Jan Philipp Kreysing
@jpkreysing.bsky.social
in cell cryo-ET and image processing enthusiast #teamtomo
PhD student in Martin Beck's group (@becklab.bsky.social) at the Max Planck Institute of Biophysics (@mpibp.bsky.social)
PhD student in Martin Beck's group (@becklab.bsky.social) at the Max Planck Institute of Biophysics (@mpibp.bsky.social)
Pinned
New preprint on 3D heterochromatin architecture in human cells! Great collab with @sergiocruzleon.bsky.social & @johannesbetz.bsky.social from @hummerlab.bsky.social, @marinalusic.bsky.social & the Turoňová lab. Many thanks to my supervisor @becklab.bsky.social. bioRxiv: tinyurl.com/3a74uanv 🧵👇
Reposted by 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
February 12, 2026 at 1:21 PM
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
Reposted by Jan Philipp Kreysing
We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉
January 13, 2026 at 2:39 PM
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.
It’s out! Using cryo-ET in Dicty cells, we take a fresh in situ look at vaults. Surprisingly, we uncover vaults associated with ER and NE membranes, and find that many vaults enclose ribosomes in defined orientations, opening new avenues to their cellular function! www.biorxiv.org/lookup/conte...
December 16, 2025 at 9:42 AM
#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)
December 12, 2025 at 5:16 PM
That is of course what I tried... With both 3D subtomos from Warp1 (Desktop) and Warp2 (unix)
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/...
github.com/3dem/relion/...
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...
github.com
December 12, 2025 at 4:38 PM
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/...
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.
December 12, 2025 at 3:38 PM
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).
December 12, 2025 at 11:44 AM
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).
December 12, 2025 at 11:43 AM
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).
Reposted by Jan Philipp Kreysing
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
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
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...
link.springer.com
December 4, 2025 at 1:58 PM
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
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.
Just published! We share an open-source workflow to measure membrane thickness from tomograms, including a tutorial with 3D visualizations. We analyze thickness variations across organelles and reflect on where to define a membrane boundary. @becklab.bsky.social #teamtomo rupress.org/jcb/article/...
November 6, 2025 at 8:37 AM
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.
Reposted by Jan Philipp Kreysing
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
🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
📍 Frankfurt | 📆 April 12–20, 2026
October 23, 2025 at 9:10 AM
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
🔗 Apply by Dec 8, 2025: meetings.embo.org/event/26-in-...
📍 Frankfurt | 📆 April 12–20, 2026
Reposted by Jan Philipp Kreysing
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🍧
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...
www.biorxiv.org
October 23, 2025 at 11:13 AM
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.
October 23, 2025 at 11:29 AM
Congrats, this is really cool! I already tried it on one of my favorite tomos and the result looks fantastic.
Reposted by Jan Philipp Kreysing
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
www.biorxiv.org/content/10.1...
#teamtomo
October 15, 2025 at 6:26 AM
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
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.
October 15, 2025 at 6:51 AM
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.
October 10, 2025 at 10:35 AM
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.
❓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...
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.
www.nature.com
October 10, 2025 at 10:35 AM
❓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...
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...
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...
www.biorxiv.org
August 23, 2025 at 9:18 AM
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...
Reposted by Jan Philipp Kreysing
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-...
August 18, 2025 at 11:29 AM
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-...
Reposted by Jan Philipp Kreysing
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...
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…
www.sciencedirect.com
July 25, 2025 at 10:14 AM
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...
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...
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
July 23, 2025 at 8:14 AM
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...
www.biorxiv.org/content/10.1...
Reposted by Jan Philipp Kreysing
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 🔬🧪
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 🔬🧪
Welcome to TomoGuide
A step-by-step Cryo-ET guide
tomoguide.github.io
May 6, 2025 at 4:27 PM
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 🔬🧪
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 🔬🧪
Reposted by Jan Philipp Kreysing
🦠🧠 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
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
April 25, 2025 at 7:28 AM
🦠🧠 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
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...
www.biorxiv.org/content/10.1...
www.biorxiv.org
April 12, 2025 at 7:29 PM
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...
www.biorxiv.org/content/10.1...
Thank you, Michaela!
April 12, 2025 at 12:27 PM
Thank you, Michaela!