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Ben Barad

@baradlab.com
1.5K followers 547 following 328 posts

Assistant Professor @ OHSU • Structural Biologist • Programmer • Coffee Roaster • he/his/him • Cryo-electron tomography, membranes, infectious bacteria, mitochondria. #teamtomo #cryoET tomo.science

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Reposted by Ben Barad
Cathy Spangler @cathyspangler.bsky.social · 22/09/2026
I'm excited to share our new preprint, where we show that fine-tuning gold nanoparticle conjugation to different Fab structural elements can produce powerful, rigidly coupled, labeling tools for in-situ cryo-ET. Take a look if you want to see an AuNP in an EM map!🔬🧠 www.biorxiv.org/content/10.6...
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Phuoc Nguyen (Fook Win) ✍️ @phuocerman.bsky.social · 14/09/2026
FT 1-1 #BAONPDX #NWSL Portland Thorns have dropped 21 points from winning positions and today is no different. Chicago Stars earned that late-stoppage time equalizer. Atrocious performance from the home side and look every bit like a one-and-done playoff team. THIS IS A LOSS.
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Caitie McCafferty @computingcaitie.bsky.social · 09/09/2026
I am looking for a lab manager for my group that I will be starting at the @fmiscience.bsky.social in February! We will use in situ structural biology to investigate dynamic ciliary processes. More info here —> bsky.app/profile/comp... #cilia #teamtomo #proteomics #protistsky
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Ben Barad @baradlab.com · 24/08/2026
@tinalope.bsky.social you getting royalties for Rose the Dragon stealing your crown?
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Matt Johnson @drmatthewcjohnson.bsky.social · 11/08/2026
Interested in a career in industry cryoEM? We're hiring! We seek a cryoEM/cryoET expert to join our team at Genentech advance our mission to provide high-resolution structural insights into biological macromolecules involved in health and disease. Apply at: careers.gene.com/us/en/job/20...
careers.gene.com
Systems Specialist II in South San Francisco, California, United States of America | Manufacturing & Engineering at Genentech
Apply for Systems Specialist II job with Genentech in South San Francisco, California, United States of America. Manufacturing & Engineering at Genentech
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Ben Barad @baradlab.com · 30/07/2026
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.
Mitochondrial membrane shown in surforama
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Ben Barad @baradlab.com · 27/07/2026
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
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Ben Barad @baradlab.com · 21/07/2026
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...
cxtoolshed.rbvi.ucsf.edu
ChimeraX Toolshed - Geopickr
Resource for Biocomputing, Visualization amd Informatics (RBVI), and its precursor, the Computer Graphics Laboratory (CGL), develops cutting-edge interactive software tools and advanced web-based comp...
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Ben Barad @baradlab.com · 17/07/2026
New tools for membrane annotation (especially the painful cleanup step) are always so welcome!
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Ben Barad @baradlab.com · 14/07/2026
Geopickr works perfectly with MorphometricsX - and is especially powerful with morphometrics preprocessing like extracting only high curvature regions or mitochondria-ER contact sites!
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ChimeraX @chimerax.ucsf.edu · 10/07/2026
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....
ChimeraX user interface for MorphometricsX
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Reposted by Ben Barad
Gregor Weiss @weiss-lab.bsky.social · 10/07/2026
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 🧵
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Ben Barad @baradlab.com · 09/07/2026
cxtoolshed.rbvi.ucsf.edu/apps/chimera... Available through the toolshed now! Thanks to the chimera team for reviewing this one very quickly.
cxtoolshed.rbvi.ucsf.edu
ChimeraX Toolshed - MorphometricsX
Resource for Biocomputing, Visualization amd Informatics (RBVI), and its precursor, the Computer Graphics Laboratory (CGL), develops cutting-edge interactive software tools and advanced web-based comp...
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Ben Barad @baradlab.com · 08/07/2026
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...
Screenshot of MorphometricsX rendering mitochondrial membrane surfaces in chimera with color-by-quantification.
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Ben Barad @baradlab.com · 08/07/2026
I love weird membranes!
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Ben Barad @baradlab.com · 27/06/2026
This is what cryo-ET is made for!
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Ben Barad @baradlab.com · 27/06/2026
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.
github.com
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 ...
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Ben Barad @baradlab.com · 24/06/2026
Anyone got a recommendation for someone I could commission for a lab logo?
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Ben Barad @baradlab.com · 19/06/2026
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...
github.com
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...
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Ben Barad @baradlab.com · 18/06/2026
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...
Geopickr enables particle picking on surfaces, spheres, tubes, and filaments interactively in ChimeraX!
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Danielle Grotjahn @nanigrotjahn.bsky.social · 16/06/2026
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
sciencedirect.com
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…
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Ben Barad @baradlab.com · 14/06/2026
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!
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Ben Barad @baradlab.com · 13/06/2026
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!
ChimeraX/ArtiaX visualization showing mitochondria-associated ribosomes connecting drives reduced IMM-OMM spacing in yeast.Surforama depiction of mitochondrial outer membrane shows membrane-associated ribosomes.
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Ben Barad @baradlab.com · 10/06/2026
Kvelling (reverse kvelling?) for my mom today!
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Connor Garrels @garrels.bsky.social · 01/06/2026
Very excited about our new work highlighting the role of lipids in mediating multi-channel assemblies of Cx-46/50!
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Jonathan Pruneda @jnpruneda.bsky.social · 04/05/2026
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...
nature.com
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.
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Helena Watson @helenawatson.bsky.social · 25/04/2026
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)
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Kimberly Beatty @beattylab.bsky.social · 20/04/2026
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).
pubs.acs.org
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...
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U-M Life Sciences Institute @umlifesciences.bsky.social · 27/03/2026
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
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Ben Barad @baradlab.com · 11/02/2026
I am getting excited about teaching at this! I think we're going to do copick, membrain-seg, morphometrics, and surforama on my day!
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Ben Barad @baradlab.com · 04/02/2026
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.com
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
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Shyamal @shyamalm.bsky.social · 20/01/2026
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!
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Sergio Cruz-León @sergiocruzleon.bsky.social · 13/01/2026
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 👇
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Ben Barad @baradlab.com · 08/01/2026
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!
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Ben Barad @baradlab.com · 26/12/2025
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/...
rupress.org
Surface Morphometrics reveals local membrane thickness variation in organellar subcompartments | Journal of Cell Biology | Rockefeller University Press
Medina, Chang et al. introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar membranes fro
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Ben Barad @baradlab.com · 13/12/2025
I had such a fun experience sharing the quantitative #teamtomo gospel at the Chemical Biology and Physiology 2025 conference. I've gotten so many ideas for perturbations and correlative tools to pair with our tools for quantitative membrane ultrastructure in situ.
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Ben Barad @baradlab.com · 13/12/2025
Hopefully as image processing in cryoET advances we can see concomitant improvements in benchmarking and validation - so we don't end up imagining features of cells that aren't there!
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Ben Barad @baradlab.com · 12/12/2025
Holy cow the Zhou lab at UCLA is cooking with Isonet 2 - www.biorxiv.org/content/10.6... Averaging-free direct visualization of ribosome translational state! #teamtomo #cryoet
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Danielle Grotjahn @nanigrotjahn.bsky.social · 07/12/2025
What an honor to see @attychang.bsky.social’s work featured in @jcb.org The Year in Cell Biology 2025 collection! Even more special that it coincides with my first #cellbio2025 conference 🙂 s/o to co-authors @baradlab.com @hamid13r.bsky.social @zidlab.bsky.social #teamtomo #cellbio25
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Kimberly Beatty @beattylab.bsky.social · 20/11/2025
PSA: NIH study section members Keep a hard copy back-up of your online written reviews. Don't learn the hard way.
media.tenor.com
a little girl is making a funny face and saying aw nuts !
ALT: a little girl is making a funny face and saying aw nuts !
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SBGrid Consortium @sbgrid.bsky.social · 17/11/2025
Join us November 18th to hear from Hui Wang, postdoc in the Hong Zhou lab at @uofcalifornia.bsky.social, Los Angeles, on TomoNet: Automatic Particle Picking of Flexible Lattice-Like Structures for CryoET. Register here: buff.ly/QAMUkym #SBGrid #StructuralBiology #Webinars
buff.ly
Webinars
The SBGrid Consortium is an innovative global research computing group operated out of Harvard Medical School. SBGrid provides the global structural biology community with support for research…
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Danielle Grotjahn @nanigrotjahn.bsky.social · 17/11/2025
Prohibitins aren’t hanging out just anywhere in the membrane — they prefer the 💁‍♀️💎✨VIP section💅🪩🥂 Lab all-star @mmedina300kv.bsky.social maps these microdomains using cryo-ET + surface morphometrics. s/o to #teamtomo #cryoET co-authors @hamid13r.bsky.social @attychang.bsky.social @baradlab.com
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Portland Thorns FC @thornsfc.com · 09/11/2025
WE SAID ALL IN 🌹
group photo of team on field
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Stumptown Footy @stumptownfooty.bsky.social · 09/11/2025
Rob Gale: "We ain't done yet." #BAONPDX
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Florian Schur @schurlab.bsky.social · 15/10/2025
ISTA @istaresearch.bsky.social is hiring a tenure-track staff scientist in Computational Structural Biology, to develop tools for cryo-EM, cryo-ET, structural prediction methods and protein interaction analysis! Please spread the word! ista.ac.at/en/job/tenur...
ista.ac.at
Tenure-based Research Staff Scientist Position in Computational Structural Biology
ISTA (www.ista.ac.at) is seeking a highly skilled Staff Scientist in Computational Structural Biology to support and advance the Institute’s structural biology research through the development and imp...
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Bronwyn Lucas @bronwynalucas.bsky.social · 30/08/2025
First pre-print from the Lucas Lab led by Matthew Giammar and @joshdcryoem.bsky.social online today! We develop a new, extensible Python implementation of 2DTM and apply it to build pixel size optimization, constrained search and characterize molecular motions in situ www.biorxiv.org/content/10.1...
biorxiv.org
Leopard-EM: An extensible 2DTM package to accelerate in situ structural biology
The ability to generate high-resolution views of cells with cryogenic electron microscopy (cryo-EM) can reveal the molecular mechanisms of biological processes in their native cellular context. The re...
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Katie Downes @dr-downes.bsky.social · 30/07/2025
Very excited to announce that my first, first author paper, is now on BioRxiv! In this paper we unambiguously show #COPII coated vesicles in unperturbed human cells for the very first time!! Make my day and check it out! www.biorxiv.org/content/10.1... #Cryo-ET #TeamTomo #Cryo-CLEM ❄️🔬❄️🔬❄️🔬❄️🔬
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Bella Rauch @rauchlab.bsky.social · 06/06/2025
I'm at the OHSU PREP research symposium and I am so impressed with our trainees, they present and know their project background better then many a graduate student. All the more I'm filled with rage about the cancellation of this wonderful #NIH program 🤬
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Danielle Grotjahn @nanigrotjahn.bsky.social · 09/04/2025
I know print journals aren't exactly on everyone's radar these days, but we’re still geeking out that our latest study—led by the brilliant @attychang.bsky.social—landed the cover of the April issue of JCB! 🤩 @zidlab.bsky.social @tomo.science @hamid13r.bsky.social
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James Fraser @fraserlab.com · 16/03/2025
Since @stephanieaw.bsky.social left the lab to start her group at Vanderbilt, we've been talking regularly on the ups and downs of academic science. We started recording... The Tortured Proteins Department open.spotify.com/show/10PHVou... (science with a small dose of running and Taylor Swift)
open.spotify.com
The Tortured Proteins Department
Podcast · Stephanie Wankowicz · A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser.
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