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.
BIAUnit
@biaunit.bsky.social
The BioImage Analysis Unit designs innovative computational methods to address challenging biological questions through rigorous quantitative approaches @Icy_bioimaging.bsky.social https://research.pasteur.fr/en/team/bioimage-analysis/ @InstitutPasteur
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
Institut Pasteur | 130 years of biomedical research@pasteur.fr · 10mo agoPour chaque vie, la science agit. Le Pasteurdon, c’est maintenant ! Soutenez la recherche et celles et ceux qui la font avancer ↘️ pasteurdon.fr #Pasteurdon
👋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
🎓 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
🎶 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
When science meets creativity: TuberKiller | My PhD at the Institut Pasteur
YouTube video by Institut Pasteur EDUCATION
youtube.com
📌 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
GdR ImaBio 🔬@gdrimabio.bsky.social · last yr.🔥 We've already received over a third of pre-registrations! #Mifobio2025 is already shaping up to be a highly attractive event... Don't delay in pre-registering! 👉 imabio-cnrs.fr @cnrs.fr @cnrsbiologie.bsky.social @cnrsingenierie.bsky.social @cnrs-inist.bsky.social
🚨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
🔬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 »
Bioimage Analysis – Retour sur le Cours Pasteur NEUBIAS
YouTube video by Institut Pasteur EDUCATION
youtube.com
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...
💡 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...
👉 Learn more: journals.plos.org/plospathogen...
Fibronectin induces a transition from amoeboid to a fan morphology and modifies migration in Entamoeba histolytica
Author summary Even though we know increasingly well how cells move in tissues, the question of whether parasites modify their migration as a function of the host tissue environment requires further i...
journals.plos.org
Maria@mmanich75.bsky.social · 2y agoBottom view of a 3D reconstruction of Entamoeba histolytica loaded on fibronectin, characterized by its fan shape with of a dorsal column of F-actin and numerous podosomes-like, and a broad cytoplasmic extension at the front. F-actin (red), nucleus (blue) & cytoplasm (green) #Icy
