Reposted by Ben BaradCathy Spangler @cathyspangler.bsky.social · 22/09/2026I'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... 14922
Reposted by Ben BaradPhuoc Nguyen (Fook Win) ✍️ @phuocerman.bsky.social · 14/09/2026FT 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. 11525
Reposted by Ben BaradCaitie McCafferty @computingcaitie.bsky.social · 09/09/2026I 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 34443
Ben Barad @baradlab.com · 24/08/2026@tinalope.bsky.social you getting royalties for Rose the Dragon stealing your crown? 120
Reposted by Ben BaradMatt Johnson @drmatthewcjohnson.bsky.social · 11/08/2026Interested 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.comSystems Specialist II in South San Francisco, California, United States of America | Manufacturing & Engineering at GenentechApply for Systems Specialist II job with Genentech in South San Francisco, California, United States of America. Manufacturing & Engineering at Genentech 01713
Ben Barad @baradlab.com · 30/07/2026Small 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. 082
Ben Barad @baradlab.com · 27/07/2026Do 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 072
Ben Barad @baradlab.com · 21/07/2026Just 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.eduChimeraX Toolshed - GeopickrResource 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... 093
Ben Barad @baradlab.com · 17/07/2026New tools for membrane annotation (especially the painful cleanup step) are always so welcome! 020
Ben Barad @baradlab.com · 14/07/2026Geopickr works perfectly with MorphometricsX - and is especially powerful with morphometrics preprocessing like extracting only high curvature regions or mitochondria-ER contact sites! 0152
Reposted by Ben BaradChimeraX @chimerax.ucsf.edu · 10/07/2026A 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.... 0207
Reposted by Ben BaradGregor Weiss @weiss-lab.bsky.social · 10/07/2026Some 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 🧵 311527
Ben Barad @baradlab.com · 09/07/2026cxtoolshed.rbvi.ucsf.edu/apps/chimera... Available through the toolshed now! Thanks to the chimera team for reviewing this one very quickly.cxtoolshed.rbvi.ucsf.eduChimeraX Toolshed - MorphometricsXResource 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... 0154
Ben Barad @baradlab.com · 08/07/2026My 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... 25612
Ben Barad @baradlab.com · 27/06/2026Just 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.comRelease 2.0.0b2 · GrotjahnLab/surface_morphometricsA 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 ... 0187
Ben Barad @baradlab.com · 24/06/2026Anyone got a recommendation for someone I could commission for a lab logo? 17140
Ben Barad @baradlab.com · 19/06/2026Just 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.comRelease Geopickr 1.1.0b1 (beta) · baradlab/GeopickrBeta 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... 171
Ben Barad @baradlab.com · 18/06/2026Inspired 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... 1385
Reposted by Ben BaradDanielle Grotjahn @nanigrotjahn.bsky.social · 16/06/2026Cryo-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/localmembranesciencedirect.comThink globally, act locally: Redefining organellar membrane environments through cryo-electron tomographyEarly enthusiasm for the “cellular revolution” in cryo-electron tomography (cryo-ET) was largely driven by the promise of resolving protein structures… 26323
Ben Barad @baradlab.com · 14/06/2026BTW, 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! 041
Ben Barad @baradlab.com · 13/06/2026I 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! 2418
Reposted by Ben BaradConnor Garrels @garrels.bsky.social · 01/06/2026Very excited about our new work highlighting the role of lipids in mediating multi-channel assemblies of Cx-46/50! 0166
Reposted by Ben BaradJonathan Pruneda @jnpruneda.bsky.social · 04/05/2026Interested 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.comFaculty Position in Molecular Microbiology and Immunology - Portland, Oregon job with Oregon Health & Science University (OHSU) - Molecular Microbiology and Immunology | 12858852The Department of Molecular Microbiology and Immunology at OHSU invites applications for a tenure-track Assistant or Associate Professor position. 03336
Reposted by Ben BaradHelena Watson @helenawatson.bsky.social · 25/04/2026BIGSMALL 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) 2214
Reposted by Ben BaradKimberly Beatty @beattylab.bsky.social · 20/04/2026New 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.orgChemoproteomic Elucidation of β-Lactam Drug Targets in Mycobacterium abscessusThe 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... 054
Reposted by Ben BaradU-M Life Sciences Institute @umlifesciences.bsky.social · 27/03/2026The 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 055
Ben Barad @baradlab.com · 11/02/2026I am getting excited about teaching at this! I think we're going to do copick, membrain-seg, morphometrics, and surforama on my day! 191
Ben Barad @baradlab.com · 04/02/2026I'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.comGitHub - 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 13815
Reposted by Ben BaradShyamal @shyamalm.bsky.social · 20/01/2026We 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! 02218
Reposted by Ben BaradSergio Cruz-León @sergiocruzleon.bsky.social · 13/01/2026We 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 👇 06115
Ben Barad @baradlab.com · 08/01/2026Happy 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! 1195
Ben Barad @baradlab.com · 26/12/2025Online 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.orgSurface Morphometrics reveals local membrane thickness variation in organellar subcompartments | Journal of Cell Biology | Rockefeller University PressMedina, Chang et al. introduce a new method based on the Surface Morphometrics pipeline to measure global and local thicknesses of organellar membranes fro 13111
Ben Barad @baradlab.com · 13/12/2025I 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. 1280
Ben Barad @baradlab.com · 13/12/2025Hopefully 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! 092
Ben Barad @baradlab.com · 12/12/2025Holy 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 210235
Reposted by Ben BaradDanielle Grotjahn @nanigrotjahn.bsky.social · 07/12/2025What 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 0478
Reposted by Ben BaradKimberly Beatty @beattylab.bsky.social · 20/11/2025PSA: NIH study section members Keep a hard copy back-up of your online written reviews. Don't learn the hard way.media.tenor.coma little girl is making a funny face and saying aw nuts !ALT: a little girl is making a funny face and saying aw nuts ! 021
Reposted by Ben BaradSBGrid Consortium @sbgrid.bsky.social · 17/11/2025Join 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 #Webinarsbuff.lyWebinarsThe 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… 053
Reposted by Ben BaradDanielle Grotjahn @nanigrotjahn.bsky.social · 17/11/2025Prohibitins 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 05718
Reposted by Ben BaradStumptown Footy @stumptownfooty.bsky.social · 09/11/2025Rob Gale: "We ain't done yet." #BAONPDX 0342
Reposted by Ben BaradFlorian Schur @schurlab.bsky.social · 15/10/2025ISTA @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.atTenure-based Research Staff Scientist Position in Computational Structural BiologyISTA (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... 01017
Reposted by Ben BaradBronwyn Lucas @bronwynalucas.bsky.social · 30/08/2025First 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.orgLeopard-EM: An extensible 2DTM package to accelerate in situ structural biologyThe 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... 88431
Reposted by Ben BaradKatie Downes @dr-downes.bsky.social · 30/07/2025Very 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 ❄️🔬❄️🔬❄️🔬❄️🔬 610031
Reposted by Ben BaradBella Rauch @rauchlab.bsky.social · 06/06/2025I'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 🤬 073
Reposted by Ben BaradDanielle Grotjahn @nanigrotjahn.bsky.social · 09/04/2025I 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 36613
Reposted by Ben BaradJames Fraser @fraserlab.com · 16/03/2025Since @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.comThe Tortured Proteins DepartmentPodcast · Stephanie Wankowicz · A deep dive into scientific discovery and the process of doing science, hosted by Stephanie Wankowicz and James Fraser. 36621