BioImage Informatics 2021 is an annual meeting in the processing, analysis, and extraction of information and knowledge from biological images. This conference will be held in virtual from November 29 to December 1, 2021, and is organised by Jean-Christophe Olivo-Marin (Institut Pasteur), Charles Kervrann (Inria), Jean Salamero (Institut Curie) and Jean-Yves Tinevez (Institut Pasteur).

This year’s edition of the BioImage Informatics conference will happen fully online, and rely on a very nice website built specially for the conference. There will be a dedicated space for poster presentations where presenters will be able to interact with the audience, leave a video or materials when they are not here, etc…

There will be a space for job fair and general announcements as well.

BioImage Informatics 2021 meeting will include, but not be limited to, the following topics:

  • Advanced analytical solutions for bioimage processing and analysis
  • Statistical spatial analysis of cellular or molecular distributions
  • Applications of machine and deep learning to analysis of cellular structure and related functions
  • Quantification of dynamic images and transport phenomena Automation of data acquisition and analysis
  • Dynamic cell imaging and biological processes
  • Reconstruction and analysis of structure and function of biological networks
  • Registration, correlation and fusion of multimodality data

BioImage Informatics will feature a variety of types of presentations: invited talks (45’), selected talks from abstracts (20’) and posters.

Invited Speakers

  • Yonina Eldar, Weissmann Institute, Israel
  • Michael Liebling, EPFL/IDIAP, Switzerland
  • Emma Lundberg, KTH Royal Institute of Technology, Sweden
  • Jong Chul Ye, KAIST, Korea

Abstract submission and Registration for BioImage Informatics 2021 are now open!

  • All abstracts for selected talk and poster consideration must be submitted by October 15, 2021 and should not exceed 350 words (excluding authors and affiliations).
  • You may submit as many abstracts as you like.
  • At least one author of each paper or poster must register and attend the conference in order to be listed in the conference programme as a presenter. Authors will have the opportunity to edit an originally-submitted abstract before it is published in conference proceedings.
  • Only accepted abstracts and fully paid registration will be printed in the PDF programme book.

More details can be found at Home – BioImage Informatics 2021

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.


This new version of TrackMate is the product of a collaboration between the IAH facility (Institut Pasteur), part of the FBI Bioimage Informatics Node , the Jacquemet lab (Turku Bioscience Centre) , and the Dumenil lab (Institut Pasteur) .

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 Tinevez bioRxiv 2021.09.03.458852; doi: https://doi.org/10.1101/2021.09.03.458852

Contact: Jean-Yves Tinevez


[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

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
  • closed loop optical neural interfaces.

 Timeline:

Abstract Due: 20 October 2021

Author Notification: 12 January 2022

Manuscript Due: 9 March 2022

Call for papers information

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.

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.

Programme préliminaire

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).

L’inscription est gratuite mais obligatoire via le formulaire ci-dessous.

Date limite pour les inscriptions pour une participation en présentiel: 15/11/2021


Les inscriptions sont ouvertes!

Meeting DATA INBS 2021

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Plan d’accès

France BioImaging primary mission is to develop, promote, disseminate and provide access to innovative instruments and imaging technologies in the field of bioimaging to scientists. Fostering the technological transfers is at the heart of this mission, and for this France BioImaging relies on a strong association of leading R&D research teams with core facilities.

However, several bottlenecks exist and often hamper or prevent successful technology transfer:

  • A lack of human resource leads to difficulties in transferring and stabilizing the technology which is not enough user-friendly
  • A technology that is too specific, with not enough user base
  • A difficulty to contract with industry through institutional offices for industrial valuation
  • In the context of image analysis: the instability of open software economical model, inter-operability, large data handling and algorithm complexity

As a way to tackle these bottlenecks, France BioImaging launched in January 2021 its first “FBI Internal Call 2021: Technology transfer from the R&D teams to the core facilities” to promote the transfer of new technologies (instrumentation, probes, staining methods, software, data analysis or data visualization) from the R&D teams to the facilities of France BioImaging, for access and service to end-users. The outcome of the transfer project had to ensure for the prototype to be usable by the end-users until the interpretation of the data. The project had also to include a sustainability plan and a training plan to guide both facility staff and end-users toward autonomy.

The project selection was organized by the National Coordination of France-BioImaging and applications were assessed according to the following evaluation criteria:

  • Innovation and originality of the proposal
  • Scientific quality, implementation, timeline
  • Competitive positioning
  • Adequacy of resources with the proposed project
  • Economic impact and tech transfer potential and perspectives
  • Estimation of the user market and potential for user adoption
  • Plan for training and sustainability.

For the first edition of the “FBI Internal Call 2021: Technology transfer from the R&D teams to the core facilities”, 5 projects were selected:

  • Icy@FBI: Jean-Christophe Olivo-Marin (IPDM Node): Broadening the scope of applications of Icy (http://icy.bioimageanalysis.org/) by implementing several key new bioimage analysis components
  • BIC-HCS-SMLM: Jean-Baptiste Sibarita (Bordeaux Node), Technological transfer of a Single-Molecule-based High Content Screening platform to the Bordeaux Imaging Center
  • CloudFISH: Marcello Nollmann (Montpellier Node), A tool for the analysis of single-molecule RNA and DNA FISH images
  • MorphoNet: Emmanuel Faure (Montpellier Node), An interactive online morphological browser to explore complex multi-scale data
  • BioImageIT: Jean Salamero, Sylvain Prigent (IPDM Node), An open source framework for integration of image data management with analysis

Each selected project was awarded with a 80k€ grant for salary and/or equipment, and several positions are currently available: https://france-bioimaging.org/jobs/

This call will be renewed in 2023.

The 6th edition of Global BioImaging annual gathering will have the theme “Imaging Research Infrastructures in a time of change” and will take place on the 8th and 9th September 2021 as an online event.

The program of the event including the titles of the talks and the line-up of speakers will be available soon via the GBI web page: https://globalbioimaging.org/exchange-of-experience/exchange-of-experience-vi

Registration is open! The registration form is available here: https://www.surveymonkey.com/r/EoEVI

Save the date! The European Research Infrastructure Euro BioImaging (EuBI) is organizing an online User Forum on “Understanding and Fighting Cancer”.  The event takes place on June 17, 2021 from 14:00-17:00 CEST and will highlight the importance of cutting-edge imaging technologies in support of cancer research and showcase the specific expertise available at the EuBI Nodes.

In addition, keynote presentations from Kevin Brindle, University of Cambridge, and Frank Winkler, DKFZ, will further reveal the potential of biological and biomedical imaging technologies to boost cancer research. 

The full program is coming soon! In the meantime, you can register here.

For more informationhttps://www.eurobioimaging.eu/news/join-us-for-the-first-euro-bioimaging-user-forum-understanding-and-fighting-cancer/

When: Thursday, June 17th, 14:00-17:00 CEST

Where: Online

Please spread the word within your network! 

Quantifying translation in space and time during development

During development, precise control of gene expression allows the reproducible establishment of patterns, leading to the formation of organs at the right time and place.

The establishment of developmental patterns has been primarily studied at the transcriptional level. In comparison, the fate of these transcripts received little attention.

Dufourt*, Bellec* et al deployed the SunTag labeling method to image the dynamics of translation of individual mRNA molecules in living Drosophila embryos. This led to the discovery of translation factories and unmasked important heterogeneities in the efficiency of translation between identical mRNAs, demonstrating a novel layer of fine-tuning of gene expression.

Imaging translation dynamics in live embryos reveals spatial heterogeneities.

Dufourt J, Bellec M, Trullo A, Dejean M, De Rossi S, Favard C, Lagha M.

Science. 29 avril 2021 doi: 10.1126/science.abc3483.

Contact:

Mounia Lagha (CNRS)

mounia.lagha@igmm.cnrs.fr

+33 434359653

twitter : drosoigmm

Institut de Génétique Moléculaire de Montpellier (Univ.Montpellier/CNRS) 1919 route de Mende, 34090 Montpellier

On May 25th, 2021, 15:00 CSET, our partner the French Network for Multidimensional Optical Fluorescence Microscopy will receive Edward S. Boyden* from the MIT, USA for a webinar on Expansion Microscopy“Tools for analyzing and repairing biological systems”.

The presentation will be broadcast live on Youtube: https://youtu.be/Xc48aDLDZDI

*invited by Tudor Manoliu (Imaging and Cytometry platform-Gustave Roussy/ FBI Paris-Sud Node)

For several weeks now, the H2P2 histopathology platform located in Rennes (France BioImaging Bretagne-Loire Node) has become the European reference for the integral solution of Cell DIVE (https://www.leica-microsystems.com/products/light-microscopes/p/cell-dive/).

Cell Dive device on H2P2 platform

This technology brings great expectations for the research teams and the private companies with which we work. Leica’s Cell DIVE technology provides an in-depth solution for characterizing the tissue microenvironment using multiplexed imaging technology. Up to 60 biomarkers can be revealed in one tissue sample. An extensive list of antibodies is already validated and users can customize their own panel! The multiplexed Cell DIVE technology is based on successive immunolabeling of 4 antibodies conjugated with 4 fluorochromes (Cy2, Cy3, Cy5 and Cy7). The slides are digitized (x20 objective) as things progress and a final compiled image is obtained and can be analysed with the Halo Image Analysis Platform. This software allows users to do segmentation to highlight clusters, to define specific cell phenotypes, to analyse neighbourhood, heatmap…

For example, in cancer treatment research, researchers need a better understanding of the cellular architecture of normal and diseased tissues to develop better treatments and more accurately predict disease progression. 

This technology has been developed by scientists for scientists over the last decade and several publications are available to date (https://www.leica-microsystems.com/products/light-microscopes/p/cell-dive/publications/).

Images from human tonsil with 9 biomarkers.

For more information about the Cell Dive technology or to discuss your project, you can contact Nicolas Mouchet nicolas.mouchet@univ-rennes1.fr

Grant Applications for organizing Virtual/Hybrid Training Schools are open!

COMULIS is now launching a call to financially support virtual and hybrid training schools fulfilling the following conditions:

  • the training school has to take place between the 1st of June and 30th of October 2021;
  • it has to be virtual (or hybrid);
  • it has to cover topics of the COMULIS network;
  • led by a COMULIS member or someone who is willing to become one;
  • COMULIS and COST support will have to be diplayed on the program, website, or any related document to the training school;
  • fees that can be covered by this grant include the technical setup of these training schools and training material:
    • If engaging a conference organiser, technician hourly rate if required on specific openings days before and during the event to assist with technical support, attendee management and monitoring, configuration and setup, communication.
    • customer support for attendees, live-stream tech support via email and/or chat.
    • pre-recording of keynotes/teaching sessions for training schools.
    • post-event process management: video editing, recording management.
    • Rental of rooms and audio-visual material
    • Consumables purchased for Training Schools
    • Photocopying and the printing of programmes, handouts, event materials, book of abstracts, book of proceedings, flyers etc

Maximum amount of a grant is 10000 euros, that will be reimbursed on presentation of invoices strictly related to eligible fees above.

Procedure

Filling an online form https://forms.gle/tJqaLmauZDA5V58o6 with check of the above conditions, (pedagogical) program, list of organizers, speakers and trainers, dates, provisional budget including usage of the COMULIS financial support in regards of one or several of the above categories of eligible expenses.

Deadline 1st of June. Notification of acceptance: 15th of June. (if needed earlier please do tell us, and we will do our best to meet you own deadline in case of co-funding).

Criteria among eligible proposals (fulfilling the above checklist) will be based on matching COMULIS objectives (www.comulis.eu) and scientific excellence. Proposal will be ranked by grade following this criteria, and funded until the available budget is used up. Three to ten possible grants, according to budget.

Contact: Perrine.paul-gilloteaux@univ-nantes.frandreas.walter@vbcf.ac.at