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Eugene Katrukha 🇺🇦

@ekatrukha.bsky.social
1.3K followers 576 following 291 posts

Biophysics, cytoskeleton and self-disorganization

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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 57m
Yoohoo, more 3D SMLM! @chenjiajiachen.bsky.social Pls try BigVolumeBrowser for point cloud data rendering, it can even deskew it
chenjiajiachen.bsky.social
Jia Chen (@chenjiajiachen.bsky.social)
Postdoc in Daniel St Johnston lab, fruitfly gastroenterologist.
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Reto Fiolka @retof.bsky.social · 6h
Y’all 🤬☠️ www.linkedin.com/posts/wenlu2...
linkedin.com
#microscopymonday | Wen Lu | 29 comments
The Unicorn Is Still Waiting 🦄🔬 #MicroscopyMonday I created this cilia-“inspired” fluorescent unicorn last week, hoping Nikon Small World’s ongoing review would bring clarity and restore confidence i...
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Octavio Reyes-Matte @octavio-rm.bsky.social · 05/10/2026
Having lots of fun with BigVolumeBrowser. Thanks @ekatrukha.bsky.social for the cool plugin! FlyBrain image from FIJI samples BOP Blue and BOP Orange LUTs from @christlet.bsky.social
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Jean-Yves Tinevez @jytinevez.bsky.social · 05/10/2026
We have a position open in our core facility in the @pasteur.fr . Please share it and / or apply! forum.image.sc/t/research-e...
forum.image.sc
Research engineer in Bioimage Analysis. Institut Pasteur, Image Analysis Hub - 2026
Dear all Below is an announcement for a permanent position as a Research Engineer in the Institut Pasteur, Paris. There is a flyer attached at the bottom. We are looking ideally for a Bioimage An...
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Minor Mobius @minormobius.bsky.social · 02/10/2026
Torusweeper and Kleinsweeper are live. It only reeeeeally works if you fix perspective and slip the game over the surface
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 02/10/2026
In any multidisciplinary meeting, in 97% of cases. The person who is struggling with audio/video not working, file problems, wrong adapter etc, would be: A) software developer; B) IT person. The rest of the crowd (managers, biologists, anyone not related directly to IT) would deliver smoothly.
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 02/10/2026
Scientific papers/literature analysis over years to see if claim is valid 1990s: Carefully read whole text, study figures, pay attention to methods 2000s: Study figures, try to find relevant text paragraphs 2010s: Browse through figures, read discussion 2020s: Browse through supplementary movies
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Heather Brown-Harding @microscopyed.bsky.social · 02/10/2026
Struggle with sharing data? @bogovicj.bsky.social shows us better options than emailing data #I2KxBINA
John at the podium with a slide titled "Sharing OME-Zarr dats with Fileglancer"
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Dale Moulding @dalemoulding.bsky.social · 01/10/2026
Having seen the news: www.bbc.co.uk/news/article... thought I'd share a cilia movie captured at UCL GOS ICH with Eriomina Shahaj & Vanesa Papastavrou using simple DIC on a Nikon Ti2 with DIC at 60x1.4. 500 fps here slowed down 20 times. Processed with Nikon's denoiseAI and an unsharp mask in Fiji.
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 30/09/2026
Really like these kind of ventures. I will not be surprised to see a post from James: "microscope connection was lagging, so I wrote a new OS. Please test it, it was my Monday after-lunch project, so not all 90s soundcards are supported yet on Macs".
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Kay Schink @kschink.bsky.social · 26/09/2026
According to the quoted email from Nikon spokesperson, AI was used for "postprocessing". However, I wonder how this lines up with this recent post on LinkedIn, which finds AI watermarks from Google AI generators. I checked this myself, and Gemini reports a watermark.
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Kirsty Wan @micromotility.bsky.social · 10/11/2024
ooh Bluesky can do videos now... here's an emergency #cilia movie
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Valentin Dunsing-Eichenauer @dunsingvalentin.bsky.social · 25/09/2026
#FluorescenceFriday: Given the recently grown interest in ciliary beating, here is a movie of beating cilia in a human airway model that I captured last week with lattice light-sheet microscopy. No AI „processing“, this is the raw data! Frame rate is ca. 170fps, displayed here at 25fps.
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Sholto David @sholtodavid.bsky.social · 20/09/2026
Today I'm posting a video about Neurodigitech LLC which has provided clearly photoshopped neurons to research teams that published these images in Nature, JBC, and more. A year after I uncovered this only one paper has been corrected. It's in Frontiers. youtu.be/4g_1_AWOVpI
youtu.be
Faked Images of Neurons in Major Journals
YouTube video by Sholto David
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Hao Yin @haoyin.bsky.social · 25/09/2026
Cilia - AI champion show🏆 Credit: GPT6-Astra Inspired by @christlet.bsky.social
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André Nadler @nadlerlab.bsky.social · 24/09/2026
Well, actually cilia are probably also hallucinations bsky.app/profile/joac...
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Agathe Chaigne @agathechaigne.bsky.social · 24/09/2026
I'm super proud of this review written (mostly) by Zoé Ducarne and @myanhtruong.bsky.social about the extraordinary genomic features of the placenta. Such a crazy organ! journals.biologists.com/dev/article/...
journals.biologists.com
The curious case of the placental genome
Summary: The placenta is the only mammalian organ that harbors a cancer-like genome while remaining functional and healthy. This Review highlights its high mutational load, structural variants, aneupl...
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Joyce Meiring @joycemeiri.bsky.social · 24/09/2026
Excited to share that our latest story on #microtubule conformation controlling cell #signaling is now out in NCB! We show that microtubule expansion by taxane chemotherapeutics releases microtubule bound GEF-H1 which in turn activates RhoA/ROCK signaling. ✨ www.nature.com/articles/s41...
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 23/09/2026
Preparing my submission for the next year's "Nikon Small World in Motion". It should qualify, since I wrote it on a PC connected to a microscope. No AI, pure GLSL GPU code www.shadertoy.com/view/f333Dj
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 23/09/2026
Very cool! Happy that Gaussian splats are finally being used in microscopy. Related, I think that the Sbalzarini group's 2018 attempt with "Adaptive Particle Representation (APR)" was a bit ahead of its time. But now splats have infiltrated computer vision, so a lot of code and tricks are available.
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
Luxar is made for 3D UMAPs. 500K Tabula Sapiens cells from 24 tissues as points coloured by organ, with a legend in the scene; hovering a cell names its cell type and tissue. Millions of points stay interactive. #SingleCell Demo: demos.luxarviewer.dev/d/tabula_sa...
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Loïc A. Royer 💻🔬🧪 @loicaroyer.bsky.social · 23/09/2026
What if any dataset, any size, any number of dimensions, opened in a browser tab from a link? 🔬🧪💻 Luxar is out today: write it in Python, share it as a link, explore it in any browser. Open source. 🧵 @biohub.org Preprint: doi.org/10.5281/zen... Code: github.com/royerlab/luxar
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Christophe 🔬 Leterrier @christlet.bsky.social · 22/09/2026
From the new info my bet is fluo labeling inference pushed to 11. Hallucinating nonsensical DAPI nuclei, mitochondria stain, membrane labeling from a kind of phase contrast image: wrong localization, wrong scale, wrong movement. Keeping this movie as SWiM winner is a disgrace to the competition
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Jean-Yves Tinevez @jytinevez.bsky.social · 22/09/2026
I'd like to introduce a piece of work we did for the paper of @ines-ssm.bsky.social and colleagues in the lab of Chiara Zurzolo in @pasteur.fr www.nature.com/articles/s41...
nature.com
Tunneling nanotubes regulate mitochondrial homeostasis between glioblastoma and astrocytes, and between tumor cells in vivo - Nature Communications
Tunneling nanotube-like (TNT) connections allow mitochondrial exchange between tumor cells and its tumor microenvironment. Here, the authors show that TNT connections mediate bidirectional mitochondri...
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Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 21/09/2026
Happy #MicroscopyMonday. I found this very pretty COS-7 cell expressing LifeAct-mCherry from my old data. Look at how dense its actin network is. Also, many of the moving dots are endosomal to seemingly push them through the cytoplasm, similar to actin comet tail, but just a lot shorter.
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 22/09/2026
There is still time to register. And maybe you can attend my #BigVolumeBrowser workshop
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Estibaliz Gómez de Mariscal, PhD @gomez-mariscal.bsky.social · 18/09/2026
🚨Our work #ReScale4DL: balancing pixel and contextual information for enhanced bioimage segmentation, with @henriqueslab.bsky.social is out today!🚀 www.nature.com/articles/s41... ReScale4DL links key concepts in DL (receptive fields)+microscopy (resolution) so they can work #bettertogether😉 Threat👇
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Ben Engel @cellarchlab.com · 18/09/2026
Duuude! What indeed?? Airway epithelia have 100s of cilia per cell (not one or two), and they aren’t 10x longer than the cells themselves. Then there’s that mysterious purple layer below… made of mitochondria? And the motion😵‍💫. It looks like #AIslop may have taken over the small world competition? 🔬🧪
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Nils Norlin @nilsnorlin.bsky.social · 17/09/2026
I am looking for postdoc candidates for two opportunities in my lab at Lund University. 1. Co-application for a two-year postdoc scholarship on method development in 3D spatial biology, with applications in lung physiology, cancer and neuroscience.
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 16/09/2026
Before a new release, adding some new and responsive initial screen shaders to #BigVolumeBrowser (I know, I know..). This one is modified from www.shadertoy.com/view/MllcD7
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 16/09/2026
Found my old "always random LUT" code for a new test of GPU upload speed. #BigVolumeViewer
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Sergey Ovchinnikov @sokrypton.org · 14/09/2026
Finally a more intuitaive way to learn pLDDT/pAE? 😎 sokrypton.github.io/protein_figh... (Character idea from @hannes-stark.bsky.social & Alex Waldherr)
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Matt Henderson @matthen.com · 13/09/2026
Approximating the Lorenz attractor with a chaotic leaky water wheel. The orange dot is the centre of mass of the water. It traces (a projection of) the familiar attractor as the wheel spins seemingly randomly left and right.
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 11/09/2026
I'm always very happy to see the #Fiji gang & co, this time during the OME-Zarr Java hackathon in Dresden (imglib2/BDV motherland?). My personal progress: increasing max # of volumes in #BigVolumeViewer from 15 to ~200. Still not high enough, but there was not enough time.
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Anna Bodzeta @annabodzeta.bsky.social · 11/09/2026
While waiting for the manuscript to be uploaded on bioRxiv, here some sneak peek #FluorescenceFriday
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paveltomancak.bsky.social @paveltomancak.bsky.social · 10/09/2026
This article seems to celebrate the shift from poor support for #software #engineers in research to pretending they aren't needed at all. Did we spend 2 decades consolidating fragmented software ecosystems into platforms only to see them dissolve through "vibe coding"? www.nature.com/articles/s41...
nature.com
Disruption of the research software landscape through AI software generation - Nature Methods
Specialized research software has historically been costly and time-consuming to create, but large language models (LLMs) have become capable enough at code generation to fundamentally change this. We...
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Anh Hoang Le, PhD 🏳️‍🌈🏴󠁧󠁢󠁳󠁣󠁴󠁿🇻🇳 @anhhle2702.bsky.social · 07/09/2026
Very happy to share my postdoc paper is out now in @natcellbio.nature.com titled "Tissue flow acts as a guidance cue for immune cell polarization and directional migration". If you love imaging and immune cells, this is for you! #microscopymonday www.nature.com/articles/s41... A 🧵: 1/n
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 04/09/2026
A very persistent, tireless cowboy! Very pretty choanoflagellates, imaged today on LLS together with Babette van Amen from @agathechaigne.bsky.social lab.
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Gaëlle Letort @gaellel.bsky.social · 03/09/2026
The final version of the paper presenting our tool EpiCure is now online: journals.biologists.com/dev/article/... !! Thanks again to all collaborators in this project
journals.biologists.com
EpiCure (Epithelial Curation): a versatile and handy tool for curation of epithelial segmentation
Summary: EpiCure is a napari plugin designed to optimise epithelia segmentation and tracking curation through automatic errors detection and ergonomic correction while being easily interoperable with ...
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Jean-Yves Tinevez @jytinevez.bsky.social · 03/09/2026
New version of #Mastodon-SC, the Fiji plugin to track and lineage cells in gigantic movies! What is Mastodon? 👉 in the preprint linked to the quote post What's new? 👇
liveimagetrackingtools.org
geff
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Manuel Thery @manuelthery.bsky.social · 01/09/2026
"La cellule" by Yves Saint Laurent.
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MwahahahahahadScientist @mads100tist.bsky.social · 29/08/2026
Do you work with microscopy images and segment to quantify or track? Do you study cell biology? development? Gather round! Let me tell you about FOCUS-3D, a segmentation algorithm that is fast, accurate and can be used on any model. We used it here to study zebrafish development. 🧪 (thread)
biorxiv.org
FOCUS‑3D: Robust, generalizable volumetric cell segmentation for three‑dimensional fluorescence microscopy
Understanding how cells establish spatial organization within tissues is a fundamental question in life sciences. While modern three-dimensional fluorescence microscopy captures large-volume tissue ar...
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Denis Chrétien @dchretien.bsky.social · 27/08/2026
It can be used for a 2D classification approach, and also to facilitate analysis of cryo-EM images of microtubules, with its companion TubuleJ. Any feedback will be welcomed. (2/2).
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jmutterer.bsky.social @jmutterer.bsky.social · 28/08/2026
I've made a video about Fig_Space, the next version of FigureJ. It has nice new features, I hope you like it. youtu.be/bTKcXN4p-JM
youtu.be
FigSpace Fiji plugin demo
YouTube video by jerome mutterer
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Paul & Virginie - Centriole Lab @centriolelab.bsky.social · 27/08/2026
Very happy to see our Nature Reviews Molecular Cell Biology Roadmap out! A fantastic collective effort, led by Carsten Janke and Zdenek Lansky, together with an amazing group of colleagues, and sparked by inspiring discussions at the Fondation des Treilles. www.nature.com/articles/s41...
nature.com
Towards a systems-level view of the microtubule cytoskeleton and its functions in physiology and disease - Nature Reviews Molecular Cell Biology
Microtubules are essential components of the cytoskeleton, yet important links between their molecular properties and organismal functions remain unresolved. In this Roadmap, Janke et al. discuss key ...
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Eugene Katrukha 🇺🇦 @ekatrukha.bsky.social · 17/08/2026
I really like this work, from imaging to analysis. Here is my 5 cents on why it is cool. In short, to acquire a shape of a beating cilium without a smear, you need to record at ~1000 fps, i.e. have time resolution of ~ 1 ms. This is a current limit of modern "high-end" scientific cameras. (1/N)
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Christophe 🔬 Leterrier @christlet.bsky.social · 04/08/2026
But a nuanced view requires distinguishing the use cases, which people lamenting the discourse here never do. I'm very vocal against AI use for churning out shit that sets what's wrong with science on overdrive. It is useful for things like coding, image analysis, etc
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Jitte @jittebug.nl · 03/08/2026
Posting this for no particular reason, but I should be doing vacation stuff and instead I'm looking through some scans I made last week. Here is a very rough brain of a Pieris brassicae butterfly 🦋, about 2 mm wide. CLSM image, visualized with BigVolumeBrowser in Fiji #Entomology
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Nicole Feng @nicole--f.bsky.social · 28/07/2026
At #SIGGRAPH2026, I presented "points as tori" (PAT) for fast pointwise evaluation of signed distance for point clouds. Some code (Python w/ C++ extensions) and demo up: github.com/nzfeng/point... Contributions from people/LLMs welcome. Explainer thread below for the project: 🧵
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Aafke Gros @aafkegros.bsky.social · 24/07/2026
Microscopy Nodes 3.1 is out for Blender 5.2! 🎉 This has cool new features for conditional masking, working with even larger data (regional upscaling), and data manipulation! Watch the new youtube tutorials that explain the features: www.youtube.com/playlist?lis...
A FIB-SEM plankton visualization where the top shows only the volumetric data of the chromosomes, and the bottom a normally sliced region of the cell. A fluorescence microscopy dataset where a region has been reloaded to be much higher resolution
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