Utz Ermel

I’m very excited to share the first big project from my PhD (my first proper-first, yay!) where we use cryoET and a fun new flavour of CLEM to study the re-organisation of photosynthetic machinery of cyanobacteria growing beyond the red limit of light. doi.org/10.64898/202...

CryoET reveals molecular organization inside cells, but annotation limits analysis at scale. SABER (Segment Anything Based Electron Recognition) pairs a foundation video model with sparse labels to segment 3D cellular structures, cutting annotation time by 10x. chanzuckerberg.github.io/saber/

Introducing CiliaBuilder2, a ChimeraX bundle to generate cilia & centriole assembly from real structures (maps, pdbs). Here's a hybrid sperm cilium (bovine sperm doublet microtubule PDB 9fqr & mouse sperm central pair PDB 9ijj)

two retroviruses | one chimeric CA

Shawn Zheng leads Biohub’s work to streamline cryo-electron tomography, which images cells in 3D at near-atomic resolution. His team’s AreTomoLive automates cryoET reconstruction and denoising in real time and cuts processing from months to days. Learn more: sbgrid.org/software/tal...

Online Now: Large-scale CryoET segmentation from minimal expert annotations with foundation video models #datascience

A wild publishing ride to get here... but finally! (first bioRxiv: January 5th, 2024 🙃) Amazing work from @lorenzlamm.bsky.social and colleagues 🤗 Special thanks to the community who jumped early on the boat, sharing feedback and training data to make MemBrain v2 a reality 🙏🏽

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

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...

New Title Alert: copick- is a cross-platform, storage-agnostic & server-less dataset API for cryoET datasets. Access to the data is provided through an object-oriented API that abstracts away the underlying storage using the fsspec-family of libraries. More here: buff.ly/ZBe5Vpd #SBGrid #Software

One cell, one tomogram! Our montage tomography workflow, MOSAIC, is out in Structure, and MontageMaker is on GitHub! MOSAIC: www.cell.com/structure/fu... MontageMaker: github.com/MPI-Dortmund... Big thanks to @maikaboiero.bsky.social, Adriana Prajica, Gavin Rice, and @raunser-lab.bsky.social!

With Cryo-ET/EM, the macromolecules we study (and biological questions we ask) are SNR-limited. Here, we share Nilas, a low-voltage milling method named after thin sea ice. Nilas produces thin (sub 50 nm in places!), minimally damaged lamellae. biorxiv.org/content/10.64898/2026.07.21.739890v1

Learn about a device that boosts the contrast in electron microscopy using the most intense laser beam yet made, and the story of its path from an idea to an invention that could open new lines of inquiry in structural biology and biochemistry. #chemsky 🧪

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...

🚨Open call to the Cell Tracking crowd out there🚨! Loïc's team at @biohub.org opened our Kaggle Challenge for 3D cell tracking, with $60k of prize money💰. Spread the news, delve into our gigabytes of imaging (zarr3) and cell tracking (geff) data of developing zebrafish embryos, and start tracking 🤩

From v0.2.0 MissAlignment now has an inference mode where you can apply the trained models from one dataset to a new dataset to skip training time. I haven't tested it extensively, so double check if the results look decent 😉 The program calls changed slightly, see here: github.com/warpem/miss-...

Inspired by Utz, I ported the old Briggs lab tools to ChimeraX in a single bundle named Geopickr, with some extra utilities (geopicking on morphometrics surfaces!). I've submitted it to the toolshed, but in the meantime: github.com/baradlab/Geo...

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...

In a series of 3 papers and preprints, we’re thrilled to share with you the working laser phase plate. In collaboration with research led by Holger Müller at UC Berkeley, this is a huge innovation in imaging to make small and faint objects inside cells visible. bit.ly/4vK9LVn

We have published a review on how contextual information can complement and enhance research using #cryoET . www.sciencedirect.com/science/arti...

Proteins are the machinery of life. Billions of their sequences have been cataloged—but the biology behind most is still unknown. Today we're releasing ESMFold2, ESMC and ESM Atlas to help change that. Open source, open to every scientist. biohub.ai/esm/protein

We're happy to announce our new preprint! 🐸 easymode: general pretrained networks for cellular cryo-ET. Segment ~20 cellular features – ribosomes, microtubules, mitochondria, nuclei & more – with zero model training. 🔗 doi.org/10.64898/202... 🧵👇

Volumetric exploration of multi-resolution CryoET data in native WebGPU. Kiln (0.3.0) adds float32 support, OME-Zarr v0.4, slice views and more. github.com/MPanknin/kil... Vibrio cholerae tomogram from CryoET Data Portal. cryoetdataportal.czscience.com #WebGPU #OME-Zarr #CryoET

Easymode: general pretrained networks for cellular cryo-ET enable flexible approaches to subtomogram averaging www.biorxiv.org/content/10.64898/2026.05.19.726344v1 #cryoEM

Thanks to @uermel.bsky.social from the @biohub.org for helping me upload my unpublished tomograms from my time at Caltech. FIB milled and cryosectionned Arabidopsis cells and Pollen tubes (thread 🧵).

Hello World :) Join us in building foundational subcellular spatial intelligence. To get this party started, we are pleased to announce inaugural call for Subspatial x DECTRIS CLOUD fellowships, apply at subspatial.org/fellowship #subspatial #fellowships #openscience #teamtomo #spatialbiology

Today we're announcing the Virtual Biology Initiative—a major new commitment to build the data foundation biology needs to power the next generation of AI models. Next-gen imaging. Molecular engineering tools. Open data infrastructure for the entire scientific community. Read more: bit.ly/3ONTkHO

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)

Excited to share our paper on the NLRP3 inflammasome condensate at the Microtubule Organizing Center (MTOC) by "precise!" cryo-electron tomography (cryo-ET), in collaboration with Jue (phyllis) Wang in the labs of Grant Jensen (BYU) and Pete Dahlberg (Stanford)! www.science.org/doi/10.1126/...

#UMAP in VR for #3DThursday! In this zebrafish embryogenesis dataset, RNA-seq + ATAC-seq across 94k+ cells reveal changing regulatory programs over time. 🥼 Yang-Joon Kim, Loic Royer @loicaroyer.bsky.social , Matthias Haury 📝 www.biorxiv.org/content/10.1... 🏛️ Biohub @biohub.org 🎬 #syGlass v2.6.0

New Title Alert: easymode- a collection of general pretrained networks for cellular cryoET. Learn more here: buff.ly/mLbcUbZ #SBGrid #SBGridSoftware

Streaming OME-Zarr data directly into syGlass for #3DThursday🌍🔬 With #syGlass v2.6.0, datasets can stream from disk, S3, or HTTPS with no massive downloads required. Huge thanks to the community building open imaging standards: @openmicroscopy.org #OMEZarr #Microscopy #OpenScience #Bioimaging

New on the CryoET Data Portal: ~27,000 tomograms of affinity-captured lysosomes from HEK293T cells across 4 physiological states. Includes raw data, AreTomo3 reconstructions & Membrain-Seg annotations. Openly available for reuse! cryoetdataportal.czscience.com/depositions/...

This one was quite the journey! The paper describing the #ChlamyDataset is finally out and on the cover of Mol Cell! This beautiful rendering made by co-author @jessheebner.bsky.social and Holly Peterson shows an instance of mitochondrial fission found in the dataset 😍 [Maybe long thread ahead]

Tired of knowing what you are looking for in your tomograms? Why not try bluesky-less Frosina's new self-supervised algorithm for semantic segmentation and particle picking for #teamtomo (includes a new denoiser without the need for odd/even tomos) Code is on GitHub if you want to try it out