Arjen Jakobi
@cryotud.bsky.social
Kavli Institute of Nanoscience Delft |
Associate Professor @Delft University of Technology | https://cryoem.tudelft.nl
Interested in #cryoEM & #cryoET methods, #membranes, intracellular/innate #immunity.
Associate Professor @Delft University of Technology | https://cryoem.tudelft.nl
Interested in #cryoEM & #cryoET methods, #membranes, intracellular/innate #immunity.
Pinned
Arjen Jakobi
@cryotud.bsky.social
· May 22
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
We finally wrote up the paper for LocScale-2.0.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
September 15, 2025 at 7:39 AM
We finally wrote up the paper for LocScale-2.0.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
edu.nl/pvhxv
Please try it out. LocScale is evolving & we are actively building in new features and improvements. Your feedback will help us shape the next steps.
Code: cryotud.github.io/locscale/
Work by @alok-bharadwaj.bsky.social and Reinier.
Together with colleagues at the Dept. of Microsystems Engineering, we are looking for a PhD student to develop methods for femtoliter-scale sample dispensing in cryoEM sample preparation.
edu.nl/h436k
If you like interdisciplinary research & fascinating physics at ultrasmall scales, please apply!
edu.nl/h436k
If you like interdisciplinary research & fascinating physics at ultrasmall scales, please apply!
September 8, 2025 at 1:48 PM
Together with colleagues at the Dept. of Microsystems Engineering, we are looking for a PhD student to develop methods for femtoliter-scale sample dispensing in cryoEM sample preparation.
edu.nl/h436k
If you like interdisciplinary research & fascinating physics at ultrasmall scales, please apply!
edu.nl/h436k
If you like interdisciplinary research & fascinating physics at ultrasmall scales, please apply!
Beautiful structures and mechanistic insight into endosomal lipid transfer!
Also a good example showcasing how contextualised map optimisation may be helpful in visualisation/interpretation of complex biological assemblies.
Also a good example showcasing how contextualised map optimisation may be helpful in visualisation/interpretation of complex biological assemblies.
June 26, 2025 at 8:30 PM
Beautiful structures and mechanistic insight into endosomal lipid transfer!
Also a good example showcasing how contextualised map optimisation may be helpful in visualisation/interpretation of complex biological assemblies.
Also a good example showcasing how contextualised map optimisation may be helpful in visualisation/interpretation of complex biological assemblies.
Reposted by Arjen Jakobi
spent some time this evening updating the teamtomo.org site - if you're interested in cryo-EM + Python you might want to take a look around!
May 30, 2025 at 8:29 AM
spent some time this evening updating the teamtomo.org site - if you're interested in cryo-EM + Python you might want to take a look around!
LocScale-SURFER is now also available for quick install via the ChimeraX toolshed:
cxtoolshed.rbvi.ucsf.edu
cxtoolshed.rbvi.ucsf.edu
LocScale-2.0 is deliberately designed to optimise contrast for both high-resolution detail & weak contextual densities such as membrane/micelle or flexible/low-occupancy regions
LocScale-SURFER is a ChimeraX plugin aiding w/ visualisation of contextual structure.
cryotud.github.io/locscale-sur...
LocScale-SURFER is a ChimeraX plugin aiding w/ visualisation of contextual structure.
cryotud.github.io/locscale-sur...
May 26, 2025 at 11:10 AM
LocScale-SURFER is now also available for quick install via the ChimeraX toolshed:
cxtoolshed.rbvi.ucsf.edu
cxtoolshed.rbvi.ucsf.edu
Want to try LocScale-2.0 without installing locally?
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
May 22, 2025 at 11:05 AM
Want to try LocScale-2.0 without installing locally?
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
Check out ColabScale: just upload your maps or enter your favourite EMDB ID and run LocScale-2.0 in the cloud.
edu.nl/ur3ge
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
May 22, 2025 at 10:10 AM
We are happy to release LocScale2.0: a tool for context-aware, confidence-weighted cryoEM map optimisation.
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
Taking two half maps as input, LcoScale-2.0 produces feature-enhanced maps along with a robust confidence score that guides objective map interpretation.
cryotud.github.io/locscale/
CEMOVIS revisited! 🙂
In-Situ High-Resolution Cryo-EM Reconstructions from CEMOVIS https://www.biorxiv.org/content/10.1101/2025.03.29.646093v1
March 31, 2025 at 10:45 AM
CEMOVIS revisited! 🙂
Daan & Radim extended our q4STEM method to lamella fabrication from frozen-hydrated cells, implemented RLM thin-film interference (inspired by @mgflast.bsky.social) on a 3-beam coincident system, and show how live thickness monitoring allows automated milling of high-quality lamella: edu.nl/f9fn3
Thickness- and quality-controlled fabrication of fluorescence-targeted frozen-hydrated lamellae
Boltje et al. demonstrate a workflow to prepare thin cellular sections in a thickness-controlled
fashion using an integrated light microscope coincident with electron and ion beams.
This reduces compl...
www.cell.com
March 31, 2025 at 8:16 AM
Daan & Radim extended our q4STEM method to lamella fabrication from frozen-hydrated cells, implemented RLM thin-film interference (inspired by @mgflast.bsky.social) on a 3-beam coincident system, and show how live thickness monitoring allows automated milling of high-quality lamella: edu.nl/f9fn3
We have an opening for a 4 yr PhD interested in membrane remodelling and cryo-EM/ET of a minimal cell division machinery: edu.nl/bukan
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.
December 10, 2024 at 2:53 PM
We have an opening for a 4 yr PhD interested in membrane remodelling and cryo-EM/ET of a minimal cell division machinery: edu.nl/bukan
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.
You will be part of the EVOLF consortium in which 30 leading biochemists/biophysicists work together to explore if and how we can build autonomous synthetic cells.
Really looking forward to welcoming & meeting the participants of our #EMBOStructBio course this morning!
Many of our speakers/tutors are here:
@moalquraishi.bsky.social
@sykhalid.bsky.social
@ezgikaraca.bsky.social
@amjjbonvin.bsky.social
@gchojnowski.bsky.social
@drmelissagraewert.bsky.social
Many of our speakers/tutors are here:
@moalquraishi.bsky.social
@sykhalid.bsky.social
@ezgikaraca.bsky.social
@amjjbonvin.bsky.social
@gchojnowski.bsky.social
@drmelissagraewert.bsky.social
November 18, 2024 at 7:07 AM
Really looking forward to welcoming & meeting the participants of our #EMBOStructBio course this morning!
Many of our speakers/tutors are here:
@moalquraishi.bsky.social
@sykhalid.bsky.social
@ezgikaraca.bsky.social
@amjjbonvin.bsky.social
@gchojnowski.bsky.social
@drmelissagraewert.bsky.social
Many of our speakers/tutors are here:
@moalquraishi.bsky.social
@sykhalid.bsky.social
@ezgikaraca.bsky.social
@amjjbonvin.bsky.social
@gchojnowski.bsky.social
@drmelissagraewert.bsky.social