Small new user-requested feature in 2.0 beta 5 - Surface Morphometrics can export obj in arbitrary voxel coordinates to make tools like Surforama easier to use.

Do any of the CryoET national centers have SPACEtomo set up for users? I've got several montaging and/or bigsmall projects I'd like to try but we have no support for either at PNCC. #teamtomo

Just uploaded a new Geopickr version with improved oversampling on surfaces, including automatic even/odd splitting by connected component when using a morphometrics surface. This is much less prone to half set particle overlap leading to overfitting. cxtoolshed.rbvi.ucsf.edu/apps/chimera...

New tools for membrane annotation (especially the painful cleanup step) are always so welcome!

Kathiravan Ezhilan@kathiravan-ezhilan.bsky.social · 3w ago

In #cryoET, separating closely apposed membrane segmentations into distinct labels can be difficult. Small artefacts may connect otherwise separate membranes, requiring tedious slice-by-slice correction. To address this, @jasmred.bsky.social and I developed MemSplit, a napari based workflow.

Geopickr works perfectly with MorphometricsX - and is especially powerful with morphometrics preprocessing like extracting only high curvature regions or mitochondria-ER contact sites!

ChimeraX@chimerax.ucsf.edu · 3w ago

A new ChimeraX tool Geopickr from Ben Barad's lab oversamples dense protein arrays on spheres, tubes, filaments, and arbitrary surfaces for geometry-assisted subtomogram averaging. Available from ChimeraX menu Tools / More Tools....

A new ChimeraX tool MorphometricsX from Ben Barad's lab colors cell membranes in electron tomography according to thickness, curvature and other properties. Available from ChimeraX menu Tools / More Tools....

Some bacteria do not live as individuals. They build multicellular filaments and connect neighboring cells through tiny cell-cell junctions. Cyanobacteria are among the most beautiful examples 😍 In our new paper, we reveal first molecuar insights on the cyanobacterial septal junction architecture 🧵

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...

I love weird membranes!

Martin Jonikas@mjonikas.bsky.social · last mo.

The algal pyrenoid turbocharges global CO2 fixation. Central to its function are specialized membranes that deliver CO2. We discovered that the protein RBMP2 makes these membranes—and found that the mysterious minitubules appear to enhance CO₂ delivery! www.biorxiv.org/content/10.6...

This is what cryo-ET is made for!

Nitish Dua@nitishdua.bsky.social · last mo.

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

Just in time for the weekend, the 2nd beta for our Surface Morphometrics 2.0 release: github.com/GrotjahnLab/.... Beyond the major API change from the first beta (which used for the michigan class!), this one includes a major overhaul of the dual gaussian fitting for thickness and refinement.

Release 2.0.0b2 · GrotjahnLab/surface_morphometrics

A quality and robustness release on top of 2.0.0b1, focused on the density-profile bilayer fitting (mesh refinement and thickness measurement), a forgiving centralized config system, and packaging ...

github.com

Anyone got a recommendation for someone I could commission for a lab logo?

Just pushed a beta release of geopickr with star (relion5 and warp) and dynamo tbl output. I don't have a pressing problem to test these out on, but if you have a workflow that would benefit from one of these, want to test it out and give me feedback? github.com/baradlab/Geo...

Release Geopickr 1.1.0b1 (beta) · baradlab/Geopickr

Beta pre-release adding multi-format particle export, plus a Place Object fix. New: export to Dynamo & RELION (issues #1, #2 — pending live-import testing) Dynamo .tbl (+ optional .vll volume-list...

github.com

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...

Utz Ermel@uermel.bsky.social · 2mo ago

Claude Code is pretty good at writing ChimeraX plugins! This one is almost entirely good context and some prompting: github.com/uermel/chime... Most likely older plugins could be ported over that way relatively easily.

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

BTW, this tutorial includes a bit of Mosaic, a membrane modeling software from the Kosinski lab a lot of tomo labs may have missed, but which I absolutely love!

Ben Barad@baradlab.com · 2mo ago

I had such a fun time teaching at the U Michigan Cryo-ET Course this week! I taught quantitative ultrastructure analysis and we made cool figures like these! My course materials are at baradlab.com/michigan_tutorial for anyone to try. Workflow include mesh refinement and thickness measurement!

I had such a fun time teaching at the U Michigan Cryo-ET Course this week! I taught quantitative ultrastructure analysis and we made cool figures like these! My course materials are at baradlab.com/michigan_tutorial for anyone to try. Workflow include mesh refinement and thickness measurement!

Kvelling (reverse kvelling?) for my mom today!

The Kavli Prize@kavliprize.bsky.social · 2mo ago

We're thrilled to announce the 2026 #KavliPrize Laureates, scientists pushing boundaries of what humanity knows in #astrophysics #nanoscience #neuroscience. They have revealed new chapters in the story of our universe, the smallest materials, and how the brain works. 1/2

Very excited about our new work highlighting the role of lipids in mediating multi-channel assemblies of Cx-46/50!

Reichow Lab@reichowlab.bsky.social · 2mo ago

Dual-channel Cx46/50 gap junction assemblies in a shared lipid-nanodisc = lipid-mediated packing and a lipid site near the NT gating region that is absent from single channels. Plus a 1.8 Å open-state single-channel benchmark! #cryo-EM 🍩’s #NIH-funded-research www.biorxiv.org/content/10.6...

Interested in microbiology, immunology, and host-pathogen interactions? Come work with us! Our department at OHSU is opening a search for a new tenure-track faculty position. See the job advertisement for details. Please share within your networks! www.nature.com/naturecareer...

Faculty Position in Molecular Microbiology and Immunology - Portland, Oregon job with Oregon Health & Science University (OHSU) - Molecular Microbiology and Immunology | 12858852

The Department of Molecular Microbiology and Immunology at OHSU invites applications for a tenure-track Assistant or Associate Professor position.

nature.com

BIGSMALL is now implemented in SPACEtomo. Setup is easy: - define low mag parameters with SerialEM Search preset - add LM + HM targets in the same beam-shift group - acquire! (5/6)

New work from my team: pubs.acs.org/doi/10.1021/... We used probes to ID targets of carbapenems in M. abscessus. 17 targets active in both carbon starved and replicating cultures. Includes validation of 9 targets. Part of a special issue ("NTM Pathogens – Biology, Infection, and Drug Discovery).

Chemoproteomic Elucidation of β-Lactam Drug Targets in Mycobacterium abscessus

The pathogen Mycobacterium abscessus (Mab) can cause severe and difficult-to-treat chronic lung infections. Despite the rising incidence and clinical concern of Mab infections, treatment options are l...

pubs.acs.org

The deadline to register for the 2026 Cryo-ET Workshop has been extended extended to April 10! Learn more about this hands-on workshop and apply at: myumi.ch/lsi-cryo-workshop-2026 @jbquerido.bsky.social @shyamalm.bsky.social

U-M Life Sciences Institute@umlifesciences.bsky.social · 6mo ago

Join us this summer for U-M's 2026 #CryoET Data Processing Workshop! This four-day workshop will introduce participants to standard image processing packages and all aspects of cryo-ET data processing. Apply by March 20: myumi.ch/lsi-cryo-workshop-2026 @jbquerido.bsky.social @shyamalm.bsky.social

I am getting excited about teaching at this! I think we're going to do copick, membrain-seg, morphometrics, and surforama on my day!

U-M Life Sciences Institute@umlifesciences.bsky.social · 6mo ago

Join us this summer for U-M's 2026 #CryoET Data Processing Workshop! This four-day workshop will introduce participants to standard image processing packages and all aspects of cryo-ET data processing. Apply by March 20: myumi.ch/lsi-cryo-workshop-2026 @jbquerido.bsky.social @shyamalm.bsky.social

I've been working on Surface Morphometrics for a new version (coming soon), and made some significant (AI-assisted) performance improvements, especially in pycurv (20-50x!). If you've had technical issues or just felt like it was too slow, give it another try! #teamtomo github.com/GrotjahnLab/...

GitHub - GrotjahnLab/surface_morphometrics: Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging.

Morphometrics for Membrane Surfaces Segmented from Cryo-ET or other volumetric imaging. - GrotjahnLab/surface_morphometrics

github.com

We are running the cryo-ET image processing workshop again this year! Come learn everything tomo: STA, segmentation, heterogeneity analysis from @baradlab.com @williamnwan.bsky.social and others! Apply!

U-M Life Sciences Institute@umlifesciences.bsky.social · 7mo ago

While everything feels flash-frozen in Michigan, it's a great time to plan for U-M's 2026 #CryoET Data Processing Workshop! This hands-on workshop will introduce participants to standard image processing packages used to analyze cryo-ET data. Apply by March 20: myumi.ch/lsi-cryo-wor...

We resolved the molecular architecture of a condensate—inside cells. 🤯 By combining in situ cryoET with multiscale simulations, we show how a single point mutation modifies molecular interactions, shifts the condensate’s material properties, and alters its biological function. Preprint 👇

Wilfling Lab@wilflinglab.bsky.social · 7mo ago

We are excited to share our new preprint which is now available to read on biorXiv: doi.org/10.64898/202... 🎉🎉🎉

Happy new year #teamtomo! We've resumed our OHSU tomo journal club, and this year I am going to be sharing it on bluesky. This week we did a roundtable, where attendees each brought a paper and did a 3-5 minute discussion of what they thought was cool about it. Here are the papers they discussed!

Online today, the journal version of our ( @nanigrotjahn.bsky.social @attychang.bsky.social @mmedina300kv.bsky.social) manuscript from earlier this year describing membrane thickness measurement in cells with #teamtomo! rupress.org/jcb/article/...