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.
Reposted by Arjen Jakobi
Excited to share what I've been working on with an incredible team! Visualisation of Asgard viruses on cell surfaces and vesicles, and a story of complex viral interactions. Preprint: www.biorxiv.org/content/10.6...
@brendanburns999.bsky.social @belindaferrari.bsky.social @xabivc.bsky.social
@brendanburns999.bsky.social @belindaferrari.bsky.social @xabivc.bsky.social
August 13, 2026 at 10:32 AM
Excited to share what I've been working on with an incredible team! Visualisation of Asgard viruses on cell surfaces and vesicles, and a story of complex viral interactions. Preprint: www.biorxiv.org/content/10.6...
@brendanburns999.bsky.social @belindaferrari.bsky.social @xabivc.bsky.social
@brendanburns999.bsky.social @belindaferrari.bsky.social @xabivc.bsky.social
Reposted by Arjen Jakobi
August issue is out! journals.iucr.org/d/issues/202...
The cover highlights SURFER, a lightweight GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal in cryo-EM maps. More at
doi.org/10.1107/S205...
The cover highlights SURFER, a lightweight GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal in cryo-EM maps. More at
doi.org/10.1107/S205...
August 6, 2026 at 1:53 PM
August issue is out! journals.iucr.org/d/issues/202...
The cover highlights SURFER, a lightweight GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal in cryo-EM maps. More at
doi.org/10.1107/S205...
The cover highlights SURFER, a lightweight GPU-accelerated extension for UCSF ChimeraX that enables rapid semantic differentiation of membrane or membrane-mimic density from macromolecular signal in cryo-EM maps. More at
doi.org/10.1107/S205...
The LocScale 2.0 and SURFER papers are now both published in final form.
LocScale 2.0: www.nature.com/articles/s41...
SURFER: onlinelibrary.wiley.com/iucr/doi/10....
Led by @alok-bharadwaj.bsky.social with contributions of former MSc/Bsc students Reinier de Bruin and Lotte Veerbeek.
LocScale 2.0: www.nature.com/articles/s41...
SURFER: onlinelibrary.wiley.com/iucr/doi/10....
Led by @alok-bharadwaj.bsky.social with contributions of former MSc/Bsc students Reinier de Bruin and Lotte Veerbeek.
July 20, 2026 at 7:34 AM
The LocScale 2.0 and SURFER papers are now both published in final form.
LocScale 2.0: www.nature.com/articles/s41...
SURFER: onlinelibrary.wiley.com/iucr/doi/10....
Led by @alok-bharadwaj.bsky.social with contributions of former MSc/Bsc students Reinier de Bruin and Lotte Veerbeek.
LocScale 2.0: www.nature.com/articles/s41...
SURFER: onlinelibrary.wiley.com/iucr/doi/10....
Led by @alok-bharadwaj.bsky.social with contributions of former MSc/Bsc students Reinier de Bruin and Lotte Veerbeek.
Reposted by Arjen Jakobi
MissAlignment is out!!! Our new software that improves reference-free tilt series alignment by mimicking human intuition. Check out Dimitry's beautiful thread for a quick summary!
And the preprint for more details: www.biorxiv.org/content/10.6...
The program: github.com/warpem/miss-...
And the preprint for more details: www.biorxiv.org/content/10.6...
The program: github.com/warpem/miss-...
May 3, 2026 at 8:17 AM
MissAlignment is out!!! Our new software that improves reference-free tilt series alignment by mimicking human intuition. Check out Dimitry's beautiful thread for a quick summary!
And the preprint for more details: www.biorxiv.org/content/10.6...
The program: github.com/warpem/miss-...
And the preprint for more details: www.biorxiv.org/content/10.6...
The program: github.com/warpem/miss-...
Reposted by Arjen Jakobi
Join #EMBOCryoEM to get a comprehensive foundation in advanced single-particle and cellular tomography techniques – we'll cover the entire workflow from sample preparation to data collection and image processing.
https://s.embl.org/cry26-01-bl
Apply by: 11 May 2026
@embo.org
https://s.embl.org/cry26-01-bl
Apply by: 11 May 2026
@embo.org
March 11, 2026 at 5:02 PM
Join #EMBOCryoEM to get a comprehensive foundation in advanced single-particle and cellular tomography techniques – we'll cover the entire workflow from sample preparation to data collection and image processing.
https://s.embl.org/cry26-01-bl
Apply by: 11 May 2026
@embo.org
https://s.embl.org/cry26-01-bl
Apply by: 11 May 2026
@embo.org
Still time to submit your abstracts for IMC21!
Many great sessions for anyone interested in (electron) microscopy. Please consider joining us in Liverpool and submit your abstract at www.imc21.org.uk.
Deadline for abstract submission is 20 March 2026.
Many great sessions for anyone interested in (electron) microscopy. Please consider joining us in Liverpool and submit your abstract at www.imc21.org.uk.
Deadline for abstract submission is 20 March 2026.
March 12, 2026 at 7:45 PM
Still time to submit your abstracts for IMC21!
Many great sessions for anyone interested in (electron) microscopy. Please consider joining us in Liverpool and submit your abstract at www.imc21.org.uk.
Deadline for abstract submission is 20 March 2026.
Many great sessions for anyone interested in (electron) microscopy. Please consider joining us in Liverpool and submit your abstract at www.imc21.org.uk.
Deadline for abstract submission is 20 March 2026.
New preprint by @alok-bharadwaj.bsky.social explaining the workings of SURFER, a simple tool to segment membrane, micelle or nanodisc densities in cryoEM maps.
Try it via the @chimerax.ucsf.edu ToolShed:
cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Despite LocScale in the name, it works on any map.
Try it via the @chimerax.ucsf.edu ToolShed:
cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Despite LocScale in the name, it works on any map.
Interactive segmentation of membrane and membrane mimic densities in cryo-EM maps www.biorxiv.org/content/10.64898/2026.02.25.707988v1 #cryoem
February 27, 2026 at 12:17 PM
New preprint by @alok-bharadwaj.bsky.social explaining the workings of SURFER, a simple tool to segment membrane, micelle or nanodisc densities in cryoEM maps.
Try it via the @chimerax.ucsf.edu ToolShed:
cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Despite LocScale in the name, it works on any map.
Try it via the @chimerax.ucsf.edu ToolShed:
cxtoolshed.rbvi.ucsf.edu/apps/chimera...
Despite LocScale in the name, it works on any map.
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/...
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!
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