iiinova — where your digital self keeps evolving

Reposted by Colin Ophus

Steve Purves @opensci.dev · 17/03/2026

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...

jupyterbook.org

The MyST AnyWidget Directive - Jupyter Book: Blog

Updates from the Jupyter Book subproject.

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Colin Ophus @cophus.bsky.social · 21/04/2026

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...

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Colin Ophus @cophus.bsky.social · 10/12/2025

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...

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Reposted by Colin Ophus

Curvenote® @curvenote.com · 12/11/2025

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

bit.ly

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.

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Colin Ophus @cophus.bsky.social · 12/11/2025

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.

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Colin Ophus @cophus.bsky.social · 06/08/2025

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/...

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Colin Ophus @cophus.bsky.social · 27/06/2025

Another cool scattering matrix inversion paper lead by Emmanuel Terzoudis-Lumsden and Scott Findlay: arxiv.org/abs/2506.21004

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Colin Ophus @cophus.bsky.social · 16/06/2025

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!

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Reposted by Colin Ophus

Philipp Pelz @philipppelz.bsky.social · 30/01/2025

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-...

pelzlab.science

PhD position open – ECLIPSE Lab

A PhD position on computational imaging in electron microscopy is available starting April 1st

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Reposted by Colin Ophus

Julie Marie Bekkevold (she/her) @juliedactyl.bsky.social · 14/05/2025

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...

elementalmicroscopy.com

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.

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Reposted by Colin Ophus

Georgios Varnavides @gvarnavides.bsky.social · 15/05/2025

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

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Colin Ophus @cophus.bsky.social · 07/04/2025

@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.

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Colin Ophus @cophus.bsky.social · 07/04/2025

Alright I'm in Seattle if anyone wants to grab dinner!

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Colin Ophus @cophus.bsky.social · 02/03/2025

Beautiful day with the dish broadcasting a rainbow!

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Colin Ophus @cophus.bsky.social · 02/03/2025

Where are we at with bird flu? This video explains: www.youtube.com/watch?v=5CyV...

youtube.com

Bird Flu is Here

YouTube video by SciShow

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Colin Ophus @cophus.bsky.social · 26/02/2025

NNI Nanometrology webinar: www.youtube.com/watch?v=gfQO...

youtube.com

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Reposted by Colin Ophus

Mark Cuban @mcuban.bsky.social · 09/02/2025

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...

globalnews.ca

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.

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Reposted by Colin Ophus

Dr Laura Clark @beamsontoast.bsky.social · 06/02/2025

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...

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Reposted by Colin Ophus

Toma Susi @mostlyphysics.net · 05/02/2025

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.

youtube.com

What if you just keep zooming in?

YouTube video by Veritasium

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Reposted by Colin Ophus

Elemental Microscopy @elementalmicrosc.bsky.social · 02/02/2025

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 🚀

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Colin Ophus @cophus.bsky.social · 30/01/2025

Nanobeam phase mapping from simulated data (so we know the ground truth) - it's a great day for open source!!

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Colin Ophus @cophus.bsky.social · 05/01/2025

Hilarious end of 2024 summary for py4DSTEM: www.wrapped.dev/repo/py4dste...

wrapped.dev

Wrapped.dev

Your Repos' 2024

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Colin Ophus @cophus.bsky.social · 04/01/2025

Nice write up of collaborative work on soft semiconductors between my group and the Salleo and Minor groups - work let by Yael Tsarfati! engineering.stanford.edu/news/researc... www.nature.com/articles/s41...

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Colin Ophus @cophus.bsky.social · 22/12/2024

First live hockey game in a very long time - Vancouver vs Ottawa, a chaotic 2:2 after the 1st!

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Reposted by Colin Ophus

Curvenote® @curvenote.com · 06/12/2024

Monday 9th 15:00 Open Science Pavilion - Big Screen, Exhibit Hall Join @row1.ca for a session on Publishing Computational Research Session #OpenScience #Jupyter @mystmd.org

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Reposted by Colin Ophus

Brent Toderian @brenttoderian.bsky.social · 08/12/2024

Just another helpful reminder that a human being on a bicycle is the most efficient amongst all animals and machines in terms of energy consumed in moving a certain distance as a function of body weight. Obvs.

Graph showing all the animals and machines in terms of energy efficiency

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Colin Ophus @cophus.bsky.social · 07/12/2024

Simulating electron diffraction combining precession and dynamical scattering!

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Colin Ophus @cophus.bsky.social · 07/12/2024

Great day for running the dish!

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Colin Ophus @cophus.bsky.social · 06/12/2024

Moire diffraction patterns! (simulated)

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Colin Ophus @cophus.bsky.social · 06/12/2024

USA is an extreme outlier in life expectancy vs healthcare spending: www.reddit.com/r/economicCo...

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Reposted by Colin Ophus

Berkeley Lab @berkeleylab.lbl.gov · 18/11/2024

🔬This image shows just 9 diffraction patterns (of 65536) from a dataset of gold nanoparticles on a carbon grid acquired for ptychographic reconstruction. 📷 Stephanie Ribet, Georgios Varnavides | @molecularfoundry.bsky.social @ucberkeleyofficial.bsky.social More: foundry.lbl.gov/2024/10/21/a...

A grid of nine images, each showing differing patterns of glowing blue dots on a dark background.

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Colin Ophus @cophus.bsky.social · 02/12/2024

Folks who give scientific talks on diffraction - here is a tutorial for rendering a physics demo movie using matplotlib and numpy, which you can run entirely in colab: drive.google.com/file/d/1uBq6... I show how to drawing pseudo-3D atoms in another tutorial: drive.google.com/file/d/1uUir...

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Colin Ophus @cophus.bsky.social · 01/12/2024

In our new paper, we describe a missing type of Dzyaloshinskii–Moriya interaction that stabilizes in-plane magnetic chirality, enabling the creation and control of topological textures like merons and bimerons with ultra-low DMI strengths! doi.org/10.1038/s414...

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Colin Ophus @cophus.bsky.social · 15/11/2024

Good / bad academic habits - spending WAY too long making figures! doi.org/10.1017/S143...

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