Some impressions from last time
(We had a good time, and aim for it again.)

Organized with the great @biaunit.bsky.social , @gaellel.bsky.social and the IAH team.

In this edition, organized with the @biaunit.bsky.social , we will focus on teaching the basics of bioimage analysis and machine learning for image analysis in Life Science.

The course is focused on beginners, with little or no experience in image analysis, but who needs it for their research

📌 Tracking cell dynamics just got smarter!
We use Bayesian linking algorithms — KOFT and SKT — implemented in our ByoTrack 🐍 Python library.
Kalman filters + optical flow for links & mitosis detection.
[PDF] celltrackingchallenge.net
#CellTracking #Python #KalmanFilter #OpticalFlow #OpenScience

Aujourd'hui ce sont les portes ouvertes de l'Institut Pasteur, venez nombreux nous y retrouver...
#institutpasteur #portesouvertes #pasteurdon @pasteur.fr

Microscopy image of a cell with labeled cytoskeleton and nuclear components

ZEISS LSM 880 microscope with incubation chamber

2 people working on the microscopes

2 men looking at monitors with microscopy images

👋Welcome to CELLIM on BlueSky!

• a core facility for advanced light microscopy @ceitec.eu @masarykuniversity.bsky.social

🔬 Follow us for:
• Updates on our microscopy platforms
• Insights into imaging methods
• Behind-the-scenes highlights
• Workshops, courses & more

#CEITECScience

Pasteur-Paris University International Doctoral Programme, The call for enrollment of students in October 2026 will be open from September 1st to October 20th, 2025

🎓 Applications for Institut Pasteur's PhD programs open Sept 1-Oct 20, 2025 for October 2026 entry.

Apply to up to 4 projects across 6 programs: PPU, PPU-IMAGINE @institutimagine.bsky.social, PPU-@ox.ac.uk, PPU-EID @upcite.bsky.social & more 🧬

Register now ✍️ www.pasteur.fr/en/education...

🌍 Excited to be present at #EUSIPCO2025 in Palermo!
📄 Deep Multitask Learning for Automated Tissue Segmentation & Cell Detection
👤 Presenter: Mohamed Mounib BENIMAM
📅 September 2025
📍 Palermo, Italy
Let’s connect around cutting-edge image processing!
#SignalProcessing #MedicalImaging #DeepLearning

When science meets creativity: TuberKiller | My PhD at the Institut Pasteur YouTube video by Institut Pasteur EDUCATION

🎶 Science meets creativity with TuberKiller! Yaëlle Wormser, PhD student featured in the My PhD at the Institut Pasteur series, raps her tuberculosis research.

Discover how music and science collide to make research unforgettable! 👏

🎧 TuberKiller is also available on Spotify!

@pasteur.fr

Yes! The code is distributed in Python in the open-source ByoTrack library. A python script (cli) is available, as well as a standalone executable for Linux/MacOs. It can be found on the CTC website associated to our submission: celltrackingchallenge.net/participants...

Exactly! In this case, we are relying on Farneback to solve our optical flow.

📌 Tracking cell dynamics just got smarter!
We use Bayesian linking algorithms — KOFT and SKT — implemented in our ByoTrack 🐍 Python library.
Kalman filters + optical flow for links & mitosis detection.
[PDF] celltrackingchallenge.net
#CellTracking #Python #KalmanFilter #OpticalFlow #OpenScience

🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource

Adeline Mallet, head of the Ultrastructural Bioimaging facility, is presenting cutting-edge technologies to visualize intraflagellar transport in Trypanosomas.
@pasteur.fr @bastinlab.bsky.social

🚀 Manual mask annotation slowing you down?
💡 SAMJ is a new ImageJ/Fiji plugin using Segment Anything (SAM) for fast, interactive segmentation — no GPU needed, one-click install, real-time results.
🔬 Perfect for large biomedical images.
arxiv.org/abs/2506.02783
#AI #Bioimaging #ImageJ #OpenSource

⏰ We've just passed the 250 pre-registration mark for #Mifobio2025 !

There's only one week left before the deadline, which won't be extended given the current numbers ! 👉 imabio-cnrs.fr/mifobio-2025...

@cnrsingenierie.bsky.social @cnrsbiologie.bsky.social @cnrs-inist.bsky.social @cnrs.fr

🚨Paper alert!
🚀 We presented SINETRA at #ISBI2025 in Houston
A new simulator for generating realistic 2D/3D neuron tracking data in moving animals like Hydra vulgaris
🧠 Helps test and improve tracking algorithms under tough conditions
📄 dx.doi.org/10.1109/ISBI...
#celltracking #syntheticdata #ISBI

Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS YouTube video by Institut Pasteur EDUCATION

🔬Le Cours Pasteur NEUBIAS propose une formation avancée en analyse d’images biologiques intégrant théorie, pratique et IA. Lina El Hajji, post-doc à Sorbonne Université, partage son expérience. La prochaine édition aura lieu en juin 2026 sous le nom « Advanced Bioimage Analysis with AI »

Zoom into a human cell infected by Shigella, the bacteria behind dysentery. Using cryo-EM, @leaswistak.bsky.social and team revealed how it pierces cells with molecular syringes. Stunning science at the nanoscale.

@enningalab.bsky.social @jytinevez.bsky.social @nanoimaging.bsky.social

#CryoEM

🚨Paper alert!
🚀 We presented SINETRA at #ISBI2025 in Houston
A new simulator for generating realistic 2D/3D neuron tracking data in moving animals like Hydra vulgaris
🧠 Helps test and improve tracking algorithms under tough conditions
📄 dx.doi.org/10.1109/ISBI...
#celltracking #syntheticdata #ISBI

Exciting news! 🎉 We propose Spatiopath, a null-hypothesis framework for cell-cell & cell-tumor interactions that distinguishes statistically significant immune cell associations from random ones.📊🔬
Check it out:😊 www.nature.com/articles/s41...
#statistics #immunology #oncology

👉To classify the dynamic behaviors governing biological particles, we developed a neural network model based on geometric trajectory descriptors and a framework to robustly detect dynamic changes in compound trajectories.
#simulation #activationpathwayofreceptorsCCR5
👉 hal.science/hal-04870375v1

The stiffness of cells and their nuclei is a biomarker of several pathologies, yet is usually reduced to a single value. In our last paper, we propose a method to estimate heterogeneous maps of stiffness inside freely moving cells using only fluorescence imaging.
ieeexplore.ieee.org/document/107...

Exciting news! 🎉 We propose Spatiopath, a null-hypothesis framework for cell-cell & cell-tumor interactions that distinguishes statistically significant immune cell associations from random ones.📊🔬
Check it out:😊 www.nature.com/articles/s41...
#statistics #immunology #oncology

👉To classify the dynamic behaviors governing biological particles, we developed a neural network model based on geometric trajectory descriptors and a framework to robustly detect dynamic changes in compound trajectories.
#simulation #activationpathwayofreceptorsCCR5
👉 hal.science/hal-04870375v1

The stiffness of cells and their nuclei is a biomarker of several pathologies, yet is usually reduced to a single value. In our last paper, we propose a method to estimate heterogeneous maps of stiffness inside freely moving cells using only fluorescence imaging.
ieeexplore.ieee.org/document/107...

Spot detection @Icy_bioimaging

💡 BioFlow is an image-based method able to extract velocities, pressure and forces inside living cells observed in fluorescence microscopy 🔬🖥️
icy.bioimageanalysis.org/plugin/biofl...
👉 The lateral movement of fan-shaped amoeboid cells is not pressure-driven ‼️

JDLL: a library to run deep learning models on Java bioimage informatics platforms.
@jytinevez.bsky.social @deepIcy_IP @deepImageJ

www.nature.com/articles/s41...