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Arjen Jakobi @cryotud.bsky.social · 17d

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 · 23d

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.

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/

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Arjen Jakobi @cryotud.bsky.social · Sep 8

Good luck!

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Arjen Jakobi @cryotud.bsky.social · Sep 8

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 · Sep 5

Where is the backpack? 😉

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Arjen Jakobi @cryotud.bsky.social · Jun 26

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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Arjen Jakobi @cryotud.bsky.social · Jun 23

Welcome to Delft, Georgios!

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Reposted by Arjen Jakobi

Alister Burt @alisterburt.bsky.social · May 30

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 · May 26

LocScale-SURFER is now also available for quick install via the ChimeraX toolshed:

cxtoolshed.rbvi.ucsf.edu

Arjen Jakobi @cryotud.bsky.social · May 22

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 · May 23

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

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Arjen Jakobi @cryotud.bsky.social · May 22

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 · May 22

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 · May 22

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 · 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/

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Arjen Jakobi @cryotud.bsky.social · Mar 31

CEMOVIS revisited! 🙂

bioRxiv Biophysics @biorxiv-biophys.bsky.social · Mar 31

In-Situ High-Resolution Cryo-EM Reconstructions from CEMOVIS https://www.biorxiv.org/content/10.1101/2025.03.29.646093v1

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Arjen Jakobi @cryotud.bsky.social · Mar 31

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

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Arjen Jakobi @cryotud.bsky.social · Mar 18

Krijg je ook borrelnootjes bij je bier? 😉

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Arjen Jakobi @cryotud.bsky.social · Dec 31

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 · Dec 31

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 · Dec 10

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

Join us! — EVOLF

www.evolf.life

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Arjen Jakobi @cryotud.bsky.social · Dec 10

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 · Nov 25

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 · Nov 23

6 hours of HADDOCKing and still going strong! ⛄️

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Arjen Jakobi @cryotud.bsky.social · Nov 18

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

https://www.embl.org/about/info/course-and-conference-office/events/stb24-01/#vf-tabs__section-programme

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