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
Please share🙏:
Our lab opens 2 PhD positions to investigate fungi's evolution: #Barcelona
Wet lab in Biochemistry/Structural Biology of cryo-tolerant fungi
www.upf.edu/documents/d/...
Computational in Physical Chemistry of cellular processes under extrem environments
www.upf.edu/documents/d/...
Our lab opens 2 PhD positions to investigate fungi's evolution: #Barcelona
Wet lab in Biochemistry/Structural Biology of cryo-tolerant fungi
www.upf.edu/documents/d/...
Computational in Physical Chemistry of cellular processes under extrem environments
www.upf.edu/documents/d/...
www.upf.edu
January 26, 2026 at 11:53 AM
Please share🙏:
Our lab opens 2 PhD positions to investigate fungi's evolution: #Barcelona
Wet lab in Biochemistry/Structural Biology of cryo-tolerant fungi
www.upf.edu/documents/d/...
Computational in Physical Chemistry of cellular processes under extrem environments
www.upf.edu/documents/d/...
Our lab opens 2 PhD positions to investigate fungi's evolution: #Barcelona
Wet lab in Biochemistry/Structural Biology of cryo-tolerant fungi
www.upf.edu/documents/d/...
Computational in Physical Chemistry of cellular processes under extrem environments
www.upf.edu/documents/d/...
How can one be scooped if one is the first to publish a preprint of a new discovery? 🤔
It is sad that we appear to consider the date of a journal stamp a more important sign of priority than the actual date of reporting your discovery to the scientific community.
It is sad that we appear to consider the date of a journal stamp a more important sign of priority than the actual date of reporting your discovery to the scientific community.
January 12, 2026 at 3:35 PM
How can one be scooped if one is the first to publish a preprint of a new discovery? 🤔
It is sad that we appear to consider the date of a journal stamp a more important sign of priority than the actual date of reporting your discovery to the scientific community.
It is sad that we appear to consider the date of a journal stamp a more important sign of priority than the actual date of reporting your discovery to the scientific community.
Congrats Kiarash! 👏🏻
December 9, 2025 at 3:41 PM
Congrats Kiarash! 👏🏻
Reposted by Arjen Jakobi
New preprint from the lab!!🎉
We show that Asgard archaea ESCRT-III proteins can trigger membrane fission and reveal its molecular mechanism, offering clues to how these cells may have built internal compartments. But do these organisms even have these compartments?
www.biorxiv.org/content/10.1...
We show that Asgard archaea ESCRT-III proteins can trigger membrane fission and reveal its molecular mechanism, offering clues to how these cells may have built internal compartments. But do these organisms even have these compartments?
www.biorxiv.org/content/10.1...
Molecular basis for cellular compartmentalization by an ancient membrane fission mechanism
The emergence of cell compartmentalization depends on membrane fission to create the endomembrane compartments. In eukaryotes, membrane fission is commonly executed by ESCRT-III, a protein complex con...
www.biorxiv.org
December 1, 2025 at 9:09 AM
New preprint from the lab!!🎉
We show that Asgard archaea ESCRT-III proteins can trigger membrane fission and reveal its molecular mechanism, offering clues to how these cells may have built internal compartments. But do these organisms even have these compartments?
www.biorxiv.org/content/10.1...
We show that Asgard archaea ESCRT-III proteins can trigger membrane fission and reveal its molecular mechanism, offering clues to how these cells may have built internal compartments. But do these organisms even have these compartments?
www.biorxiv.org/content/10.1...
CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!
Giles and Burnley: Ten years of the CCP-EM Spring Symposium ##Cryoem##ElectronCryoMicroscopy##CCPEM... ##IUCrhttps://journals.iucr.org/paper?S2059798325010496
Ten years of the CCP-EM Spring Symposium
This article reviews the growth over the last ten years of the CCP-EM Spring Symposium. The conference is now established as a popular meeting for practitioners of life-science cryoEM and highlights new methods and exemplar applications.
journals.iucr.org
November 29, 2025 at 7:06 PM
CCP-EM Spring Symposia have become key venues for methods-focused cryo-EM advances and an annual fixture for structural biologists worldwide. Their early adoption of online talks set the bar for inclusive meetings, and even as they have grown over the years, they have kept a family feel. Kudos!
Not sure if this is what you are looking for, but in zenodo you can specify parent repositories as “related works” including the DOI to the original repository. This way you could link a subset of data (a particle stack in your case) back to its original source (the EMPIAR deposition).
September 21, 2025 at 5:14 PM
Not sure if this is what you are looking for, but in zenodo you can specify parent repositories as “related works” including the DOI to the original repository. This way you could link a subset of data (a particle stack in your case) back to its original source (the EMPIAR deposition).
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!
Where is the backpack? 😉
September 5, 2025 at 10:01 PM
Where is the backpack? 😉
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.
Welcome to Delft, Georgios!
June 23, 2025 at 7:02 PM
Welcome to Delft, Georgios!
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
Uups, our bad. Please try again (cryotud.github.io/locscale-sur...); it should work now.
Installation - LocScale-SURFER
Documentation for LocScale-SURFER
cryotud.github.io
May 23, 2025 at 3:40 AM
Uups, our bad. Please try again (cryotud.github.io/locscale-sur...); it should work now.
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
This is work led by @alok-bharadwaj.bsky.social with contributions by Reinier de Bruin and Lotte Verbeek.
Preprint(s) with detailed description underway. In the menatime we are happy for any feedback.
Preprint(s) with detailed description underway. In the menatime we are happy for any feedback.
May 22, 2025 at 10:10 AM
This is work led by @alok-bharadwaj.bsky.social with contributions by Reinier de Bruin and Lotte Verbeek.
Preprint(s) with detailed description underway. In the menatime we are happy for any feedback.
Preprint(s) with detailed description underway. In the menatime we are happy for any feedback.
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 22, 2025 at 10:10 AM
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...
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
Krijg je ook borrelnootjes bij je bier? 😉
March 18, 2025 at 7:03 PM
Krijg je ook borrelnootjes bij je bier? 😉
Klopt! Ik had er tot voor kort niet eerder van gehoord maar heb onlangs een interessante lezing bijgewoond in het Green Village van de TU. Er is ook een interessant verslag van Deltares: www.deltares.nl/expertise/pr...
December 31, 2024 at 8:08 PM
Klopt! Ik had er tot voor kort niet eerder van gehoord maar heb onlangs een interessante lezing bijgewoond in het Green Village van de TU. Er is ook een interessant verslag van Deltares: www.deltares.nl/expertise/pr...
Goed voornemen, Cees! Ik gebruik sinds enkele jaren co2offset.atmosfair.de/co2offset#/f... om mijn vluchten te compenseren. Dit is enkele malen door de Duitse en Zwitserse consumentenbond als meest betrouwbare/transparante berekening uitgeroepen.
co2offset.atmosfair.de
December 31, 2024 at 7:46 PM
Goed voornemen, Cees! Ik gebruik sinds enkele jaren co2offset.atmosfair.de/co2offset#/f... om mijn vluchten te compenseren. Dit is enkele malen door de Duitse en Zwitserse consumentenbond als meest betrouwbare/transparante berekening uitgeroepen.
In this project you will collaborate closely with the groups of @ceesdekker.bsky.social, @cg-martini.bsky.social and @ettema.bsky.social.
Many other interesting PhD/PD openings within the consortium here: www.evolf.life/join-us
Many other interesting PhD/PD openings within the consortium here: www.evolf.life/join-us
Join us! — EVOLF
www.evolf.life
December 10, 2024 at 3:08 PM
In this project you will collaborate closely with the groups of @ceesdekker.bsky.social, @cg-martini.bsky.social and @ettema.bsky.social.
Many other interesting PhD/PD openings within the consortium here: www.evolf.life/join-us
Many other interesting PhD/PD openings within the consortium here: www.evolf.life/join-us