Hello Yu, I’m glad to meet you! Where are you from?

I am originally from Jiangsu Province, China. Currently, I live in Dortmund, Germany, where I work at the Leibniz Institute for Analytical Sciences (ISAS).

What is your background and your professional activity?

My professional background is in biomedical image processing, where I focus on applying AI algorithms to analyze and enhance imaging data. A key aspect of my work is improving efficiency, such as using model quantization and pruning to reduce inference energy consumption, as well as applying biomedical image compression to lower storage and bandwidth costs. Recently, I have also been exploring research in foundational models for omics data, aiming to bridge different modalities in biomedical research.

Why did you decide to participate in the France-BioImaging challenge “Light My Cells”?

I learned about the Challenge “Light My Cells” through my supervisor, who discovered the competition on X and shared it with me. I had never participated in a competition on the Grand Challenge platform before, so I wanted to experience the full process of such a challenge. Also we found the problem itself very interesting, and thanks to a previous project, we were already somewhat familiar with this topic.

What was the most challenging part of the competition for you?

The most challenging part of the competition was data processing. We used a semi-automated approach that combined an automated pipeline with manual curation for data filtering. This process was quite time-consuming.

How did you manage your time during the competition?

For the experimental phase, our team worked in parallel on several tasks: data cleaning, trying different network architectures, and conducting hyperparameter searches. However, when it came to writing the final paper, we were somewhat rushed as we had only about two weeks left to complete it.

What are your thoughts about Challenge 2 “Fuse My Cells”?

What excites me most about this challenge is its innovation. Predicting a fused 3D image directly from a single view bypasses some potential issues of multi-view fusion, such as light toxicity. Additionally, with a well-constructed dataset, the solution could be more generalizable, enabling models to perform image restoration across all the various 3D perspectives.

Do you have any advice for the participants of Challenge 2?

1. Pay attention to the data.
2. Keep an open mind and be willing to explore different strategies, including model selection and training methods.
3. Manage your time wisely by balancing the experimental phase and paper writing.

Thank you very much for your time, Yu! I’m sure your testimony will be useful for the participants of Challenge 2.

For those interested in taking part in the “Fuse My Cells” challenge, find more information here!

Hello Marek, I’m glad to meet you! Where are you from?

I am from Poland – currently working both in Poland (AGH University of Kraków) and Switzerland (HES-SO Valais).

What is your background and your professional activity?

I have a PhD in Biomedical Engineering & Computer Science from AGH University of Kraków and I am currently working as PostDoc in HES-SO Valais. I have worked in the field of medical image analysis, computer vision, machine & deep learning for more than 7 years so far.

Why did you decide to participate in the France-BioImaging challenge “Light My Cells”?

Taking part in scientific challenges is a great way to explore previously unknown subfields and gain valuable experience in new topics. When I came across the challenge on the IEEE ISBI website, I immediately recognized it as an opportunity to deepen my expertise in biological imaging and expand my research network.

What was the most challenging part of the competition for you?

As in every challenge – to fully understand the goal, the data, and the associated challenges. The most time-consuming part in scientific challenges work is to explore the dataset and understand which challenges related to the data are the most important, e.g. in the Light My Cells challenge it was connected with significant dataset imbalance, both at the study and organelles level.

How did you manage your time during the competition?

I started with exploring the data and thinking how the problem should be addressed. The process took me more than half of the time I spent on the challenge. Then, I implemented and debugged the training and evaluation scripts. Finally, I queued all ablation studies on our supercomputing platform (ACK Cyfronet Athena) and chose the best model.

Do you have any projects or aspirations related to imaging or research after this competition?

The competition improved my experience related to image-to-image translation tasks that could be further used in different downstream applications I am working on, e.g. MR-to-CT translation in radiology. I continue to work both in digital pathology and radiology where I develop novel deep learning techniques.

What are your thoughts about Challenge 2 “Fuse My Cells”?

Definitely the most difficult aspect of the Fuse My Cells challenge is the timeline – there is only 1.5 months to develop and evaluate the solution.

Do you have any advice for the participants of Challenge 2?

I suggest starting with exploring the data and understanding the associated challenges. Then, it is wise to explore the current state-of-the-art to understand the best-performing solutions and improve them. The practical part related to developing the scripts and  performing ablation studies is usually significantly less influential.

Thank you very much for your time, Marek! I’m sure your testimony will be useful for the participants of Challenge 2.

For those interested in taking part in the “Fuse My Cells” challenge, find more information here!

France-BioImaging’s “Preclinical Microscopy” Working Group is organizing its next webinar on February 6th, 2025, from 14:00 to 16:00. The main objective of this Working Group is to advance multimodal microscopy of thick samples for preclinical studies.

During this webinar, you will have the opportunity to discuss the latest research, technologies, and regulatory frameworks related to photonic microscopy, spanning from the scale of organs/organoids to live animals.

Program:

14:00 – Welcoming and introduction

14:05 – “Exploring Mammary Gland Remodeling and Breast Cancer Therapies Through 3D Organoid Imaging” by Thomas Pelé (CRCI2NA, Nantes)

14:55 – Presentation on animal ethics (title to be confirmed) by Magali Jacquier (IPBS, Toulouse)

15:45 – Open discussion

Join the webinar:

Click here to join the Microsoft Teams meeting.

Please connect using your last name and first name so we can update the participants’ list.

This workshop will take place at the Institut Fresnel (FBI Marseille node) from November 12^th to 14^th , 2024.

Fluorescence polarization microscopy allows measurements of the orientation of molecules probed by various techniques. Through hands-on experiments, we will demonstrate their suitability for biological applications on a range of sample types, including cells and organisms.
The Institut Fresnel is a pioneer in this field, developing unique microscopes to probe molecular orientation – an intrinsic property of molecules that is measurable with all types of microscopes but often remains inaccessible.

The workshop aims to offer (1) a theoretical basis for understanding how one can probe molecular orientation, (2) ample time for practical experiments, and (3) opportunities for formal and informal discussions on technical details and biological applications.

Interested in attending this workshop? Please complete the following form by October 1^st, 2024:
FLUORESCENCE POLARISATION MICROSCOPY WORKSHOP 2024 | Framaforms.org

Limited to 16 participants.

Free registration includes accommodation, transport, and meals (except for the evening of November 13^th).

Candidates whose research projects align best with the workshop’s focus will be selected,
with preference given to members of the France-BioImaging (FBI) infrastructure.

Flyer & Programme

The France-BioImaging CLEM working group is pleased to announce the organization of the next CryoCLEM Workshop, to be held from October 14 to 15, in Bordeaux.

This workshop is the ideal event to be introduced to, and to gain knowledge of, the cryoCLEM technology, with the aim of applying it to your research project.

It will be composed of a theoretical part, presented by experts in this technology, and a practical part covering the entire cryoCLEM workflow (from sample preparation to correlative microscopy in cryogenic conditions).

Programme

In order to ensure the best conditions for this workshop, the event is limited to 4 participants.

The selection will be made on the possibility of rapid implementation of the cryoCLEM technology for your research project.

A pre-registration questionnaire is therefore available until 31st August 2024 :  CryoCLEM Workshop

This training covers lunches and accommodation.

For more information, please contact :

noemie.pied@u-bordeaux.fr 

monica.fernandez-monreal@u-bordeaux.fr

Banner picture copyrights: images 1 & 3 R. Anger, image 4 P. Lapios, image 2 N. Pied

The first meeting of the FBI Mechanobiology WG will take place on the 2 and 3 of December 2024 at the Centre for Integrative Biology (https://cbi-toulouse.fr/fr/) in Toulouse..

The programme will include a seminar by Matthieu Piel (Institut Curie/Institut Pierre Gilles de Gennes), presentations by participants and practical mechanobiology workshops (a choice of 3 workshops from a dozen: optical tweezers, bioprinting, microfluidics, AFM, Brillouin, finite element modelling, mechanical confinement, force measurements, etc.).

Registration is free, but places are limited and priority will be given to contributors whose abstracts have been selected.

Preliminary Programme:

Workshops

Call for abstracts

Abstract submission open until 15/09

TYPES OF PRESENTATIONS

• Oral presentations: If you are selected for an oral presentation, you will have 15 minutes, including discussion (12 minutes presentation + 3 minutes Q&A).
• Posters: If you are selected to present a poster, you will present your work at the dedicated poster session on December 2nd, afternoon.

Selected contributors will be notified at the end of September.

Registration/Abstract submission form

This form is currently closed for submissions.

On November 20th and 21th 2024, we have the pleasure to invite you to our Annual Meeting, to be hosted by our brand new FBI Alsace Node at the Bibliothèque Nationale et Universitaire (BNU) de Strasbourg (6 Pl. de la République, 67000 Strasbourg).

We will be happy to celebrate yet another year of achievements and developments in bioimaging with all the members of the community.

With a focus on “Live functional imaging: From chemical synthesis of the probes to instrumentation”, this edition aims to bring together chemists, microscope builders and biologists developping tools to probe life.

The scientific sessions will explore the development of new probes (organic, inorganic, nanoparticles, fluorescent proteins, hybrid materials), how to leverage their optical properties (spectra, quantum yield, lifetime, photostability, switching between dye states, etc…) and new instrumentations taking advantage of these new probes for life science.

France-BioImaging Mission Officers,  Technology WGs, facilities or R&D teams are invited to present news, innovations or any achievements to the community with a poster. We strongly encourage you to submit an abstract for a poster presentation during your registration!

Registration is free but mandatory. Please note that the BNU capacity is limited and registrations will be accepted on a first come first served basis.

We look forward to meeting you there!

Programme

Registation Form

This form is currently closed for submissions.

Poster