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)
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).
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.
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.
Thank you, Michaela!
April 12, 2025 at 12:27 PM
Thank you, Michaela!