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ekatrukha.bsky.social
Biophysics, cytoskeleton and self-disorganization
90 posts 1,035 followers 356 following
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Preprint: IntAct-U-ExM enables robust, isoform-specific expansion microscopy of actin networks in yeast and mammalian cells. A cool study led by @anubhavdhar.bsky.social in collaboration with Sudarshan and Deepak Nair. www.biorxiv.org/content/10.1...

submitted 7 days ago • 2 comments

Image normalization: trivial enough to automate, impactful enough to quietly sabotage your results. Here’s a Jupyter notebook I wrote on how, why & when normalization matters, feedback 💛ly welcome. 👇 haesleinhuepf.github.io/BioImageAnal...

submitted 7 days ago • 0 comments

Today I will be working on the import of glTF format to #bigdatabrowser. It is a common format to store 3D scenes and object (meshes), so it would be nice to have it. As a datasource, real life and 3D model, I will be using this guy. Let's see how far I can go (1/N)

submitted 8 days ago • 1 comment

Introducing warpfield, an open source Python library for GPU-accelerated non-rigid 3D registration. Warps and aligns gigavoxel volumes within seconds (not hours). For 3D microscopy, region-to-region and cell-to-cell matching. A collaboration with @mh123.bsky.social 🚀 github.com/danionella/w...

submitted 11 days ago • 7 comments

Our work “AI4CellFate: Interpretable Early Cell Fate Prediction with Generative AI” is finally out in @biorxivpreprint.bsky.social !!! 😍❤️ biorxiv.org/content/10.1... @scilifelab.se , @crick.ac.uk . More about it in the thread #AI4CellFate (1/n)⬇️

submitted 9 days ago • 1 comment

Thanks to a dose of activation energy from @dpshepherd.bsky.social, I've finally cleaned up my Biggs–Andrews accelerated version of our automatic parameter-free deconvolution code and made it available at beryl.mrc-lmb.cam.ac.uk/rlgcba_noteb.... This is ~2.75× faster than the previous version. 1/4

submitted 13 days ago • 1 comment

Some early attempts to show 3D SMLM data in #bigvolumebrowser : 4M points from @shuangfu-shawn.bsky.social re-analysis of our LLS-paint data (see recent retweet). It can be overlaid with any volumetric data input. @christlet.bsky.social are you still interested in Fiji SMLM renderer?

submitted 10 days ago • 3 comments

A beautiful reconstruction of LLS-motor-PAINT dataset using LUNAR

submitted 36 days ago • 0 comments

Hey #TeamTomo, Ever been in need of a tutorial about the fundamentals of cryo-electron tomography? From preprocessing raw frames to high-res subtomogram averaging? That's why @florentwaltz.bsky.social and I made this website! tomoguide.github.io Follow the thread 1 /🧵 #CryoET #CryoEM 🔬🧪

submitted 16 days ago • 5 comments

This desperate attempt to sort diffusing motors is a fight against entropy and disorder. Life shall win. Numerical simulation by Floran Lavrilleux.

submitted 17 days ago • 2 comments

A dream come true: the first expansion microscopy images of C. flexa 🤩 Generated by Mylan & Uzuki who learned from the best (@hiralshah.bsky.social @gautamdey.bsky.social @dudinlab.bsky.social). We will learn so much from these!

submitted 30 days ago • 18 comments

Postdoc position in my lab: investigating how the microtubule motor protein dynein-2 works in cilia. Here's dynein-2 at work translocating microtubules - how is this activity regulated? How does dynein-2 malfunction in disease? Find out more and apply: my.corehr.com/pls/uoxrecru...

submitted 23 days ago • 2 comments

Imported mesh of a very short filament traced in Imaris to #bigvolumebrowser. And wow, look at how nice those rounded end segments are! Good job, @oxfordinstruments.bsky.social programmers, nice attention to details! Data comes from a post at the forum forum.image.sc/t/open-wrl-f...

submitted 24 days ago • 1 comment

🚀 Excited to share that our work on BiaPy has been published today in Nature Methods! BiaPy makes deep learning accessible for bioimage analysis, from small datasets to terabyte-scale 3D images. 👇 (1/7) 🔗 www.nature.com/articles/s41... #DeepLearning #BioimageAnalysis #OpenSource #BiaPy

submitted 24 days ago • 1 comment

New lab preprint! Unveiling the Molecular Architecture of T Cells and Immune Synapses with Cryo-Expansion Microscopy (Cryo-ExM). A fantastic collaboration with Dr. Benita Wolf. Congratulations to all authors, especially Florent Lemaitre, for leading this amazing work! www.biorxiv.org/content/10.1...

submitted 30 days ago • 3 comments

The STIM paper is out! We build on established computer vision techniques to automatically create 3D volumes of spatial transcriptomics datasets with human-level accuracy, and useful, interactive visualizations. www.sciencedirect.com/science/arti... @hhmijanelia.bsky.social @mdc-bimsb.bsky.social

submitted 31 days ago • 0 comments

Today I had a lot of fun implementing different types of mesh rendering for #bigvolumebrowser As usual with GLSL, something as simple as a wireframe render was the most difficult to implement.

submitted 30 days ago • 1 comment

Our PhD student Louis Romette is optimizing long-term live-cell imaging. He just casually dropped this 65-hour movie of a growing neuron (div 3 to 6) with knocked-in actin 🔥🕶️ #realtimemicroscopy

submitted 36 days ago • 14 comments

Moving obituary of David Stephens, "in many ways, the perfect academic" journals.biologists.com/jcs/article/...

submitted 38 days ago • 0 comments

We've updated our preprint that reports on a "mTurquoise2-based glucose biosensor" with data of HeLa cells - the movie shows the effect of adding 5 mM of Glucose www.biorxiv.org/content/10.1...

submitted 42 days ago • 1 comment

Why do lower-resolution images sometimes yield better results in deep learning for bioimaging analyses? 🤔📉 Mariana Ferreira's new preprint on #ReScale4DL explores this paradox and introduces optimal resolution design! @gomez-mariscal.bsky.social brainchild🧑‍🔬✨ Check: www.biorxiv.org/content/10.1...

submitted 42 days ago • 5 comments

Some "should be simple" features of a 3D viewer, like "focus" and positioning of a cube in the center of the view, can be notoriously complex (well, for me). Here is my current work in progress. I thought I could do all math in my head, but eventually had to add debugging geometry. #bigvolumebrowser

submitted 43 days ago • 3 comments

We have a new review out! In this Microscopy & Microanalysis piece, Louisa Mezache and I survey some of the latest commercially available microscope technologies: Nikon NSPARC, Re-scan Gaia, CSR Biotech MI-SIM, refinements to STED, SMLM from Bruker and Abbelight… Check it out with free access:

submitted 44 days ago • 2 comments