Fabrice Senger

Capillary interactions drive the self-organization of bacterial colonies - Nature Physics Bacteria tend to live in thin layers of water on surfaces. Now the capillary forces in these layers are shown to help organize the bacteria into dense packs.

Dreaming of a swimming pool? Bacteria are surrounded by water! Water capillary forces organize bacterial colonies into gas, nematic streams, or droplet states. New paper @natphys.nature.com led by Matt Black and Chenyi Fei, with Ned Wingreen and Josh Shaevitz!

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

Cell state-specific cytoplasmic density controls spindle architecture and scaling - Nature Cell Biology Kletter et al. show that cell state-specific cytoplasmic density controls spindle architecture and scaling in neural differentiation, suggesting that the physical properties of the cytoplasm are a det...

🍹Kletter et al. show that cell state-specific cytoplasmic density controls spindle architecture and scaling in neural differentiation, suggesting that the physical properties of the cytoplasm are a determinant in #organelle size control.
bit.ly/4mhMvsU

Data scientists, experimental biologists, mathematical modelers, and biophysicists interested in using machine learning to study cytoskeletal dynamics, cell migration, and mitosis are invited to join us for an upcoming workshop!

Apply today at www.nitmb.org/cytoskeletal...

Besides that in fluorescence microscopy you get the feeling the black part is empty...

Pulsatile flow dynamics determine pulmonary arterial architecture BACKGROUND Single ventricle congenital heart disease (SV-CHD) is a uniformly lethal condition. Survival depends upon the Glenn surgery, which shunts venous blood directly to the pulmonary arteries wit...

Happy to share our work on the role of biomechanical PULSATILITY on lung vessels.

Following surgery to alleviate overload in kids with single ventricle hearts, lung arteries form AVMs. #DevBio #EndothelialCell #CHD

Beautiful work from Steve Spurgin. #DevBio 🫁 🫀 ❤️‍🩹

www.biorxiv.org/content/10.1...

Cytoplasmic crowding acts as a porous medium reducing macromolecule diffusion Intracellular transport of macromolecules is crucial for the proper functioning of most cellular processes. Although intracellular crowding is known to strongly alter macromolecule mobility, how cytop...

To what extent does crowding modulate diffusion across the cytoplasm?
Thrilled to contribute to this study alongside O. Destrian, M. Chabanon, and B. Goyeau!
www.biorxiv.org/content/10.1...

Caption+Credit: EMBL’s AI Strategy aims to transform life sciences by integrating AI across research areas like genomics, drug discovery, and imaging. Creative team/ EMBL

🌐 EMBL’s new initiative is set to transform life science research through full AI integration – from genomics to drug discovery.

💡 Funding from the Hector Foundation is dedicated to attracting interdisciplinary talent, boosting infrastructure, training, & innovation.

www.embl.org/news/connect...

Precise 3D Tracking of Highly Non-planar Eukaryotic Flagellar Beating Patterns using Digital Holographic Microscopy https://www.biorxiv.org/content/10.1101/2025.07.28.666810v1

Congratulations

Waouw

The power of custom opto-mechanics AND custom software!

-> Here's a RAMM epi (REPI) microscope I put together. It's just a 2D fluorescence microscope with fast triggering that's mobile and relatively easy to modify. The real advantage here is full programmatic control!

github.com/amsikking/RE...

Fig. 5. Emergence of cellular orientation parallel to the tissue interface originates in the basal epithelium and propagates to the internal mesenchymal cells. (A) Diagrams showing explant interface and predicted axis of elongation and sectioned explant showing apical epithelium, basal epithelium and first layer of inner mesenchymal cells in the z-axis. (B) Images and segmentations with cell orientation representation for three z-positions at time point ti. (C) Representative close-up of segmented cells and corresponding nematic order Q score for each z-position. Data are mean±s.d. N=3. No outer mesenchymal cells were quantified at this time point as mesenchymal cells are predominantly covered by epithelium. (D) Images and segmentations with cell orientation representation for three z-positions and at time point 2. (E) Representative close-up of segmented cells and corresponding nematic order Q score for each z-position Data are mean±s.d. N=3.

Read the Research Article, 'Epithelial-mesenchymal interface guides cell shapes and axis elongation in embryonic explants' here:
journals.biologists.com/dev/article-...

YouTube video by Brian Northan Pixi and Napari-Easy-augment-Batch-DL

I just published a new video demonstrating how to use Pixi and Napari-Easy-Augment-Batch-DL for repeatable and reproducible deep learning segmentation. In this example, I use Pixi to set up a Python environment then launch Napari to explore and compare Cellpose3 and Micro-SAM. youtu.be/3ObAnSTBri8

Alternatives to the statistical mass confusion of testing for "no effect." Josh Morgan discusses how progress in cell biology is hindered by significance testing and the need for a shift to effect size estimation. rupress.org/jcb/article/...

#Technology #Reproducibility #Statistics

Good read imho

interestingly, the group is mainly working with animal tracking data (fish for example) and the analysis highlights collective behaviour ...should work great with cells though

Data Analysis & Visualization Group Data Analysis & Visualization Group has 25 repositories available. Follow their code on GitHub.

thinking aloud , some nice tools here : github.com/dbvis-ukon

it is intriguing and if you're not aware , here the paper : arxiv.org/pdf/1909.07872

has someone already analyzed tracking data with sktime ?

🤩

📢Accepted manuscript!

From cells to pixels: a decision tree for designing bioimage analysis pipelines.

With @mycroscopy.bsky.social, @haesleinhuepf.bsky.social, @kbias.bsky.social and pushed through by David Legland @inrae-france.bsky.social

Coming soon to J Microsc. @royalmicrosoc.bsky.social

Wound repair in plants guided by cell geometry Mathew et al. show that growth conflicts reshape cells after injury, forming rhomboidal geometries that trigger diagonal divisions. This reorients cell files to restore tapered morphology. A two-step ...

Our new paper is out!
1/14 How does an organ rebuild its shape after injury? It's not just about making new cells, but aligning them in the right direction — like bricks shaping a structure. We show that it's all driven by Cell Geometry!

www.cell.com/current-biol...

Human interpretable grammar encodes multicellular systems biology models to democratize virtual cell laboratories We developed a plain text modeling language—a cell behavior hypothesis grammar—to easily build virtual cell models and connect them to data, helping scientists to unlock the hidden dynamics of tissues...

Really excited to share our new @cellpress.bsky.social Cell paper with @fertiglab.bsky.social and colleagues. 1/n

www.cell.com/cell/fulltex...

@jktgfoundation.bsky.social @itcrtraining.bsky.social @smbmathbiology.bsky.social #mathbio #mathonco @mathonco.bsky.social @deniswirtz.bsky.social

Tested once at #Mifobio. Beautiful and indeed, huge files

Nice new toy

À must read if you're into monolayers

Ben tiens

“A #SPADarray in any laser scanning #microscope”. That is the latest effort from a group of people that shared this mantra. Proud of all of them.
@erc.europa.eu
#imagescanningmicroscopy #photonresolvedmicroscopy
#superresolution
#BrightEyes_ERC

doi.org/10.1038/s415...

I was allready thinking to run the soft in batch on a per-frame basis as it can be called by python ... maybe not elegant but it should work and csv files are not that heavy ;)

very interesting read even though i'm not into SMLM