Colin Ophus
@cophus.bsky.social
Associate Professor at Stanford University. Using data science and electron microscopy to solve research problems. Views my own. colab.stanford.edu elementalmicroscopy.org
After some upstreaming work by @curvenote.com and further work by the @mystmd.org core team, `anywidget` directive is now natively supported in `mystmd` and Jupyter Book 🎉 jupyterbook.org/blog/posts/2...
The MyST AnyWidget Directive - Jupyter Book: Blog
Updates from the Jupyter Book subproject.
jupyterbook.org
With the help of AI, I built a new package for making disordered supercells: tricor.readthedocs.io/en/latest/ex... tricor.readthedocs.io/en/latest/ex...
Another exciting paper - Using implicit neural representations to make electron tomography easier, more accurate and more robust! arxiv.org/pdf/2512.08113 Tutorials available too, example: github.com/electronmicr...
When the Microscopy Society of America set out to launch Elemental Microscopy, we partnered with them to make it happen fast - an interactive, open-access journal where readers can explore data and code while MSA maintains full control of the publishing process. Read the full story → bit.ly/3LxMAff
MSA | Curvenote
A web-first experience that brings science and data to the surface. Enhance comprehension and maximize impact and reach of your research using rich metadata and interactive figures.
bit.ly
Our new DGP ptychography methods paper is online on the arxiv! arxiv.org/abs/2511.07795 Code + tutorial notebooks available if you want to try it out for your own ptychography experiments.
We've just posted an open faculty search in MSE at Stanford! facultypositions.stanford.edu/en-us/job/49...
Stanford | Faculty Positions: Details - Assistant or Untenured Associate Professor in Materials Science and Engineering
facultypositions.stanford.edu
In this paper, we show that neutral gallium clusters from a Ga-FIB microscope’s liquid metal ion source can create nanopores in thin samples and damage. Because these clusters aren’t stopped by the beam blanker, your samples could be exposed to them without your knowledge! doi.org/10.1093/mam/...
Another cool scattering matrix inversion paper lead by Emmanuel Terzoudis-Lumsden and Scott Findlay: arxiv.org/abs/2506.21004
Another week, another great paper led by @stephanieribet.bsky.social ! Multi-angle precession electron diffraction (MAPED): a versatile approach to 4D-STEM precession arxiv.org/abs/2506.11327 Serial precession finally!
I have an opening for a Doctoral Researcher working on adaptive sampling and faster 3D imaging in electron microscopy. Please spread the word pelzlab.science/posts/25-01-...
PhD position open – ECLIPSE Lab
A PhD position on computational imaging in electron microscopy is available starting April 1st
pelzlab.science
Hello! Who's up for some more 4D-STEM? Maybe a 2-day workshop on applications of 4D-STEM in sunny Yorkshire is just your jam? Hop over to the @royalmicrosoc.bsky.social for info, www.rms.org.uk/rms-event-ca... We look forwards to seeing you there with @bmatb.expmicromech.com @cophus.bsky.social
Workshop on the Applications of 4D-STEM
The purpose of this workshop is to highlight the applications of 4D-STEM across a broad range of materials classes, both hard and soft, and by demonstrating the micro- and nano-structural information ...
rms.org.uk
Excited to share this interactive pre-print investigating the information transfer of phase retrieval techniques in STEM 🔬 Now everyone has an open-access tool to optimise their experimental parameters ✨ Feel free to share and play around with it 🧪 www.elementalmicroscopy.com/articles/EM0...
Evaluating the Transfer of Information in Phase Retrieval STEM Techniques - Elemental Microscopy
Evaluating the transfer of information in various phase retrieval STEM techniques using analytical and numerical methods.
elementalmicroscopy.com
Super proud of this work, which showcases modern scientific publishing for open science 🧪 Inspired by the insights of the interactive CTF widgets, we propose a novel phase-retrieval algorithm which achieves robust information transfer on sub-sampled datasets 🙌 @elementalmicrosc.bsky.social
Julie Marie Bekkevold (she/her)@juliedactyl.bsky.social · last yr.Excited to share this interactive pre-print investigating the information transfer of phase retrieval techniques in STEM 🔬 Now everyone has an open-access tool to optimise their experimental parameters ✨ Feel free to share and play around with it 🧪 www.elementalmicroscopy.com/articles/EM0...
@materials-mrs.bsky.social great job with the badge pickup guys - I think there are only 1000+ people ahead of me in line. And I tried to pick it up last night and was turned away.
What a completely unpredictable turn of events!! cleantechnica.com/2025/04/05/c...
China Just Turned Off U.S. Supplies Of Minerals Critical For Defense & Cleantech - CleanTechnica
In response to new Trump tariffs, China cut dysprosium, terbium, and tungsten exports—hitting U.S. EVs, wind, and military systems hard.
cleantechnica.com
Where are we at with bird flu? This video explains: www.youtube.com/watch?v=5CyV...
Bird Flu is Here
YouTube video by SciShow
youtube.com
Another great atomic electron tomography paper, lead by Prof Jihan Zhou! Check out these amazing reconstructions. www.nature.com/articles/s41...
Strain release by 3D atomic misfit in fivefold twinned icosahedral nanoparticles with amorphization and dislocations - Nature Communications
The crystallographically forbidden fivefold symmetry in icosahedra remains a long-standing mystery. Here, the authors resolve the three-dimensional atomic structure of Janus-like icosahedral nanoparti...
nature.com
This is the most relevant article to NIH and research cuts I’ve seen. Imagine if this was today , how many people would be saying “Why are we studying Gila Monsters and their impact on diabetes ? That’s wasted money !” globalnews.ca/news/9793403...
How a Canadian scientist and a venomous lizard helped pave the way for Ozempic - National | Globalnews.ca
In 1984, Dr. Daniel Drucker, an endocrinologist from the University of Toronto, discovered a hormone that helped pave the way for popular diabetes drugs such as Ozempic.
globalnews.ca
If you know someone who might also like to live in the chocolate city & develop 4D-STEM imaging, there's funding open & I'd be happy to chat -Roy Soc Newton International Fellowship royalsociety.org/grants/newto... -Marie Curie Fellowship marie-sklodowska-curie-actions.ec.europa.eu/actions/post...
Morning commutes living downwind of the chocolate factory 😋 #CommuteWithAView
Very cool explainer video on my field of electron microscopy! I still remember the first times I just kept zooming in and zooming in... and seeing atoms.
What if you just keep zooming in?
YouTube video by Veritasium
youtube.com
Hey there 🦋🧪, we're a new open access microscopy journal and wanted to introduce ourselves! EM aims to modernize scientific publishing for microscopy, by prioritizing open science, transparency, and accessibility and using open-source formats and interactive notebooks 🙌 @curvenote.com @mystmd.org 🚀
Nanobeam phase mapping from simulated data (so we know the ground truth) - it's a great day for open source!!
