iiinova — where your digital self keeps evolving

Arjen Jakobi @cryotud.bsky.social · 06/10/2026

State-selective nanobodies to probe Guanylate-binding protein coat assembly and function Lennart & Tanja identified and validated conformation-selective nanobodies to probe and interfere w/ GBP coat formation on intracellular bacteria. Led by @lpagani.bsky.social. www.biorxiv.org/content/10.6...

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Arjen Jakobi @cryotud.bsky.social · 22/09/2026

If you would have not said otherwise I would have thought this is a beautiful example of µSOLIST (MicroSurgical On-Lamella In-situ Sample Takeout) 😉

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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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Arjen Jakobi @cryotud.bsky.social · 26/02/2026

Your thinking is too parallelised, Sjors 😅

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Arjen Jakobi @cryotud.bsky.social · 15/02/2026

Great way to further increase the economic divide.

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Arjen Jakobi @cryotud.bsky.social · 11/02/2026

Completely with you, but BioRxiv versioning is not unlike Git assuming most recent version is ‘most correct’ (also in Git older versions kept & crawlable). As such BioRxiv in principle already allows having a ‘living document’. I can see though how explicitly tracking changes as in Git adds value.

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Arjen Jakobi @cryotud.bsky.social · 11/02/2026

Does BioRxix not already allow you/us to do exactly that? Indexed repository, version-controlled updates, transparent options for peer feedback and author replies. Each version can have updated author contributions to document individual contributions.

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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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Arjen Jakobi @cryotud.bsky.social · 12/01/2026

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.

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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 · 21/09/2025

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).

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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 · 23/05/2025

Uups, our bad. Please try again (cryotud.github.io/locscale-sur...); it should work now.

cryotud.github.io

Installation - LocScale-SURFER

Documentation for LocScale-SURFER

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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

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.

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

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...

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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 · 18/03/2025

Krijg je ook borrelnootjes bij je bier? 😉

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Arjen Jakobi @cryotud.bsky.social · 31/12/2024

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...

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Arjen Jakobi @cryotud.bsky.social · 31/12/2024

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

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

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

evolf.life

Join us! — EVOLF

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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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Arjen Jakobi @cryotud.bsky.social · 25/11/2024

Maya, Jan and I had a great time with you all! So many exciting projects - we are looking forward to seeing the results pop up here in the future 🙂

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Arjen Jakobi @cryotud.bsky.social · 23/11/2024

6 hours of HADDOCKing and still going strong! ⛄️

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