iiinova — where your digital self keeps evolving

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 · 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 · 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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Ben Barad @baradlab.com · 18/06/2026

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

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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 · 26/12/2025

Of note, for the peer reviewed edition we added a super cool collaboration with Neal Waxham and Fred Heberle, who have been doing thickness measurements in vitro for years with extruded vesicles. We showed that using the same sample, our measurement matches theirs within 2%!!

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Ben Barad @baradlab.com · 26/12/2025

Membrane thickness is a super interesting parameter of ultrastructure, and we don't know a ton about its impact yet. We've found some very interesting correlations with high curvature in cells; the journal version adds a control to show this is different in vitro!

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Ben Barad @baradlab.com · 26/12/2025

We got really excited after developing the thickness measurement tools to see really strong variance between organelles and even within organellar subcompartments we could see significant changes despite being in a continuous membrane environment.

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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 · 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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Ben Barad @baradlab.com · 02/05/2025

So far, no organelle we've seen comes close to the replication organelles from langatvirus infections: www.biorxiv.org/content/10.1...

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Ben Barad @baradlab.com · 07/03/2025

Happy to share that the final version of record for our ( @nanigrotjahn.bsky.social) #teamtomo mitochondrial cotranslation story is online at @jcb.org! We combined STA with surface morphometrics to learn how ribosomes bind to and alter mitochondrial membranes in yeast. rupress.org/jcb/article/...

Subtomogram Averaging of a mitochondrially co-translating ribosome

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Ben Barad @baradlab.com · 16/12/2024

Tomorrow(!) morning at 9AM pacific, I am giving a webinar for EMS discussing the surface morphometrics pipeline and our approach to contextual structural biology #teamtomo. Free to attend, hope to see you all there! us06web.zoom.us/webinar/regi...

Example series showing the surface morphometrics workflow

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Ben Barad @baradlab.com · 06/12/2024

It has been clear all week in portland, which makes for some VERY cold bike rides but also some incredible views from my office!

Photo of the Portland skyline with Mt St Helens in the background

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Ben Barad @baradlab.com · 26/11/2024

The Arc Reactor of the 4th floor genentech hall at UCSF:

A back staircase of my old apartment showing a coffee roaster in action

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Ben Barad @baradlab.com · 22/11/2024

In cloudflare DNS, it goes in the "Name" section. I am not showing the "Content" since that could be used to hijack, but it is the bit that starts with "did="

Cloudflare DNS entry w/ only the Type and Name

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Ben Barad @baradlab.com · 19/11/2024

Last week I had the unique and special experience of presenting a scientific mentoring award in honor of my late grandfather, George Martin, for the American Federation of Aging Research. I was touched by how fondly he is remembered as a friend and mentor for so many. www.afar.org/george-m-mar...

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Ben Barad @baradlab.com · 15/09/2024

My streak of @nytimes.com crosswords hit four years today!

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Ben Barad @baradlab.com · 17/07/2024

Finally got around to making one! Works great.

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Ben Barad @baradlab.com · 03/04/2024

First hotend failure on the bambu (polycarbonate clog managed to push the hotend right off the heat break). Anyone know if its possible to reassemble and reuse, assuming I am even able to clear this clog? Polycarbonate is tough as nails once its cooled!

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Ben Barad @baradlab.com · 21/03/2024

We have autoclavable, biocompatible grid holders for #teamtomo! And also a great lesson in crystal mosaic packing.

A tray of 233 "crystal-packed" cryoEM grid holders for cell culture on a 3d printing build plate.

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Ben Barad @baradlab.com · 20/03/2024

Progression of polycarbonate printing - ready for grid holders!

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Ben Barad @baradlab.com · 23/02/2024

I'm still not used to how beautiful Portland is

Aerial Tram with Mt Hood in the background

View of Portland with Mt St Helens in the background

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Ben Barad @baradlab.com · 21/02/2024

Lots of game left but player of the match tonight for the #uswnt is sealed up for me.

Picture of midge purce smoking a cigar with her MVP trophy and the championship trophy

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Ben Barad @baradlab.com · 14/12/2023

Still don't totally get why it's famous but this is home now!

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Ben Barad @baradlab.com · 04/12/2023

Last day on a Scripps microscope is in the books with some post-TEM fluorescence so I can CLEM all the things!

Fluorescence image showing GFP puncta within a FIB-milled lamella

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Ben Barad @baradlab.com · 30/11/2023

TEM or Coffee Machine?

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Ben Barad @baradlab.com · 27/11/2023

Discovered a typo/error in our surface morphometrics paper a year after the final publication and 2 years after the preprint - I will never unsee this.

Equation with an accidentally subscripted letter a

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Ben Barad @baradlab.com · 22/11/2023

SerialEM crashing and leaving low-dose mode unexpectedly is giving me a nice direct visualization of how small my "extra-tight" beam setting really is. I want fringe free so we can get even more shots per lamella!

A hole in a lamella, shown by a low-magnification TEM image, shows where the beam burned (accidentally). A rectangle shows the area captured by the K3 camera.

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Ben Barad @baradlab.com · 22/11/2023

We're starting to get great results from the next tool in the Surface Morphometrics toolkit and I am so excited about it! Its going to be a while before I get the UX nailed down so it is as plug and play as the rest of the quants, but we're gonna have a preview with a collaborator coming out soon™!

Violin plot with a significant (p<0.0001) change between two conditions. x and y axis labels are intentionally removed.

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Ben Barad @baradlab.com · 15/11/2023

Almost like I'm already in the PNW!

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Ben Barad @baradlab.com · 12/10/2023

10/10 worth the boredom

SEM image overlayed with green fluorescence showing 33 targeted sites and 27 polished lamellae

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Ben Barad @baradlab.com · 13/09/2023

I feel lucky to have been able to attend a symposium this week in remembrance of my grandfather, George Martin. I knew him as a family member, and it was a joy to see the lives he touched as a scientist and mentor and to learn more about his beloved field of aging research.

Seminar honoring Dr. George Martin at UW

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