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.
Join a young lab with great ideas and a kind mentor!
Matti Pronker@mfpronker.bsky.social · 2w agoWe have a PhD position at Sanquin Research in Amsterdam involving protein engineering, de novo design and antibody development related to bleeding disorders. Please share this with anybody to whom this may be relevant! 🩸 🧬 🧪 🧫 www.sanquin.nl/en/working-a... www.linkedin.com/jobs/view/44...
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.
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
Dimitry Tegunov@dtegunov.bsky.social · 3mo agoWe're super excited to share MissAlignment: a new ML-based approach to reference-free tilt series alignment, spearheaded by @martenchaillet.bsky.social. We think it's going to make your cryo-ET life a lot better. Preprint: www.biorxiv.org/content/10.6... Code: github.com/warpem/miss-... 🧶 Thread:
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
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.
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.
cryoEM papers@cryoempapers.bsky.social · 5mo agoInteractive segmentation of membrane and membrane mimic densities in cryo-EM maps www.biorxiv.org/content/10.64898/2026.02.25.707988v1 #cryoEM
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
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...
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...
biorxiv.org
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!
Structural Biology@actacrystd.iucr.org · 8mo agoGiles and Burnley: Ten years of the CCP-EM Spring Symposium #Cryoem #ElectronCryoMicroscopy #CCPEM ... #IUCr https://journals.iucr.org/paper?S2059798325010496
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 · last yr.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/
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!
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.
Brett Collins@brettcollins.bsky.social · last yr.Interesting new structure of the Tweety protein TTYH2 complexes with delipidated ApoE www.nature.com/articles/s41...
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
Arjen Jakobi@cryotud.bsky.social · last yr.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...
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
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/
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...
cell.com
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.
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
