G2 200kV FEI
Congratulations to the winners!
Explore all the images submitted here:
As stated in the Terms & Conditions of the contest, foreign participants non-affiliated to a French institution are featured in the gallery, but were not evaluated as part of the contest.
Euro-BioImaging first open call for user projects is open! If you have an idea for a biological or biomedical imaging project that you, your student or your close colleague could carry out in one of Euro-BioImaging Nodes, including France-BioImaging, now is the time to make this project come true with financial support from the Euro-BioImaging Access Fund.
How it works:
Submit your project proposal through the Euro-BioImaging web portal between October 20 and December 15, 2021, and indicate that you want to apply for the Euro-BioImaging Access Fund in order to be considered for a grant of up to 5.000 Euros to access the imaging services at a Euro-BioImaging Node. Projects will be evaluated by a committee of independent reviewers. Successful applicants will be notified by late January 2022 and successful projects should be started before July 2022.
What the funding covers:
The Euro-BioImaging Access Fund covers the user’s travel and accommodation costs as well as access and consumable costs at the imaging facilities that are part of Euro-BioImaging Nodes. For remote access projects shipment costs are also covered. Each successful applicant is eligible for up to 5.000 Euros of support.
Who is eligible:
All academic scientists, regardless of gender, nationality, home institution, career phase, or field of interest, are eligible to apply. We strongly encourage early career researchers to apply for this grant.
Projects should include transnational access to a Euro-BioImaging Node, i.e. the applicant’s home institution is in a different country than the Node where the project is to be performed. Due to the current sanitary situation, projects with non transnational access are elligible but transnational access will have priority.
All the external users/collaborators of France BioImaging facilities/labs are eligible:
any users from outside the institutional perimeter of France BioImaging nodes (i.e. from outside the following institutions: Aix-Marseille Université, Université de Montpellier, Université de Bordeaux, Université de Nantes, Université de Rennes 1, Université Paris-Saclay, Université de Paris, Université PSL -Paris Sciences & Lettres-, Généthon, Ecole Polytechnique, Institut Pasteur) who would like to use imaging technologies in one of FBI nodes: Paris Centre, Paris Ile-de-France-Sud, Marseille, Montpellier, Bordeaux, Bretagne-Loire. They can be French or international users – EU and non-EU
or users from a France BioImaging regional Node who want to access an equipment available in another FBI regional node.
Evaluation:
All applications will be evaluated for scientific excellence by a committee of independent reviewers. Selected projects will be assessed for technical feasibility and if needed receive technical advice from the Node providing the service.
How to apply:
Applicants are invited to visit our website to discover the range of technologies provided by Euro-BioImaging Nodes. Applicants will then follow the user access process described here: https://www.eurobioimaging.eu/about-us/how-to-access and indicate that they wish to apply for the Euro-BioImaging Access Fund in the application form.
Le club des Infrastructures Nationales en Biologie et Santé (INBS) organise son premier symposium autour d’une thématique qui les concernent toutes, la vie des données qui sont générées en leur sein.
Information pour les personnes inscrites:
Si vous avez opté pour une participation en présentiel:
En ce qui concerne les restrictions sanitaires, la présentation du pass sanitaire est requise et celui-ci sera contrôlé. Il peut être présenté sous forme numérique (sur téléphone) ou papier et consiste en soit un schéma vaccinal complet, soit la preuve d’un test négatif de moins de 48 heures. Aucune donnée vous concernant ne sera enregistrée.
Le renforcement des mesures sanitaires sur le campus ne permettra malheureusement pas d’assurer de pauses café ou de restauration sur place.
Si vous avez opté pour une participation en distanciel :
Ce symposium sur deux demi-journées aura de multiples objectifs:
Présentations des pratiques et développements en cours ou mis en place par les INBS ou des Infrastructures de Recherche d’autres disciplines autour des modalités de gestion de nos données (PGD de structure),
Pistes d’amélioration et de cohésion pour le futur, en ce qui concerne l’accès aux structures de stockage et de calcul scientifique,
Responsabilité morale et éthique vis-à-vis de ces données (FAIRisation, OpenScience éthique…) et leur valorisation,
Enfin, nous axerons aussi ce premier meeting sur les échanges d’expériences entre les INBS avec nos tutelles respectives.
Ce symposium est ouvert à tous. Il est cependant dédié en priorité à tous les personnels de nos communautés, c’est-à-dire à tous ceux qui participent à l’élaboration, la mise en œuvre des infrastructures nationales en Biologie-Santé et à l’accès aux prestations et services sur les différents sites qui les constituent.
La situation sanitaire évolue mais reste complexe. Le symposium se déroulera en mode hybride dans l’Amphithéâtre Durand, Espace Esclangon sur le campus de Jussieu (Sorbonne Université), et en fonction des jauges imposées (inscriptions d’un nombre limite de participants en présentiel (60 personnes) + inscriptions pour le distanciel).
SPAOM is a joint effort from Red Española de Microscopía Óptica Avanzada (REMOA) and the Portuguese Platform of Biomedical Imaging (PPBI), to organize an annual congress covering new applications in optical microscopy and image analysis. This year’s programme offers 5 plenary sessions + 5 community workshops + numerous workshops and tech bites from commercial partners.
REGISTRATION AND ATTENDANCE IS FREE FOR ALL PARTICIPANTS
There will be also flash-talks, and a prize for the best communication from the submitted abstracts! The full list of speakers and scientific programme can be found here: https://igc.events.idloom.com/spaom2021
(the event will be online, through the Hopin platform, transmitted from Oeiras @IGCiencia)
Going to Rendez-Vous Carnot 2021? Drop by our booth and say hello!
In one week from today, we will be travelling to Lyon to attend the Rendez-Vous Carnot 2021! This is the third time we’ll attend the Rendez-Vous Carnot as an exhibitor, in the Research Infrastructures Village. We are going to present France-BioImaging R&D ecosystem and the multiple advanced biological imaging technology developments taking place on FBI imaging platforms and R&D teams.
If you’re in Lyon between November 17 and November 18 attending the Rendez-Vous Carnot as well, be sure to drop by our booth and meet some of our colleagues at the venue:
Etienne Henry, France-BioImaging R&D and Tech-Transfer mission Officer
Jean Salamero, France-BioImaging Inter-Infrastructures Activities mission Officer
Besides getting to see in person what services France-BioImaging can offer in terms of R&D and tech transfer in the field of biological imaging, we also invite you to attend the Research Infrastructures special events:
On Nov. 17th 15h00 – 15h40: Flash presentations of successful academia-industry collaborations. France-BioImaging will present the success story of the “Nikon Imaging Center@Institut Curie-CNRS: 15 years of collaboration and integration in France-BioImaging”.
On Nov. 18th 14h00 – 17h00: Research Infrastructures and Health special event, in partnership with the Ministère de l’Enseignement Supérieur et de la Recherche.
What’s the RIs impact on Covid19 research and cancer research?
How can RIs work more closely with the France Health Innovation 2030?
What is France’s strategic investment plan in health & disease?
Euro-BioImaging is pleased to announce that the next special edition of the Virtual Pub, organized by Euro-BioImaging and the Euro-BioImaging Industry Board, will take place on December 10, 2021. In line with the season, this edition will focus on the theme of “COLD” in imaging.
They are inviting abstracts for 5 minute Flash talks about “COLD” in imaging. Be creative! Possible interpretations of “COLD” include:
Biology of the cold – from cold receptors and arctic organisms to brain reactions to cold and infections with common cold viruses
Cold-related metabolism including fat metabolism
Cold technologies – from cooling and freezing samples to low-temperature and cryo-imaging techniques
Keeping your sample or equipment cool – from reducing laser output and keeping high-power magnetic coils cool to incubating your sample at controlled low temperatures
The club of INBSs is an informal consortium of the coordinations from 16 Research Infrastructures. It was initiated one year ago.
Why a CLUB?
Past institutional initiatives (DGRI, ANR…) stopped in 2019
Specificities and problems common to INBS (mostly distributed with complex perimeters and parent institutions). 21 Infrastructures in the 2018 roadmap of the Ministry of Research (16 members of the Club in October 2021) out of 70, for all disciplines.
Sharing of information on: MESRI WGs, ESFRI, Calls (from competition, to coordinated actions)
Overlapping service offer instead of benefiting from complementary technologies and skills between INBSs
New roadmaps (national, European). Régine (FLI) and Isabelle (IDMIT) propose themselves as facilitators. Changed to “Feedback from ESR/equipex+ for INBS RIs”.
February 23rd 2021
Meso-Centers and Data Center / Data management and openness. Perrine (FBI) and Jean François (IFB) as facilitators with invited participants.
April 6th 2021
Full costs and pricing “upcoming exercises”. Members of the MESRI WG on pricing, Myriam Ferro (Profi) and Yann Herault (Cellphedia) as facilitators
May 31st 2021
First propositions for the organization of a DATA-INBS symposium in December 2021
July 7, 2021
Indicators and Impact (Facilitated by MetaBoHUB, FBI and Cellphedia with invited participants): Automated Indicator Harvesting; Hierarchizing Relevant Indicators for INBS; KPIs and Impacts ; Sustainable Development Goals, are we concerned?
September 7th, 2021
Focus on year-end meetings:
The NSAF (New Africa-France Summit in Montpellier. October) presentation of INBSs initiatives
Organization of the 1st open Meeting of the CLUB, 16 and 17 of December: « Les données des Infrastructures en Biologie et Santé: enjeux et perspectives ».
More information and free but mandatory registration at:
Deadline for face to face registration: 15th of November
The National Infrastructures in Biology and Health (INBS) club is organizing its first symposium on a theme that concerns them all: the life of the data generated within them.
This two half-day symposium will be in French and will have multiple objectives:
Practices and developments in progress or implemented by INBS or Research Infrastructures of other disciplines around the management of our data (PGD structure),
Ideas for improvement and cohesion for the future, regarding access to storage and scientific computing structures,
Moral and ethical responsibility towards these data (FAIRisation, ethical OpenScience…) and their valorisation,
Finally, we will also focus this first meeting on the exchange of experiences between the INBS and with our respective Institutions.
Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes.
To overcome these obstacles, an international team of scientists from France, Spain and Germany, under the leadership of Charles Kervrann, from France BioImaging BioImage Informatics Node, developed a deep learning-based framework to quickly identify multiple classes of macromolecules in cryo-ET volumes. This DeepFinder program, now published in Nature Methods, builds upon convolutional neural networks that have already proven highly valuable in the microscopy field.
Overview of DeepFinder (from Moebel, E., et al., Nat Methods18, 1386–1394 (2021).
a) The DeepFinder workflow consists of a training stage (stage I) and an analysis (or inference) stage (stage II). These two stages correspond to five steps (represented by blue boxes) to locate macromolecular complexes within crowded cells.
b) Ribosome localization with DeepFinder in a cryo-electron tomogram of a C. reinhardtii cell. Tomographic slice with superimposed segmented cell membrane (gray) and ribosomes classified with respect to their binding states: membrane-bound (blue) and cytosolic (yellow).
c) Tomographic slices showing coordinates of detected ribosomes (colors correspond to b). The positions and classes were determined by analyzing the segmentation map shown in b. This analysis used 48 tomograms for training, one for validation and eight for testing. Scale bar, 60 nm.
Once trained, the inference stage of DeepFinder is faster than template matching and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (roughly 3.2 MDa), ribulose 1,5-bisphosphate carboxylase–oxygenase (roughly 560 kDa soluble complex) and photosystem II (roughly 550 kDa membrane complex) with an accuracy comparable to expert-supervised ground truth annotations. DeepFinder is therefore a promising algorithm for the semiautomated analysis of a wide range of molecular targets in cellular tomograms. It also serves as a prime example illustrating the importance of developing efficient, customized AI tools to accelerate knowledge generation in the biomedical life sciences.
DeepFinder has been implemented as a free, open-source program with an accessible graphical user interface.
The team is currently working on adapting it to fluorescence microscopy.
Moebel, E., Martinez-Sanchez, A., Lamm, L. et al. Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms. Nat Methods18, 1386–1394 (2021). https://doi.org/10.1038/s41592-021-01275-4
The France BioImaging Image Contest is back for its 3rd edition!
This image contest is open to all within the imaging community: core facility staff and users, R&D labs teams and co-workers, students… Submit your best microscopy images for a chance to showcase your skills, research and creativity to the French bioimaging community and beyond, allowing people to see the visual appeal of the life sciences. Images from the contest will be featured on France BioImaging communication tools, online and in print.
France BioImaging and all the French community aims to develop and promote innovative imaging technologies and methods. But microscopy images can also take an artistic, creative look and make the invisible world beautiful.
We are all eager to see your work !
Prizes
1 to 3 images will be awarded depending on the quantity and quality of the entries submitted. France BioImaging will cover the registration fees for one 2022 microscopy related event of the winners’ choice (FOM, ELMI, EMC, COMULIS conference, etc.).
Important: Only French or foreign participants affiliated to a French institution can enter the contest. Foreign participants non-affiliated to a French institution can submit images and will be featured in the gallery, but will not be evaluated as part of the contest.
Submission deadline: Friday, October 15th, 2021, 23h59 UTC+2.
A new version of TrackMate is available now, with major changes that improve its versatility. TrackMate now integrates state-of-the-art segmentation algorithms from machine-learning and deep-learning such as StarDist, Ilastik and Weka.
TrackMate[1] is a Fiji plugin that address cell or organelle tracking in Life-Science microscopy images. Its main goals are to be user-friendly, interoperable and to serve as a platform to accelerate the development of novel tracking algorithms and analysis pipelines.
With this new version we rewrote almost entirely TrackMate so that it can integrate state-of-the-art segmentation algorithms and benefit from their output. For instance, TrackMate can now store, display, save, load and exploit object contours in 2D.
We also made a new application programming interface that will facilitate and accelerate reusing TrackMate in other analysis pipelines and allow 3rd party contributors to add new segmentation algorithms in TrackMate in an easy way. We used this API ourselves to add 7 new segmentation algorithms to TrackMate:
For instance, the StarDist[2] algorithm is integrated as two different detectors. The first one uses the built-in deep-learning model that can segment cell nuclei in fluorescence image in a wide range of situation. The robustness of the StarDist algorithm in turn positively impacts the robustness of tracking and allows for better detection of cell divisions with TrackMate tracking algorithms. This will facilitate cell migration studies.
The TrackMate StarDist integration also allows for specifying and using a custom deep-learning model. For instance, we trained a specific model to detect T-cells imaged in bright-field microscopy and track them over time. Before the emergence of such detection algorithms, the tracking of label-free cells was difficult.
We also integrated the ilastik[3] segmentation software. A TrackMate user can input an ilastik classifier to detect objects then track them. We used them to study the bacterial growth of Neisseria meningitidis clones. The output of this analysis pipeline offers the lineage of each single cell along with its morphology and how it evolves across cell divisions.
The new capabilities of TrackMate can be used to address applications beyond tracking. For instance, it is now possible to use TrackMate to perform the segmentation of 3D objects using a slice-by-slice approach. This approach consists in segmenting objects in each 2D section of a 3D stack, then merging the segmentation results along Z in a subsequent step. This can be done in TrackMate, using the tracking step for merging. We implemented a novel tracking algorithm to foster this application, the overlap tracker. We could use this approach combining the cellpose[4] algorithm in 2D to segment 3D images of Arabidopsis thaliana floral meristem.
There are several other algorithms that are now offered to the TrackMate user, within a user-friendly software meant to interoperate with the key software of bioimage analysis. More importantly, TrackMate is an open-source academic software, and its new API will foster the development of new analysis pipeline with TrackMate and the integration of new algorithms by other developers, increasing the breadth of applications it can address for Life-Science researchers.
Bringing TrackMate in the era of machine-learning and deep-learningDmitry Ershov, Minh-Son Phan, Joanna W. Pylvänäinen, Stéphane U. Rigaud, Laure Le Blanc, Arthur Charles-Orszag, James R. W. Conway, Romain F. Laine, Nathan H. Roy, Daria Bonazzi, Guillaume Duménil, Guillaume Jacquemet, Jean-Yves TinevezbioRxiv 2021.09.03.458852; doi: https://doi.org/10.1101/2021.09.03.458852
[1] https://imagej.net/plugins/trackmate/
[2] Alejandro F. Frangi, Julia A. Schnabel, Christos Davatzikos, Carlos Alberola-López, and Gabor Fichtinger Uwe Schmidt, Martin Weigert, Coleman Broaddus, and Gene Myers. Cell detection with star-convex polygons. In Alejandro F. Frangi, Julia A. Schnabel, Christos Davatzikos, Carlos Alberola-López, and Gabor Fichtinger, editors, Medical Image Computing and Computer Assisted Intervention – MICCAI 2018, pages 265–273, Cham, 2018. Springer International Publishing. doi:10.1007/978-3-030-00934-2_30.
[3] Stuart Berg, Dominik Kutra, Thorben Kroeger, Christoph N Straehle, Bernhard X Kausler, Carsten Haubold, Martin Schiegg, Janez Ales, Thorsten Beier, Markus Rudy, Kemal Eren, Jaime I Cervantes, Buote Xu, Fynn Beuttenmueller, Adrian Wolny, Chong Zhang, Ullrich Koethe, Fred A Hamprecht, and Anna Kreshuk. ilastik: interactive machine learning for (bio)image analysis. Nature Methods, 16(12):1226–1232, 2019. ISSN 1548-7105. doi:10.1038/s41592-019-0582-9.
[4] Carsen Stringer, Tim Wang, Michalis Michaelos, and Marius Pachitariu. Cellpose: a generalist algorithm for cellular segmentation. Nature Methods, 18(1):100–106, jan 2021. doi:10.1038/s41592-020-01018-x.
Abstract submission is open for the Neurophotonics II Conference that will take place at Photonics Europe on April 3-7, 2022, in Strasbourg, France.
Please note that the submissions made to your conference can be viewed via your SPIE account. Details on how to access this information are listed at the end of this e-mail.
This conference focuses on cutting edge research and techniques used to investigate the brain and nervous system. Multiscale imaging and manipulating the living and intact brain are becoming important topics in neurophotonics. In this context, it’s mandatory to provide new strategies for optical measurements of neural function and develop tools such as optogenetics to enables the control of cellular function with light. Also, in terms of imaging, furthermore it’s often important to image the samples from nanoscale to whole organism scales, bridging the gap between technologies.
The conference aims to bring together engineers, optical and medical scientists, biologists, chemists, neuroscientists and physicians, bringing together researchers working in all aspects of neurophotonics. It will also serve as a forum to discuss existing and emerging techniques.
Topics include but are not limited to:
hybrid and multimodal approaches to neuroimaging
optical hemodynamic imaging and neuro-vascular interactions
mesoscopic, microscopic, and endoscopic imaging of neural structure and function
tissue scattering, clearing and de-scattering
superresolution microscopy and nanoscopy of the nervous system
novel reporters and actuators, optogenetics, bioluminescence
data analysis, machine learning, and image processing
analyzing circuitry, network function, and information processing
optics and brain disease
light shaping in the brain, holography
dissemination and commercialization of BRAIN technologies
The first practical workshop « Imaging Organoids: from the bench to the microscope » will take place in Bordeaux, from Mon 27th Sept to Fri 1st Oct 2021.
The aim of this workshop encompasses most of the workflow steps from the 3D-sample preparation (organoids, spheroids, encapsulated 3D cultures), how to process them (histology, staining), how to mount them (for upright, inverted etc…), and finally how to image them with various microscopy techniques (from super resolution microscopies -liveSR or STED- to microscopies dedicated to thick samples (two-photon, ultramicroscope), from fast optical scanning spinning-disk to High Content Screening -HiTech and LowTech-).
Bench work is possible thanks to the TBM Core Facility, and the microscopes are provided by the BIC facility and the LP2N (home-made setup).
This workshop is open to all (PhD students, Postdocs, Engineers, Technicians, Researchers and Teaching Assistants) who would like to learn how to prepare their 3D samples for photon microscopy.
The number of attendees will depend on the rules that will prevail at this time. Seats will be limited.
Each seminar will be preceded by a talk from our industry partners: Corning, StemCell, TreeFrog Therapeutics and Idylle. They will be accessible freely on a dedicated streaming platform, upon ad-hoc registration which will be set soon.
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