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/
Reposted by Arjen Jakobi
We will continue our joint investment with TU Delft in the Kavli Institute of Nanoscience Delft (KIND) for the next decade. Cynthia Friend (TKF) and Tim van der Hagen (TU Delft) have signed an agreement that will enable the development of a new, exploratory research program.
🔗https://bit.ly/4ijBSoZ
🔗https://bit.ly/4ijBSoZ
The Kavli Foundation and TU Delft's Joint Nanoscience Investment
The Kavli Foundation and TU Delft have committed to additional support for the Kavli Institute of Nanoscience Delft (KIND) for the next decade
bit.ly
November 26, 2025 at 4:24 PM
We will continue our joint investment with TU Delft in the Kavli Institute of Nanoscience Delft (KIND) for the next decade. Cynthia Friend (TKF) and Tim van der Hagen (TU Delft) have signed an agreement that will enable the development of a new, exploratory research program.
🔗https://bit.ly/4ijBSoZ
🔗https://bit.ly/4ijBSoZ
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