www.biorxiv.org/content/10.6...

Fluorescent Biosensors for Cryogenic Correlative Light and Electron Microscopy

Cryogenic electron tomography provides nanometer-scale views of subcellular structures but lacks essential physiological context, such as the metabolic state or ion concentration. To bridge this gap, ...

biorxiv.org

In-cell cryo-electron tomography reveals differential effects of type I and type II kinase inhibitors on LRRK2 filament formation and microtubule association

In-cell cryo-electron tomography reveals differential effects of type I and type II kinase inhibitors on LRRK2 filament formation and microtubule association

Type I and type II inhibitors differentially affect LRRK2 filament formation around microtubules, revealing an important consideration for Parkinson’s disease drug development.

buff.ly

Make natural language requests to ChimeraX with the new Pellaeon plugin developed by Yam Amir that works with many free and paid large language models. Get Pellaeon using ChimeraX menu Tools / More Tools.... cxtoolshed.rbvi.ucsf.edu/apps/chimera...

Excited to share our latest work on understanding CTLH-MKLN1 substrate recruitment. Stay tuned for the paper 🤗

bioRxiv Biochemistry@biorxiv-biochem.bsky.social · 2mo ago

Multimodal substrate recruitment enables CTLH-MKLN1 E3 ligase to target N-, C-, and internal degrons https://www.biorxiv.org/content/10.64898/2026.09.10.750665v1

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

Luminescent-reaction-enabled super-resolution imaging - Nature

A new chemistry-based super-resolution imaging framework is described, enabling 3D, laser-free, highly sensitive and ultralong-term imaging of live cells which overcomes the limitations in spatiotempo...

nature.com

Imaging large fields-of-view at high resolution in cryo-ET with square beam montaging www.biorxiv.org/content/10.64898/2026.08.27.747605v1 #cryoEM

A Kaggle challenge for particle picking in cryo-ET data spurred the development of new algorithms that outperform state of the art software. www.nature.com/articles/s41...

Lessons learned from a Kaggle challenge for particle picking in cryo-electron tomography - Nature Methods

A Kaggle challenge for particle picking in experimental cryo-electron tomography data delivered new machine learning algorithms that outperformed state-of-the-art software and provides a critical refe...

nature.com

Now on Arxiv: arxiv.org/abs/2608.10029 Led by grad student Matthew Giammar and collaborator Alex Strang, we provide a fast algorithm to calculate a low rank approximation to large (>100 million row) matrices with high fidelity that will accelerate template matching.

A fast diagonalization algorithm to enable singular value decomposition of large matrices for efficient template matching

Many computational problems possess the following three features: (1) the problem could be solved efficiently if a linear operator could be diagonalized, (2) direct diagonalization is infeasible due t...

arxiv.org

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 · 4mo 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 · 5mo 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...