iiinova — where your digital self keeps evolving

Reposted by Arjen Jakobi

Julia Meltzer @juliameltzer.bsky.social · 13/08/2026

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

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Reposted by Arjen Jakobi

Structural Biology @actacrystd.iucr.org · 06/08/2026

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...

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Arjen Jakobi @cryotud.bsky.social · 20/07/2026

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.

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Reposted by Arjen Jakobi

Marten Chaillet @martenchaillet.bsky.social · 03/05/2026

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-...

biorxiv.org

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Reposted by Arjen Jakobi

EMBL Events @events.embl.org · 11/03/2026

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. s.embl.org/cry26-01-bl Apply by: 11 May 2026 @embo.org

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Arjen Jakobi @cryotud.bsky.social · 12/03/2026

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.

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Arjen Jakobi @cryotud.bsky.social · 27/02/2026

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.

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Reposted by Arjen Jakobi

Gallego Lab @gallegolab.bsky.social · 26/01/2026

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/...

upf.edu

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Reposted by Arjen Jakobi

Javier Espadas @javierespadas.bsky.social · 01/12/2025

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...

biorxiv.org

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...

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Arjen Jakobi @cryotud.bsky.social · 29/11/2025

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!

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Arjen Jakobi @cryotud.bsky.social · 15/09/2025

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.

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Arjen Jakobi @cryotud.bsky.social · 08/09/2025

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!

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Arjen Jakobi @cryotud.bsky.social · 26/06/2025

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.

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Reposted by Arjen Jakobi

Alister Burt @alisterburt.bsky.social · 30/05/2025

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!

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Arjen Jakobi @cryotud.bsky.social · 26/05/2025

LocScale-SURFER is now also available for quick install via the ChimeraX toolshed: cxtoolshed.rbvi.ucsf.edu

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Arjen Jakobi @cryotud.bsky.social · 22/05/2025

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

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Arjen Jakobi @cryotud.bsky.social · 22/05/2025

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/

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Arjen Jakobi @cryotud.bsky.social · 31/03/2025

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

cell.com

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...

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Arjen Jakobi @cryotud.bsky.social · 10/12/2024

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.

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