Sign in

Marten Chaillet

@martenchaillet.bsky.social
653 followers 254 following 54 posts

CryoET open-source software developer 🤓 Postdoc to tackle tilt-series alignment with deep-learning. Working in Arjen Jakobi's lab at the technical university of Delft. interests outside of work: DnD, cooking, road-cyling!

PostsRepliesMedia
Reposted by Marten Chaillet
Casper Berger @casperberger.bsky.social · 23/09/2026
We developed Adaptive Polishing for the consistent preparation of ~150 nm thin FIB-lamellae. This was done by using imaging feedback to adjust parameters for each lamella, or Adaptive Milling, rather than applying a fixed recipe. Preprint: doi.org/10.64898/202...
12813
Reposted by Marten Chaillet
Prof. Stefan Rahmstorf @rahmstorf.bsky.social · 19/09/2026
Sommer 2026: 16.000 Hitzetote 🥵 alleine in 🇩🇪. Dürre. Brände. 🤯 Die Bundesregierung subventioniert jetzt mit 2.500.000.000 € von unseren Steuergeldern die Ursache der Hitze: fossile Brennstoffe. Unfassbar. 🤯🤯🤯 Das meiste Geld landet dann wieder bei den Ölkonzernen, der Lobby gegen Klimaschutz.
832118933
Reposted by Marten Chaillet
simon-alkema.bsky.social @simon-alkema.bsky.social · 17/09/2026
Releasing TOMATO, the TOMogram Annotation TOol! A lightweight Python GUI for going through hundreds of cryo-ET tomograms. Flag what's in each one, grade its quality, and end up with a table you can filter and act on. github.com/alkemasimon/...
15825
Reposted by Marten Chaillet
Andrew Dessler @andrewdessler.com · 14/09/2026
On The Climate Brink: The Atmosphere Just Set a Water Vapor Record. Aug. 2026 probably had more water vapor in the atmosphere than any month in the last few thousand years, if not a 100,000 years. www.theclimatebrink.com/p/the-atmosp...
theclimatebrink.com
The Atmosphere Just Set a Water Vapor Record
More water vapor means more rocket fuel for extreme rain — so this record is not good news
11282163
Reposted by Marten Chaillet
Joy Jeongyoon Choi @joyjoychoi.bsky.social · 14/09/2026
Excited to share our new preprint on in situ chromatin structure of the inactive X chromosome in differentiated female mouse embryonic stem cells. www.biorxiv.org/content/10.6... 🧵1/8
611743
Reposted by Marten Chaillet
Arthur Oldeman @arthuroldeman.bsky.social · 14/09/2026
We gaan zeer waarschijnlijk de NLse klimaatdoelen niet halen en dat komt door politieke keuzes, zo stelt het PBL. De NLse doelen zijn eigenlijk al niet toereikbaar. Dus dit is een slechte ontwikkeling. www.pbl.nl/actueel/nieu...
pbl.nl
Grote kloof tussen ambitie en beleid richting 2040; emissiereductie 2030 stagneert
Nederland heeft een grote kloof te overbruggen om in 2040 in de buurt te komen van de Europese ambitie van 90 procent minder Europese broeikasgasemissie dan in 1990.
031
Reposted by Marten Chaillet
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)
727698
Reposted by Marten Chaillet
David Ho @davidho.bsky.social · 12/09/2026
I resigned from ExxonMobil today. I spent the last three years doing fossil fuel extraction research at both BP and ExxonMobil. Neither company is acting responsibly. They are racing to maximize extraction while the window to act closes, and gambling with our lives. More below.
145136944893
Reposted by Marten Chaillet
Arthur Oldeman @arthuroldeman.bsky.social · 09/09/2026
In Europa zagen we een record hoeveelheid hittegolven deze zomer. En onze premier, die zogenaamd een klimaatdrammer zou zijn, gaat in diezelfde zomer op werkbezoek bij Shell. Vind jij dat ook verkeerd? Kom deze zaterdag naar de klimaatmars, in Amsterdam.
021
Reposted by Marten Chaillet
Daniel Hurdiss @danielhurdiss.bsky.social · 09/09/2026
Our first #cryoEM map from the Krios 5 recently installed at Utrecht University as part of the EMPower-funded upgrades to NeCEN. Hopefully the first of many more!
4258
Reposted by Marten Chaillet
Guillaume Gaullier @guillawme.eurosky.social · 07/09/2026
"How contemporary academic structures constrain scientific creativity and hold back early-career researchers" doi.org/10.1038/s415... #AcademicChatter #Academia
doi.org
How contemporary academic structures constrain scientific creativity and hold back early-career researchers - Nature Human Behaviour
In this Perspective, Haubrock et al. argue that today’s scientific structures constrain creativity and that strategic conformity is a rational response. They discuss how this holds back early-career r...
031
Reposted by Marten Chaillet
Arthur Oldeman @arthuroldeman.bsky.social · 31/08/2026
The Himalayas are melting. In the valley where a piece of glacier broke off on Wednesday, a quarter of the ice mass is already gone. We can - unfortunately - keep expecting devastating floods like in Nepal. Until the glaciers are gone. @klimaatveranda.bsky.social klimaatveranda.nl/2026/08/31/n...
klimaatveranda.nl
Nu overstromingen en later waterschaarste door smeltende gletsjers in de Himalaya
Een snel opwarmend klimaat en terugtrekkende gletsjers vergroten het risico op een gebeurtenis zoals die van afgelopen week in Nepal, ongeacht of we deze specifieke ramp uiteindelijk aan klimaatver…
023
Reposted by Marten Chaillet
bioRxiv Molecular Biology @biorxiv-molbio.bsky.social · 28/08/2026
Imaging large fields-of-view at high resolution in cryo-ET with square beam montaging www.biorxiv.org/content/10.64898/20…
01810
Reposted by Marten Chaillet
Jeff Berardelli @weatherprof.bsky.social · 17/08/2026
Watch as the East Pacific Morphs into a Monster El Niño - the strongest ever observed! This shows how surface and subsurface temperatures have heated dramatically since (relative to) last fall. The heat travels there under the surface from an overheated West Pacific Warm Pool… 1/
717385
Reposted by Marten Chaillet
Kashish Singh @kashishsingh.bsky.social · 13/08/2026
Very happy to see the final version of our work on the structure and composition of cytoplasmic lattices in mouse embryos, previously shared on bioRxiv, now published in The EMBO Journal! Many thanks to our editor, Ieva Gailite, and the reviewers for their constructive input.
15019
Reposted by Marten Chaillet
c0nc0rdance @c0nc0rdance.bsky.social · 11/08/2026
The /largest/ animal in the oceans is the blue whale, but it may not be the LONGEST animal in the ocean. Colonial siphonophores like this feather boa siphonophore (Erenna richardi) can be 475 feet long (145 m), a slender wall of stinging death. Let's talk about them. (📷: MBARI, linked below)
522864
Reposted by Marten Chaillet
Bronwyn Lucas @bronwynalucas.bsky.social · 12/08/2026
Now on Arxiv: arxiv.org/abs/2608.10029 Led by grad student Matthew Giammar and collaborator Alex Strang, we provide a fast algorithm to calculate a low rank approximation to large (>100 million row) matrices with high fidelity that will accelerate template matching.
arxiv.org
A fast diagonalization algorithm to enable singular value decomposition of large matrices for efficient template matching
Many computational problems possess the following three features: (1) the problem could be solved efficiently if a linear operator could be diagonalized, (2) direct diagonalization is infeasible due t...
2228
Reposted by Marten Chaillet
Jamie Blaza @jnb-lab.bsky.social · 10/08/2026
Permanent academic position as a Lecturer in cryo-ET open at York. We are looking for someone to lead a research program making the most of the stunning advances occurring in cryo-ET. It's a research and teaching post but with a focus on research in the early years. jobs.york.ac.uk/vacancy/lect...
jobs.york.ac.uk
Jobs - The University of York
13838
Reposted by Marten Chaillet
Ricardo D. Righetto @lifeonthewedge.bsky.social · 08/08/2026
And here we are, getting cooked to death.
131
Reposted by Marten Chaillet
Florent Waltz @florentwaltz.bsky.social · 07/08/2026
We've been seeing a lot of "in situ" lately in titles from fancy journals (not pointing any fingers 👀). I’ve delayed posting this, but as more and more come out, I'm afraid "in situ" is becoming an empty buzzword, much like "near-atomic" was for SPA 🔬 1/n #cryo-ET #cryo-EM #cryoET #cryoEM 🧪
85616
Reposted by Marten Chaillet
Jack Ryan 🙏🧪 @jacksonwryan.com · 07/08/2026
🧪 A problem that seemed to have disappeared is still haunting new scientific papers. ...and why don't publishers just tell us the results of investigations into the weird stuff they let slip into the literature? nobreakthroughs.com/more-fishin/
nobreakthroughs.com
More Fishin'
A minor update on Latin fishies infiltrating the scientific literature.
1218
Reposted by Marten Chaillet
napari @napari.org · 31/07/2026
And it's a wrap! The hackathon was a fantastic success! 🥳 You can look forward to a longer post about all we did, and one of our biggest releases yet in 0.9.0! Huge thanks to all the participants 🤩, and we hope to see you at the next one!
Hackathon participants discussing a new feature demo.Jules Vanaret shows off slicing of volumes with non-orthogonal transforms.The naPLari hackathon crowd: Wouter-Michiel Vierdag, Grzegorz Bokota, Tim Monko, Giannis Liaskas, Draga Doncila Pop, Lorenzo Gaifas, Aroj Hada, Brian Northan, Jules Vanaret, Zuzana Čočková, Curtis Rueden, Juan Nunez-Iglesias, and Margot Chazotte.Celebratory drink after the last full day of the hackathon. 🍻
0223
Marten Chaillet @martenchaillet.bsky.social · 29/07/2026
Roep een halt op de bouw van nieuwe datacenters door deze petitie te tekenen: www.fossielvrij.nl/stop-datacenters
fossielvrij.nl
Stop nieuwe datacenters!
De gasprijzen gaan door het dak en we hebben een watertekort. Toch stampen techmiljardairs als Elon Musk en Jeff Bezos stroomslurpende datacenters uit de grond. ⛔ We moeten nu de pauzeknop indrukken ...
010
Reposted by Marten Chaillet
Laina Hall @lainahall.bsky.social · 25/07/2026
With Cryo-ET/EM, the macromolecules we study (and biological questions we ask) are SNR-limited. Here, we share Nilas, a low-voltage milling method named after thin sea ice. Nilas produces thin (sub 50 nm in places!), minimally damaged lamellae. biorxiv.org/content/10.64898/2026.07.21.739890v1
biorxiv.org
Optimized cryo-FIB milling strategy to generate thin, minimally damaged biological lamellae
Focused ion beam (FIB)-milling has been adapted to thin frozen cells for visualization of macromolecular structures in situ with cryogenic electron microscopy. However, only a few large and abundant c...
13814
Reposted by Marten Chaillet
Emil Gustavsson @emilgustavsson.bsky.social · 23/07/2026
Well, that's comforting...
011
Reposted by Marten Chaillet
Hubrecht Institute @hubrechtinstitute.bsky.social · 23/07/2026
Are you excited to redefine our understanding of molecules, cells, tissues and organisms? Then we are looking for you! Applications for the Hubrecht International PhD program (HIPP) are now open and will be accepted until September 15th. Read more here 👉 www.hubrecht.eu/hipp/
034
Reposted by Marten Chaillet
Arthur Oldeman @arthuroldeman.bsky.social · 23/07/2026
Het is niet alleen het gebrek aan regen, maar ook de intense verdamping door de extreme hitte die de droogte in Europa extra opzweept. ⤵️ www.theguardian.com/environment/...
theguardian.com
Climate crisis-driven heat ‘sucking soils dry’ as extreme drought hits Europe
Analysis shows how heatwaves are making atmosphere thirstier, damaging water supplies, food production and power generation
032
Reposted by Marten Chaillet
Mihris Naduthodi @mihrisn.bsky.social · 22/07/2026
(1/16) Nearly two-thirds of ocean carbon fixation flows through a diverse organelle: the pyrenoid. Our new paper maps its 3D architecture in the alga Chlorella and identifies new proteins — expanding the toolkit to engineer this CO2-concentrating machine into crops🧵 #Pyrenoid #CCM #Photosynthesis
13418
Reposted by Marten Chaillet
Arjen Jakobi @cryotud.bsky.social · 20/07/2026
The LocScale 2.0 and SURFER papers are now both published in final form. LocScale 2.0: www.nature.com/articles/s41... SURFER: onlinelibrary.wiley.com/iucr/doi/10.... Led by @alok-bharadwaj.bsky.social with contributions of former MSc/Bsc students Reinier de Bruin and Lotte Veerbeek.
03811
Reposted by Marten Chaillet
Matti Pronker @mfpronker.bsky.social · 20/07/2026
We have a PhD position at Sanquin Research in Amsterdam involving protein engineering, de novo design and antibody development related to bleeding disorders. Please share this with anybody to whom this may be relevant! 🩸 🧬 🧪 🧫 www.sanquin.nl/en/working-a... www.linkedin.com/jobs/view/44...
linkedin.com
Sanquin hiring PhD Candidate: Antibody Therapy for Bleeding Disorders in Amsterdam, North Holland, Netherlands | LinkedIn
Posted 10:24:43 AM. The Division of Research and Lab Services of Sanquin is home to 250 researchers, including over 60…See this and similar jobs on LinkedIn.
178
Reposted by Marten Chaillet
Emily M. Bender @emilymbender.bsky.social · 17/07/2026
For ideas on how to do that, see: buttondown.com/maiht3k/arch... /fin
buttondown.com
How to talk about "AI" without adding to the anthropomorphization
Emily M. Bender and Nanna Inie In our op-ed for Tech Policy Press ("We Need to Talk About How We Talk About 'AI'"), we made the case against the...
25112
Reposted by Marten Chaillet
cryoEM papers @cryoempapers.bsky.social · 17/07/2026
Quinoa: Efficient and Robust CTF Estimation for CryoET Tilt Series www.biorxiv.org/content/10.64898/2026.07.15.738674v1 #cryoEM
0103
Reposted by Marten Chaillet
SAHASA 🐙🪸 @sculptedreef.com · 05/07/2026
Did you know octopuses are technically colorblind? 🌈 One photoreceptor, no color vision, should only see in grayscale. So how are they perfect color matching camouflage artists? 🐙 A thread 🧵 (with sources at the end, of course 😋) 🦑🐡
13370150
Reposted by Marten Chaillet
Daniel Hurdiss @danielhurdiss.bsky.social · 02/07/2026
We are looking for an Assistant or Associate Professor to join us at the @utrechtvirology.bsky.social. Interested in building an independent research programme in a collaborative #virology environment? Please take a look and share with anyone who might be a good fit! www.uu.nl/en/organisat...
uu.nl
Assistant or Associate Professor in Virology
0138
Reposted by Marten Chaillet
Utz Ermel @uermel.bsky.social · 29/06/2026
I had a custom version of this and so far it seemed to work (N=4 Datasets, trained on 50% of the tilt series). Cool to see a native implementation!
111
Marten Chaillet @martenchaillet.bsky.social · 29/06/2026
From v0.2.0 MissAlignment now has an inference mode where you can apply the trained models from one dataset to a new dataset to skip training time. I haven't tested it extensively, so double check if the results look decent 😉 The program calls changed slightly, see here: github.com/warpem/miss-...
github.com
1269
Reposted by Marten Chaillet
Arthur Oldeman @arthuroldeman.bsky.social · 26/06/2026
nos.nl/artikel/2620...
nos.nl
Deze hittegolf was vrijwel onmogelijk zonder klimaatverandering, zeggen wetenschappers
De hittegolf die Europa teistert was zonder klimaatverandering vrijwel onmogelijk geweest. Zelfs in 2003 zou een soortgelijke hittegolf overdag ongeveer 2 graden koeler zijn geweest.
125
Reposted by Marten Chaillet
Katharina Geißler @kgeissler.bsky.social · 26/06/2026
What is the best way to distribute the electron dose across your tilt series in cryo ET? Thanks to Maarten Tuijtel, we finally know --> head over to eLife for the publication! doi.org/10.7554/eLif...
doi.org
Optimising the tilt-increment for in situ cryo-electron tomography
1178
Reposted by Marten Chaillet
Edward T Eng @edwardteng.bsky.social · 25/06/2026
What if learning structural biology felt more like playing a game? Meowtabolism aims to make the structural sciences more interactive, accessible & fun. If you have educational applications let Muyuan (or me) know. store.steampowered.com/app/4045010/... #CryoEM #ScienceOutreach #STEMEducation
0207
Reposted by Marten Chaillet
bioRxiv & medRxiv @biorxiv-medrxiv.bsky.social · 25/06/2026
Community Reviews are science in real time! Check out this new and recent example of open feedback in action: @cb99-lewis.bsky.social et al.’s preprint just got reviewed by a community-organized group through preLights! 📄 doi.org/10.64898/202... (@dbhella.bsky.social) #Preprints #openRxiv
Announcement of a new Community Review on bioRxiv (the preprint server for biology).
A screenshot of the preprint page for “Inhibition of VP2-mediated entry: a potential antiviral strategy to treat or prevent calicivirus disease" by Lewis et al. (doi:10.64898/2026.05.10.723473 ) showing the Community Reviews tab in the Reviews and Context dashboard. A link to a review from preLights is visible and highlighted with an arrow.
The footnote on the image says "bioRxiv and medRxiv are preprint servers of openRxiv."
142
Reposted by Marten Chaillet
Nikolai Slavov @slavov-n.bsky.social · 24/06/2026
Since the 1960s, the genetic code has been used to predict protein sequences from DNA and mRNA sequences. Our @nature.com article demonstrates that these predictions miss thousands of protein sequences present in human tissues. www.nature.com/articles/s41... 1/
28337
Reposted by Marten Chaillet
Caitie McCafferty @computingcaitie.bsky.social · 22/06/2026
I will be hiring at all levels so if you are interested and want to learn more, please get in touch! 📻 ❄️ 🔬 🦠 🧬 #cilia #cryoet #proteomics #exm #protistsonsky
2219
Marten Chaillet @martenchaillet.bsky.social · 19/06/2026
"With these capabilities in place, the question has shifted from 'what do we see?' to 'what have we learned?'." Fully agree, very insightful review from @nanigrotjahn.bsky.social
160
Reposted by Marten Chaillet
Ben Engel @cellarchlab.com · 18/06/2026
OK— so @phaips.vd.st & @florentwaltz.bsky.social have been testing extensively, and it's pretty clear that MissAlignment may be the best thing to happen to #TeamTomo in the last couple years. One issue: we have to re-process all our data again, hopefully for the last time 😅. Congrats and THANK YOU!!
34412
Reposted by Marten Chaillet
Jo Judernatz @jojudernatz.bsky.social · 12/06/2026
Glad to see the work of my PhD on the manchette microtubule now out in @embojournal.org: doi.org/10.1038/s443...
doi.org
SPACA9 and MNMIP1 bridge the seam of spermatid manchette microtubules - The EMBO Journal
The manchette is a transient microtubule (MT)-based structure that is vital for the correct shaping of sperm during spermiogenesis. Throughout spermiogenesis, the manchette retains structural integrity for several days, raising the question of how its MTs are regulated. Here, using cryo-electron tomography of manchettes isolated from rat testes, we find that manchette MT ends are structurally diverse. We show that the MT-binding protein CLASP2 is present throughout the manchette and likely regulates both MT ends. Using cryo-electron microscopy single particle analysis and super-resolution microscopy, we reveal that SPACA9 and MNMIP1 (SH3D21) bind to the seam of manchette MTs from the luminal side. SPACA9 binds to both α- and β-tubulin of protofilament 1 but does not interact directly with protofilament 13, while MNMIP1 binds directly to protofilament 13. MNMIP1 further extends and threads through the MT lattice at the seam. Our study reveals a novel seam MT inner protein complex with a unique binding mode, providing a plausible explanation for MT regulation that maintains manchette integrity over an extended period.
32913
Reposted by Marten Chaillet
Hubrecht Institute @hubrechtinstitute.bsky.social · 09/06/2026
Group leader Miguel Leung has been awarded the Young Scientists Award 2026 from @heinekenprizes.bsky.social . With his group, he investigates the 3D structure of protein complexes, tiny machines at work inside each of our cells. Congratulations, Miguel! Read more: www.hubrecht.eu/heineken-you...
0174
Reposted by Marten Chaillet
Josh Dickerson @joshdcryoem.bsky.social · 06/06/2026
XLPP in practice www.biorxiv.org/content/10.6...
biorxiv.org
053
Reposted by Marten Chaillet
Reese Richardson @reeserichardson.bsky.social · 05/06/2026
The Thermo Fisher situation keeps getting worse. We've now collected 450+ problematic images presented as verification data in TF's antibody catalog. This includes: 🖌️ Dozens more images with duplications or painting 🖨️ Hundreds of blots that all share the same background (behold slideshow below)
18590366
Reposted by Marten Chaillet
Daniel Gorelick @danielgorelick.bsky.social · 03/06/2026
Paying peer reviewers works. Expanded Fast & Fair experiment @biologyopen.bsky.social: • 5.5 vs 37.7 working days to decision with reviews • ~3 vs ~9 reviewer invitations per manuscript • no reduction in editor-assessed review quality • similar acceptance rates www.biorxiv.org/content/10.6...
Scatter plot showing that Fast & Fair peer review reached first decision with reviews much faster than conventional peer review: mean 5.5 versus 37.7 working days. Most Fast & Fair manuscripts met the 7-working-day target, while conventional manuscripts were slower and more variable, up to 116 working days.
8232117
Reposted by Marten Chaillet
Max Renner @maxrenner.bsky.social · 29/05/2026
www.science.org/content/blog...
001