iiinova — where your digital self keeps evolving

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...

093

Ben Barad @baradlab.com · 17/07/2026

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

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!

0152

Ben Barad @baradlab.com · 13/07/2026

Def worth it to sign up for tsa pre touchless with all your regular carriers - it's applied when you buy the ticket

Ben Barad @baradlab.com · 13/07/2026

Also, announcers saying weaver is back in practice? Wonder how long the gap will actually be for our 3 wingers...

100

Ben Barad @baradlab.com · 13/07/2026

It would have been alidou, she moved to get more minutes. I would guess we might see forward muller a bit and let lyles and Harvey take over some midfield duties. McKenzie is coming along but not ready to start...

100

Ben Barad @baradlab.com · 12/07/2026

Turner is on crutches, amazing how much we miss her - she has developed into such a good piece.

110

Reposted by Ben Barad

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

0207

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 🧵

311527

Ben Barad @baradlab.com · 10/07/2026

She was a good contributor, but our midfield is being asked to take on a lot of defensive responsibility with our current tactics, and she was less suited to that. When we had Coffey there was less pressure... Not a good fit for our current direction doesn't mean she wasn't a good Thorn!

Ben Barad @baradlab.com · 08/07/2026

Gonna miss her, felt like she was almost there for us, but obviously hard for her to get minutes ahead of our established attacking group (with quite a few more coming back from injury soon™)

040

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.

25612

Ben Barad @baradlab.com · 08/07/2026

I love weird membranes!

040

Ben Barad @baradlab.com · 05/07/2026

Believe they can't use the logos but I'd love the jolly Roger w/ sword and rose on a flag

100

Ben Barad @baradlab.com · 27/06/2026

This is what cryo-ET is made for!

070

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 ...

0187

Ben Barad @baradlab.com · 24/06/2026

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

17140

Ben Barad @baradlab.com · 19/06/2026

Note - I probably won't submit this one to the toolshed for a while, as I want to make sure all the output formats are really robust.

000

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...

171

I started with just a basic port (plus stopgap star files), but will start adding in more modern/standard output formats over the next week or three.

000

It's volume tracer, pick particle, and place object all in one.

Yep - started as a direct tkinter to qt port then added a few extra features but overall it's still Kun Qu's stuff.

100

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!

1385

Update: its looking pretty good so far! Even added arbitrary surface picking for morphometrics meshes...

Ben Barad @baradlab.com · 17/06/2026

Was just wondering if I could pure vibe code the transition

000

Ben Barad @baradlab.com · 17/06/2026

Almost certainly neither - if we want this, we will need to make the software ourselves for chimeraX!

100

Reposted by Ben Barad

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…

26323

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!

041

Ben Barad @baradlab.com · 13/06/2026

My day of the class used the 2.0.0beta1 release of surface morphometrics, which is packed full of a TON of new features, and is 40-50x faster than the 1.0 release. Expect a manuscript later this summer!

060

Ben Barad @baradlab.com · 13/06/2026

Fwiw this was true for me in fable from the US even before the global ban - anything even remotely bio related was hitting a hard wall.

110

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.

2418

Ben Barad @baradlab.com · 10/06/2026

Kvelling (reverse kvelling?) for my mom today!

Ben Barad @baradlab.com · 05/06/2026

Hmm probably shouldn't teach people easymode on my day!

Ben Barad @baradlab.com · 04/06/2026

What's the best back support pick in southeast?

100

Ben Barad @baradlab.com · 02/06/2026

Gotham, by comparison, has yet to beat a playoff team. I expect they will do fine once the season kicks into high gear for them, but the difference is stark.