How are competitive new grants looking ?

Cannot recommend the talk by Louis Smith enough. It's been such an amazing project!

Really neat math that I use a lot. Well done @pilarcossio.bsky.social, Wai Shing, Jeff and Adi!

It’s been fun to put together and write up cryoJAX. Hooray for open-source cryo-EM software! Now it’s time to use it…

GitHub - michael-0brien/cryojax: A cryo-electron microscopy image simulation library for building data analysis in JAX A cryo-electron microscopy image simulation library for building data analysis in JAX - michael-0brien/cryojax

github.com/michael-0bri...

Go use cryojax ! It's awesome! I can't wait to see what people do with it.

Quantifying distributions of cryo-EM projections We propose a numerical measure to quantify the deviation of a distribution of cryo-EM 2D views from the uniform distribution. This approach allows the traditional two-dimensional projection diagrams to be complemented with quantitative characteristics and simple, easily generated curves that are straightforward to analyze.

Alexandre G. Urzhumtsev: Quantifying distributions of cryo-EM projections #CryoEM #AngularDistributionOfViews #NonUniformDistribution ... #IUCr https://journals.iucr.org/paper?S2059798325011611

Thank you for writing it @fraserlab.com! It was super valuable and detailed.

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge pubmed.ncbi.nlm.nih.gov/41280101/ #cryoEM

CryoLike: a Python package for cryo-electron microscopy image-to-structure likelihood calculations pubmed.ncbi.nlm.nih.gov/41258998/ #cryoEM

Hello world! It's been a true joy to work on this with Michael. Both him and cryoJAX are things to keep an eye on. They're going to make amazing things happen in cryo and beyond.

CryoJAX - A Cryo-Electron Microscopy Image Simulation Library in JAX www.biorxiv.org/content/10.1101/2025.10.23.682564v1 #cryoEM

Phew!

Restriction on Entry of Certain Nonimmigrant Workers BY THE PRESIDENT OF THE UNITED STATES OF AMERICA A PROCLAMATION The H-1B nonimmigrant visa program was created to bring temporary workers into the United

The text of the order says it's a one time charge for new petitions, renewals and transfers.

www.whitehouse.gov/presidential...

This one is a bit of a departure from the usual and definitely a work in progress!

We found that by using ab initio reconstruction at very high res, in very small steps, we could crack some small structures that had eluded us - e.g. 39kDa iPKAc (EMPIAR-10252), below.

Read on for details... 1/x

I'm very excited to announce that I've just joined Steve_Bonilla's lab at @rockefelleruniv.bsky.social. With the help of @pilarcossio.bsky.social and colleagues at @flatironinstitute.org. I'll be developing cryoEM into a quantitative method to study RNA biophysics.

The results of the first #cryoEM heterogeneity challenge are up on biorxiv!
www.biorxiv.org/content/10.1...

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...

Link that works
www.biorxiv.org/content/10.1...

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...

Omg thank you. Oops

www.biorxiv.org/content/10.1...

The Inaugural Flatiron Institute Cryo-EM Conformational Heterogeneity Challenge Despite the rise of single particle cryo-electron microscopy (cryo-EM) as a premier method for resolving macromolecular structures at atomic resolution, methods to address molecular heterogeneity in v...

Omg thank you. Oops

www.biorxiv.org/content/10.1...

GitHub - flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1: The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge The Inaugural Flatiron Institute Cryo-EM Heterogeneity Community Challenge - flatironinstitute/Cryo-EM-Heterogeneity-Challenge-1

You can also check out the analysis workflow and the datasets themselves if you'd like to learn more github.com/flatironinst...

www.simonsfoundation.org/flatiron/cen...

This has been so much work from my coauthors Geoff Woollard and David Silva-Sanchez, mentors @sonyahanson.bsky.social
and @pilarcossio.bsky.social , Misha Kopylov at NYSBC, and all the participants who have continuously given us excellent feedback on the study and the manuscript. Thanks everybody!

The last metric we used calculates the likelihood that a given ensemble of volumes is contained in a set of images. This one is really exciting because we don't need any ground truth to compare to. We see the same trends between the simulated and experimental datasets.

The next is based on optimal transport. By calculating the differences between maps in a submission and the ground truth, we can calculate how close a submission is to the truth. We can also see how far from optimal participants estimated their populations.

Now comes the real work. Comparing all this amazing data! We came up with three novel ways of comparing series of volumes. With the first we simply perform PCA on the voxel maps and compare their bases. Turns out to be a super useful way of comparing motions between submissions.

We had amazing participation. Almost every method in the literature submitted to this challenge. We've chosen to keep the identity of the submissions anonymous (you'll see them in the manuscript denoted by icecream flavor hehe).

We asked each participant to give us two things. 80 volume maps which they thought gave a good representation of the molecular states in the data. And relative populations between those molecular states.

That's why we launched this challenge. We made two datasets, one experimental and one simulated. The simulated one was made with structures from molecular dynamics simulations. Here we hid a triple Gaussian for participants to discover. (Movie credit David Herreros).

There has been an explosion of methods to determine molecular ensembles from single particle cryo-EM datasets. However, these methods all use totally different algorithms and it's currently unknown how to assess their accuracy without ground truth structures to compare with.