New preprint from the lab! Led by graduate student @lainahall.bsky.social we show a new method to thin cells for cryo-EM imaging with minimal damage. www.biorxiv.org/content/10.6...

Optimized cryo-FIB milling strategy to generate thin, minimally damaged biological lamellae

Focused ion beam (FIB)-milling has been adapted to thin frozen cells for visualization of macromolecular structures in situ with cryogenic electron microscopy. However, only a few large and abundant c...

biorxiv.org

cxtoolshed.rbvi.ucsf.edu/apps/chimera... Available through the toolshed now! Thanks to the chimera team for reviewing this one very quickly.

Ben Barad@baradlab.com · 4w ago

My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...

My personal summer of code continues with another ChimeraX plugin - this time, MorphometricsX! Load quantified meshes from morphometrics (or pycurv) in ChimeraX with color-by-quantification and display alongside tomos and particles. Coming to the toolshed soon! #teamtomo github.com/baradlab/mor...

Really hyped to share our pre-print on mtDNA replication-fission ! @nanigrotjahn.bsky.social (doi: doi.org/10.64898/202...) 🧵with details below ⤵️

ATAD3A structurally links mtDNA replication and mitochondrial fission

Mitochondrial function depends on the maintenance of its genome, and disruptions in copy number and distribution are hallmarks of mitochondrial disorders. Mitochondrial DNA (mtDNA) replication is spat...

doi.org

Super excited to share my first paper from my PhD in the @dodonova-sveta.bsky.social lab. We visualise how chromatin from archaeal cells is organised using cryo-ET and SPA. Big thanks to everyone involved in this project!

Svetlana Dodonova@dodonova-sveta.bsky.social · 2mo ago

Excited to share our new preprint! 🧬❄️ by brilliant @mdreimann.bsky.social and great collaborators! Using cryo-ET&EM, we reveal archaeal chromatin in a near-native state: variable-beads-on-a-string fibers shaped by growth phase and histone composition #ArchaeaSky www.biorxiv.org/content/10.6...

Cryo-ET gives unparalleled views of cellular structures, but targeted sample preparation by cryo-FIB milling has been a constraint. No longer! A new workflow yields close to 100% targeting success for centrioles & other small structures. Read the preprint ⤵️ www.biorxiv.org/content/10.6...

Cryo-ET is often framed as a tool for in situ protein structure. But what if the real revolution is contextualization? I explore how #teamtomo is redefining what "local" means in organelle biology, revealing membrane states rather than just protein structures. tinyurl.com/localmembrane

Think globally, act locally: Redefining organellar membrane environments through cryo-electron tomography

Early enthusiasm for the “cellular revolution” in cryo-electron tomography (cryo-ET) was largely driven by the promise of resolving protein structures…

sciencedirect.com

AreTomoLive: a preprocessing pipeline for cryo-ET that streamlines tomographic alignment, reconstruction and contrast enhancement. www.nature.com/articles/s41...

AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput - Nature Methods

AreTomoLive is an accelerated preprocessing pipeline for cryo-electron tomography that streamlines tomographic alignment, reconstruction and contrast enhancement. This pipeline prioritizes automation ...

nature.com

New preprint alert! Ever wonder if cells can talk to each other? Tunneling nanotubes (TNTs) are tiny bridges between cells used to pass organelles, nucleic acids, proteins & even viruses but we've never seen inside them clearly. Until now! 👇🧵 biorxiv.org/content/10.64898/2026.05.27.728322v1

Sub-cellular chemical mapping using correlated cryogenic electron and mass spectrometry imaging online @natmethods.nature.com, led by Hannah Ochner, collaboration with @catfranco.bsky.social and @kiranrpatil.bsky.social labs doi.org/10.1038/s415...

www.nature.com/articles/s41...

In situ cryo-ET defines the ultrastructure of ER exit sites in human cells - Nature Cell Biology

Downes et al. use in situ cryo-electron tomography and super-resolution fluorescence microscopy to define ER exit site architecture in unperturbed human cells. They visualize ribosome-exclusion zones ...

nature.com

The architecture of carriers formed by AP3:ARF1 for lysosomal membrane protein transport: www.science.org/doi/10.1126/.... Work from @jggkaufman.bsky.social, in collaboration with @dgershlick.bsky.social and David Owen. @mpibiochem.bsky.social @thecimr.bsky.social

Architecture of clathrin-independent AP3:ARF1-coated carriers

AP3 generates clathrin-free carriers on endosomes by organizing via ARF1 dimers into elongated membrane-deforming arrays.

science.org

Recent advances in integrative cryoEM/ET toward visualizing the molecular sociology of cellular organelles pubmed.ncbi.nlm.nih.gov/42134003/ #cryoEM

In situ structure of the human gap junction | Science Advances www.science.org/doi/10.1126/...

In situ structure of the human gap junction

In situ cryo-ET reveals how gap junction channels organize into plaques via the interactions between intracellular domains.

science.org

Wow - this is just amazing. Hui Guo and colleagues from John Briggs’ lab use cryoEM helical reconstruction to discover how filamentous influenza virion assembly is directed by multiple conformations of M1 - explaining how NA is concentrated at the proximal pole. www.biorxiv.org/content/10.6...

Automated LN2 refill device for uninterrupted cryoFIB-SEM operations. www.biorxiv.org/content/10.64898/2026.05.06.723155v1 #cryoEM

TomoSwin3D: a Swin3D Transformer for the Identification and Classification of Macromolecules in 3D Cryo-ET Tomograms pubmed.ncbi.nlm.nih.gov/42079087/ #cryoEM

We'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:

www.biorxiv.org/content/10.1... In situ cryo-ET defines the ultrastructure of ER exit sites in human cells

View Tomo: Context-aware targeting and analysis in electron cryo-tomography www.biorxiv.org/content/10.64898/2026.04.21.719727v1 #cryoEM

Cryo-FIB lamellae enable ultra-high excitation laser intensities for cryogenic super-resolution fluorescence imaging www.biorxiv.org/content/10.64898/2026.04.20.719589v1 #cryoEM

Several state-of-the-art deep-learning methods which aim to improve the interpretability of cryo-ET reconstructions are evaluated #DeepLearning #CryoElectronTomography #ContrastEnhancement doi.org/10.1107/S205...

Preprint 🧵! I’m really excited to introduce BIGSMALL, an interleaved multi-magnification cryo-ET scheme bridging molecular and cellular scales in a single acquisition! BIGSMALL = 𝐁road 𝐈nformation 𝐆athering 𝐒trategy by 𝐌ultiscale 𝐀cquisition of lame𝐋𝐋a www.biorxiv.org/content/10.6... (1/6)

#HHMIInvestigators Eric Gouaux & Michael Rosen are using AI to turn a powerful cellular imaging tool into a molecular detective, revealing hidden molecular details in cryo-ET images to better understand how cellular structures work, & how they may malfunction: bit.ly/47Q5u9v.

How do you get a charged drug into a cell when charged molecules can't cross the membrane? You don't — you let the cell do the charging. Check our new paper "Charged molecular glue discovery enabled by targeted degron display" in Nature Chemical Biology. ❕Publication: www.nature.com/articles/s41...

Excited to share our work on the structure and function of cytoplasmic lattices within mouse embryos. A collaborative effort with @niakanlab.bsky.social and work led by @kashishsingh.bsky.social and @inaharasimov.bsky.social . It is now out on BioRxiv: www.biorxiv.org/content/10.6...

In situ cryo-ET of mammalian embryos reveals cytoplasmic lattices contain ubiquitin-charged E2-E3 ligase assemblies www.biorxiv.org/content/10.64898/2026.03.22.713481v1 #cryoEM

The E3 ubiquitin ligase mechanism specifying target-directed microRNA degradation (TDMD) is now published! 🎉🍾 We, @bartellab.bsky.social and Schulman lab, describe how 2-RNA factors control protein degradation by recruiting an E3 ligase. @mpibiochem.bsky.social www.nature.com/articles/s41...

We're excited to announce the beta-release of #RELION-5.1! 🥳 This release has important updates on our #amyloid processing pipeline, as described in this preprint: doi.org/10.64898/202... There are also some tweaks for #teamtomo. #OpenSoftwareAcceleratesScience

Cryo-EM image processing of amyloid filaments in RELION-5.1 www.biorxiv.org/content/10.64898/2026.03.17.712386v1 #cryoEM