Jan Philipp Kreysing

Ready to TANGO? 💃 In our new publication, Beata Turoňová & Markus Schreiber (@ms314.bsky.social, @becklab.bsky.social) present TANGO: the first cryoET framework to analyze the relation between particle positions and orientations 🪩 All in a single user-friendly package! #CryoET #OpenScience

We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉

#teamtomo strikes again! Check out our new preprint on the enigmatic vault and its newly discovered association with membranes in situ.

That is of course what I tried... With both 3D subtomos from Warp1 (Desktop) and Warp2 (unix)

unexpectedly small, yet non-zero sigma2 value · Issue #1191 · 3dem/relion 3D refinement with subvolumes gives the error cited. Subvolumes extracted from WarpTools 2.0.0/dev28. reconstruct_particle gives a very nice reconstruction. mpirun --np 5 --oversubscribe relion_ref...

Interesting! They haven't worked for me at all. This is the exchange on the git repo that I mentioned where it is stated these 3D warp subtomos cannot be used in relion5.
github.com/3dem/relion/...

So, for my test case the pseudosubtomos (3D option in Relion5) already provided a better map than the 2D stacks but still not as detailed and complete as warp 3D subtomos in Relion3.

Can you use 3D subtomos in Relion5? I recall a message from Sjors at some point that this is no longer supported which matches my experience (from maybe 6 months ago).

I currently still use 3D warp subtomos in Relion3 because either version of 2D input data (pseudosubtomos or 2D stacks) give considerably worse results in Relion5 (tested for small particles).

Lenacapavir-induced capsid damage uncovers HIV-1 genomes emanating from nuclear speckles - The EMBO Journal Following cell entry, HIV-1 capsids enter the nucleus by passage through nuclear pores and reach nuclear speckles with subsequent uncoating of the reverse-transcribed genome and its integration into s...

New paper out!

How can we force HIV genomes out of their capsid shells and what can we learn about HIV biology doing so?

Hint: capsid inhibitors actively re-route nuclear HIV complexes, and expose genomes via intriguing structural effects!
open access:
link.springer.com/article/10.1...
read below

Exciting new paper from my colleague @deglushk.bsky.social in the @becklab.bsky.social! It introduces a fast, robust tool for measuring membrane thickness in tomograms #TeamTomo.

Orange and green poster of the In-situ structural biology by Cryo-FIB and Cryo-ET in Frankfurt am Main, with EMBO logo. The poster promotes childcare grants, travel grants and that this is a sustainable event.

Have you registered to the next EMBO Practical Course on In-situ structural biology by Cryo-FIB and Cryo-ET? 🧊 Join us in Frankfurt for hands-on training on cryo-techniques and networking with experts!

🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
📍 Frankfurt | 📆 April 12–20, 2026

Icecream: High-Fidelity Equivariant Cryo-Electron Tomography Cryo-electron tomography (cryo-ET) visualizes 3D cellular architecture in near-native states. Recent deep-learning methods (CryoCARE, IsoNet, DeepDeWedge, CryoLithe) improve denoising and artifact cor...

Our colleagues Vinith Kishore and Valentin Debarnot from the @ivandokmanic.bsky.social lab have come up with an amazing deep learning tool for denoising and filling the missing wedge in #cryoET data. I'm pleased to introduce Icecream🍧

Congrats, this is really cool! I already tried it on one of my favorite tomos and the result looks fantastic.

Figure 1 from the preprint

Check out our preprint! With new molecular mechanisms, 140 subtomogram averages, and ~600 annotated cells under different conditions, we @embl.org were able to describe bacterial populations with in-cell #cryoET. And there’s a surprise at the end 🕵️

www.biorxiv.org/content/10.1...
#teamtomo

Great work! So cool to see how far the field has already advanced in just a few years.

The software acts as a computational shortcut to denser sampling, which is often not feasible due to radiation damage limits. → Better angular sampling, sharper segmentation, improved particle localization.

cryoTIGER: deep-learning based tilt interpolation generator for enhanced reconstruction in cryo electron tomography - Communications Biology Deep learning-based interpolation using cryoTIGER enhances angular sampling in cryoET, improving 3D reconstructions, particle localization, and structural recovery without increasing electron dose.

❓What if you could peek between your tilt series ❓ We are proud to introduce cryoTIGER -- deep-learning based tilt interpolation for enhanced reconstruction in cryo-ET. A great collaboration between Turoňová lab, @becklab.bsky.social, @hummerlab.bsky.social #teamtomo www.nature.com/articles/s42...

Optimal tilt-increment for cryo-ET Cryo-electron tomography (cryo-ET) enables high-resolution, three-dimensional imaging of cellular structures in their native, frozen state. However, image quality is limited by a trade-off between ang...

More great cryo-ET benchmarking work from my colleagues Maarten Tuijtel, Tomáš Majtner, Beata Turoňová, & @becklab.bsky.social: Systematic study of how tilt increment choice affects downstream TM & STA. Preprint has the optimally balanced tilt increment. #TeamTomo www.biorxiv.org/content/10.1...

We’re hosting the @embo.org Practical Course on In-situ structural biology by CryoFIB and CryoET in April 2026! 🧬❄️ You can expect hands-on training, cutting-edge methods, and a chance to work alongside leading experts in structural biology. 🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...

Automated removal of corrupted tilts in cryo-electron tomography Cryo-electron tomography (cryo-ET) enables the visualization of macromolecular structures in their near-native cellular environment. However, acquired…

AI for Cryo-ET 🌟 Our new paper presents a deep-learning framework that cleans up faulty tilt series in a more automated, precise and powerful way! 💪 Read more here: www.sciencedirect.com/science/arti...

Twist and Scout: Analysis and Curation of Particles in Cryo-Electron Tomography Using TANGO Cryo-electron tomography (cryo-ET) enables the visualization of cellular structures in near-native environments, but its potential for spatial analysis has been underutilized due to a lack of versatil...

New from my colleagues Markus Schreiber & Beata Turoňová: TANGO, an #opensource tool for more holistic spatial analysis of cryo-ET particles. It can clean or cluster particles, analyze lattices, and identify patterns. #TeamTomo
www.biorxiv.org/content/10.1...

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 🔬🧪

🦠🧠 MemBrain update! 🧠🦠
We’ve updated our preprint! It now covers the full MemBrain v2 pipeline for end-to-end membrane analysis in #CryoET: segmentation, particle picking, and spatial statistics.
🔗 Preprint: doi.org/10.1101/2024...
🔗 Code: github.com/CellArchLab/...
🧵(1/6) #TeamTomo

Looking for a tool to measure membrane thicknesses in tomograms (#TeamTomo)? Or curious about thickness differences within and across organelles? Check out my fellow @becklab.bsky.social PhD student @deglushk.bsky.social's excellent preprint:
www.biorxiv.org/content/10.1...

Thank you, Michaela!

Thanks!

Finally, we selected a representative fragment of chromatin, modelled it including histone tails, and performed all-atom MD simulations on it. The simulation showed an overall stable molecular arrangement with H4 tails mediating a stacking interaction.

Examining the 3D heterochromatin organization, we found a 37 nm edge-to-edge distance between connected nucleosomes and two trinucleosome arrangements: a smaller stacked population and a larger one with longer nucleosome distances, suggesting no strict long-range order for native heterochromatin.

We then used a physics-based model to predict DNA linkers between the nucleosomes obtained by cryo-ET. This allowed us to visualize kbp-long chromatin fragments from inside human cells.

Meta-analysis on the nucleosome coordinates revealed dense chromatin patches with local concentrations exceeding 200 mg/mL and showed native chromatin behaves like an intermediate between liquid and gas with some short-range order.