Eugene Katrukha ๐บ๐ฆ
@ekatrukha.bsky.social
๐ค 1087
๐ฅ 413
๐ 135
Biophysics, cytoskeleton and self-disorganization
reposted by
Eugene Katrukha ๐บ๐ฆ
George Campbell
3 days ago
Time to add some ExM to
#FluorescenceFriday
! Sample description in alt-text.
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A cell finding its way through the matrix, imaged with
@joycemeiri.bsky.social
on LLS.
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3 days ago
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Eugene Katrukha ๐บ๐ฆ
Aafke Gros
3 days ago
I gave a talk at Blender Conference yesterday, showing how biological volumes work, and how to visualize them in Blender ๐
youtu.be/WPajSWX730o?...
#bcon25
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Microscopy Nodes: handling large biological volumes โ Blender Conference 2025
YouTube video by Blender
https://youtu.be/WPajSWX730o?si=pJARGAkd8LQpMlpv
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What is this sorcery
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3 days ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Christophe ๐ฌ L
5 days ago
Our new preprint is up! This is the main postdoc work of
@wiesner-t.bsky.social
focusing on exocytosis along the axon shaft and its regulation by the sub membrane actin-spectrin scaffold:
www.biorxiv.org/content/10.1...
Read the thread below for a summary of our findings ๐งต1/11
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reposted by
Eugene Katrukha ๐บ๐ฆ
Joachim Goedhart
7 days ago
Had the pleasure of teaching a workshop on
#Shiny
today. The {shiny} package can be used to make a web-app that uses R (or Python) under the hood. Ideal for interactive
#dataViz
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reposted by
Eugene Katrukha ๐บ๐ฆ
Shweta Nandakumar
8 days ago
Despite their high rigidity, microtubules (MTs) dynamically bend and buckle in cells. MT-self repair is inherent to their metastable nature, but it remains unclear whether just inherent repair mechanisms are sufficient to maintain MT integrity๐งต (1/9)
www.biorxiv.org/content/10.1...
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reposted by
Eugene Katrukha ๐บ๐ฆ
James Manton
7 days ago
We present a simple method to easily increase the imageable depth of an expansion microscopy gel on a typical inverted microscope ten-fold, using some carefully placed FEP film and a water dipping objective lens:
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Nice, some MTs splaying to individual protofilaments upon bending with two optical traps.
www.nature.com/articles/s41...
10 days ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Subham Biswas
13 days ago
Excited to share that my paper on TauโMicrotubule interactions is now published in Nature Physics!๐ Our work shows that tau goes beyond stabilizing microtubulesโit also promotes the removal of defects in the microtubule lattice.
www.nature.com/articles/s41...
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Tau accelerates tubulin exchange in the microtubule lattice - Nature Physics
Beyond its known role in stabilizing microtubules, it is now shown that tau protein actively promotes lattice defect repair by enhancing tubulin turnover at topological defects.
https://www.nature.com/articles/s41567-025-03003-7
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reposted by
Eugene Katrukha ๐บ๐ฆ
bioRxiv Cell Biology
12 days ago
Microtubule lattice conformation and integrity regulate ฮฑ-tubulin acetylation
https://www.biorxiv.org/content/10.1101/2025.09.09.675099v1
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reposted by
Eugene Katrukha ๐บ๐ฆ
Misha Ahrens
14 days ago
WHOLISTIC reveals many phenomena, including traveling waves along the kidney,
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reposted by
Eugene Katrukha ๐บ๐ฆ
Kristen Verhey
about 1 month ago
I never thought watching microtubules break could be so interesting! I learned so much about mechanics and modeling in this work and am extremely grateful to Archie Geng for leading the way. Also huge thanks to Franรงois Nรฉdรฉlec for creating Cytosim and providing advice along the way.
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Our new preprint is about the airway epithelium microtubule network, cilia, basal body protein composition, averaging of volumetric fluorescence data, and expansion microscopy. Four years of very hard work from our very talented Emma van Grinsven.
www.biorxiv.org/content/10.1...
(1/N)
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17 days ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
18 days ago
We are all super happy and proud to see our work on the function and evolution of the
#cephalic
#furrow
published in
@nature.com
. Let me say a few things about the background and history of this work on the
#Evolution_of_Morphogenesis
(1/12)
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reposted by
Eugene Katrukha ๐บ๐ฆ
Cedric Allier
24 days ago
github.com/allierc/MPM_pytorch
@HHMIJanelia pytorch version of
github.com/yuanming-hu/...
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reposted by
Eugene Katrukha ๐บ๐ฆ
Nicolas Chiaruttini
24 days ago
Nice cell division observed on Zeiss LLS7 yesterday! Sample:
@romainguiet.bsky.social
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SMLM quantification of microtubule fixation protocol. Looks like a classic extraction is the best
onlinelibrary.wiley.com/doi/full/10....
25 days ago
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I rarely see the "depth of field effect" for 3D microscopy datasets rendering. Tried to implement it as a weekend project. Curious, if it can be useful
#bigvolumebrowser
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26 days ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Kyle Harrington
27 days ago
Better ML for cryo-ET starts with better benchmarks. We built a phantom cryo-ET dataset (~500 tomograms) + hosted a Kaggle challenge. The result: community models beat expert tools. Read more in the
@natmethods.nature.com
article that just came out: ๐
doi.org/10.1038/s415...
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A realistic phantom dataset for benchmarking cryo-ET data annotation - Nature Methods
A standardized, realistic phantom dataset consisting of ground-truth annotations for six diverse molecular species is provided as a community resource for cryo-electron-tomography algorithm benchmarki...
https://doi.org/10.1038/s41592-025-02800-5
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reposted by
Eugene Katrukha ๐บ๐ฆ
Anh Hoang Le ๐ณ๏ธโ๐
27 days ago
YO, what's up with all these almost-witchcraft techniques?? In this paper, they develop a way to freeze cells so quickly that it preserves Calcium waves midway!! WHAT??? HELLO??? So now you can do 3D reconstruction of calcium waves with just a normal confocal.
www.nature.com/articles/s41...
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reposted by
Eugene Katrukha ๐บ๐ฆ
Loรฏc A. Royer ๐ป๐ฌ๐งช
28 days ago
๐งฌ๐ฌ๐งช ๐ Our team at @czbiohub is thrilled to share TWO companion papers out today in @NatureMethods! ๐ฆ Ultrack โ robust, scalable nD cell tracking ๐ inTRACKtive โ a beautiful, open-source web viewer for lineage exploration Letโs dive in! ๐
www.nature.com/articles/s41...
www.nature.com/articles/s41...
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reposted by
Eugene Katrukha ๐บ๐ฆ
Lucien Hinderling
about 1 month ago
Automated optogenetic control of hundreds of cells in parallel. Each cell is individually steered, collectively acting as a "tissue printer". Preprint & code out!
www.biorxiv.org/content/10.1...
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reposted by
Eugene Katrukha ๐บ๐ฆ
Lucien Hinderling
about 1 month ago
๐ฌ๐ง Our paper on smart microscopy & the issue of interoperability!
www.biorxiv.org/content/10.1...
LONG THREAD WARNING: Smart microscopy uses real-time image analysis to automatically guide the acquisition or perturbation of the sample (closed feedback-control loop). Many applications exist:
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Very nice new tool, kind of like CryoDRGN, but for volumetric and SM localization data.
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about 1 month ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Siรขn Culley
about 2 months ago
For giggles, we also discovered that you can deliberately force images to be structurally wacky while still getting high scores on quality metrics (please don't try this at home) (4/5)
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reposted by
Eugene Katrukha ๐บ๐ฆ
Christophe ๐ฌ L
about 1 month ago
Happy to contribute to this new work from
@micoxscopy.bsky.social
et al, helping apply SSQUASH to analyse the shape of spectrin rings along axons. Data analysis is the next frontier in SMLM, and I'm always up for chatting, sharing data and see how we can push things further!
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reposted by
Eugene Katrukha ๐บ๐ฆ
Sauer Lab
about 1 month ago
๐จ New Preprint! Ex-dSTORM resolves fine details of the molecular architecture of CCPs, the 8-nm periodicity of microtubules, and the docking site of synaptic vesicles at the presynapse of hippocampal neurons. โถ๏ธ
www.biorxiv.org/content/10.1...
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Oh, nice, just found a paper from
@joergenderlein.bsky.social
and co on blind estimation of IRF for FLIM measurements
pmc.ncbi.nlm.nih.gov/articles/PMC...
It should be useful!
about 1 month ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Izzy Jayasinghe
about 1 month ago
Closing soon - an opportunity to come and work with me and my colleagues developing our new curriculum in cellular and molecular biophysics. ๐งช Applications close on the 24th of Aug, Aus EST.
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reposted by
Eugene Katrukha ๐บ๐ฆ
Lucien Hinderling
about 1 month ago
trypanosoma parasites before/after expansion microscopy from neighbor lab. having fun at the institute
@izb-unibern.bsky.social
! (btw there is an open assist. prof position - can def. recommend if you enjoy late night recreational microscopy)
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reposted by
Eugene Katrukha ๐บ๐ฆ
about 2 months ago
Our first
#Hydra
paper. @anaisbailles.bsky.social all the way, with crucial theory contributions from Carl Modes and
@zechnerlab.bsky.social
Hydra maintenance by Heino Andreas and HCR by Giulia Serafini. Teamwork. Many thanks to the generous Hydra research community.
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reposted by
Eugene Katrukha ๐บ๐ฆ
Yiming Li
about 2 months ago
Weโre excited to share LiteLoc โ a lightweight and scalable deep learning framework for high-throughput single-molecule localization microscopy, enabling analysis speed of >500โฏMB/s on 8ร RTX 4090 GPUs without compromising accuracy.
rdcu.be/eztp6
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Scalable and lightweight deep learning for efficient high accuracy single-molecule localization microscopy
Nature Communications - This study presents LiteLoc, a lightweight and scalable AI model for efficient and accurate single molecule localization microscopy data analysis, bringing real-time...
https://rdcu.be/eztp6
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reposted by
Eugene Katrukha ๐บ๐ฆ
Ben Gallusser
about 2 months ago
Bonus: I added a 3D version, here is an example on the C. elegans dataset from the Cell Tracking Challenge.
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Last feature for
#bigvolumebrowser
before vacation: "inverted" clipping
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about 2 months ago
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Interestingly, the (s)CMOS (+BSI) camera revolution of the last 5-6 years has also reached the field of high-speed cameras. It seems that in 2020, their price was still around 150k for a max speed of ~2000 fps. These days, one can buy 50000 fps camera for just 60k. The videos are pretty amazing
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about 2 months ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Nicolas Chiaruttini
2 months ago
Hey, it's out!
doi.org/10.1016/j.ce...
Aligning Big Brains and Atlases, ABBA in short, is published in Cell Reports
@cp-cellreports.bsky.social
.
@biancasilvalab.bsky.social
's lab added an analysis pipeline on top of it (BraiAn) and did all the relevant biological work. What is it ? Short thread:
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reposted by
Eugene Katrukha ๐บ๐ฆ
Freya Holmรฉr
2 months ago
spline tip!! prolong the life of your splines by regularly brushing them with premium proximity test bristles
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reposted by
Eugene Katrukha ๐บ๐ฆ
Florian Levet
2 months ago
As hinted earlier, the biggest change in
#PoCA
to date: support for 2D/3D image data! ๐งฉ๐ผ๏ธ In fine, point clouds will be no longer the only game in townโPoCA is evolving into a more general spatial analysis platform. This (maybe too long) movie shows what's coming!
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reposted by
Eugene Katrukha ๐บ๐ฆ
Juan Nunez-Iglesias
2 months ago
Well,
@superresolusian.bsky.social
has shown that this *mostly* doesn't work, see e.g.:
youtu.be/vmEgPqF0ivg?...
However, it indeed depends on the workflow. But it's important to have a quantitative understanding of its effects on *your* workflow, rather than taking the restoration at face value.
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Siaฬn Culley: Quantifying quality in fluorescence microscopy
YouTube video by EPFL Center for Imaging
https://youtu.be/vmEgPqF0ivg?t=2203
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reposted by
Eugene Katrukha ๐บ๐ฆ
Anton Goloborodko
2 months ago
We found a new asymmetry in the large-scale chromosome structure: sister chromatids are systematically shifted by hundreds of kb in the 5โฒโ3โฒ direction of their inherited strands! The work was led by Flavia Corsi, in close collaboration with the Daniel Gerlich lab.
www.biorxiv.org/content/10.1...
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reposted by
Eugene Katrukha ๐บ๐ฆ
Jean-Yves Tinevez
2 months ago
Are you developing with TrackMate? If yes let's get in touch: I plan to make API breaking changes in the future version (v8, soonish) that will break existing detector and segmentation algorithms integration. Details on the forum:
forum.image.sc/t/upcoming-b...
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Upcoming breaking changes in TrackMate v8
Hello TrackMate developers, This post is only important if you are developing TrackMate extensions yourself, in particular TrackMate spot detectors and segmentation modules. If not you can skip it en...
https://forum.image.sc/t/upcoming-breaking-changes-in-trackmate-v8/114687
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reposted by
Eugene Katrukha ๐บ๐ฆ
Kirsty Wan
2 months ago
Excited to share that we have received significant funding from the
@wellcometrust.bsky.social
for a new interdisciplinary consortium project on
#cilia
coordination and function across scales and organisms! ๐๐ฅ@lsiexeter.bsky.social
news.exeter.ac.uk/living-syste...
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Multi-million project to โcrack the codeโ of cilia โ tiny structures with big impact on human health
An international team of researchers, led by the University of Exeter, have been awarded a Wellcome Discovery Award grant of almost ยฃ5 million to investigate one of the bodyโs most fascinating microsc...
https://news.exeter.ac.uk/living-systems-institute/multi-million-project-to-crack-the-code-of-cilia-tiny-structures-with-big-impact-on-human-health/
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Somehow this poster illustration choice reflects my (I admit, unsubstantiated) skepticism towards denoising: all giraffe's spots are gone, but look! Our method works!
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2 months ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Brady Johnston
3 months ago
Playing around with ligands and emission lighting
#MolecularNodes
#GeometryNodes
#b3d
#motm
#SciArt
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While people explore cutting edge AI network architectures, I am still fighting framebuffers and trying to render multiple 3D transparent objects properly.
3 months ago
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reposted by
Eugene Katrukha ๐บ๐ฆ
Joyce Meiring
3 months ago
Excited to share that our fast & reversible chemical and optogenetic vimentin pulling tools are now published in JCB! ๐ฅณ We show a subset of organelles are displaced with vimentin pulling to the cell centre and cells become much softer despite little or no effect on actin/MTs
doi.org/10.1083/jcb....
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reposted by
Eugene Katrukha ๐บ๐ฆ
Vladimir Volkov ๐บ๐ฆ
3 months ago
New preprint from the lab - the first paper made (almost) entirely here
@qmul.bsky.social
We report how human outer kinetochore complexes Ndc80 and Ska form cooperative oligomers, that together stabilise microtubule ends against shortening.
www.biorxiv.org/content/10.1...
Key results below: (1/7)
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Microtubule end stabilisation by cooperative oligomers of Ska and Ndc80 complexes
During mitosis, properly aligned chromosomes stabilise microtubule ends with the help of kinetochores to ensure timely segregation of chromosomes. Microtubule-binding components of the human outer kinetochore, such as Ndc80 and Ska complexes, are present in multiple copies and together bind several microtubule ends, creating a highly multivalent binding interface. Whereas Ndc80:Ndc80 and Ndc80:microtubule binding is crucial for interface stability, Ndc80 alone in absence of Ska is unable to support stable kinetochore-attachments. Using cryoET, we demonstrate that oligomeric Ndc80:Ska assemblies stabilise microtubule ends against shortening by strengthening lateral contacts between tubulin protofilaments at microtubule plus-ends. We further identify a point mutation within the SKA1 microtubule-binding domain that does not affect microtubule-binding of individual Ska molecules, but does abolish Ska:Ska interactions. Finally, we report that oligomerisation of Ska, in a cooperative fashion together with the Ndc80, is necessary to maintain stable microtubule attachments both in vivo and in vitro. ### Competing Interest Statement The authors have declared no competing interest. BBSRC, BB/X014975/1, BB/W019698/1 Wellcome Trust, https://ror.org/029chgv08, 308895/Z/23/Z
https://www.biorxiv.org/content/10.1101/2025.07.06.663352v1
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reposted by
Eugene Katrukha ๐บ๐ฆ
Christophe ๐ฌ L
3 months ago
Just out: we used SReD to measure the periodicity of spectrin rings along axons, finely capturing the effect of actin depolymerization. This and many more applications โก๏ธ
www.nature.com/articles/s41...
Another great collab with
@henriqueslab.bsky.social
, congrats
@afonsomendes92.bsky.social
et al ๐
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reposted by
Eugene Katrukha ๐บ๐ฆ
Ricardo Henriques
3 months ago
๐งโ๐ฌ๐ฐ๐
#RxivMaker
is here! A framework automating the creation of publication-ready scientific
#preprints
from simple Markdown. Goodbye manual formatting, and hello gorgeous manuscripts! A great adventure with
@guijacquemet.bsky.social
's lab ๐:
zenodo.org/records/1575...
๐จโ๐ป:
github.com/HenriquesLab...
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