some background: in my phd, i'm working towards bridging protein and cellular scale behaviors in microtubule self-organization. the problem is that the scale of individual proteins is extremely difficult to observe in situ.
thank you to all my co-authors and contributors to our open source code base! (and thanks @miroastore.bsky.social for making this movie)
this has led me to cryo-EM and inspired my development of cryoJAX. i think cryo-EM data has great promise to inform physics models, but leveraging the data is computationally burdensome and a challenge of high-dimensional statistical inference.
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…
hey bsky! excited to share what i've been working on for a few years now.
cryoJAX: A Cryo-EM Image Simulation Library In JAX
www.biorxiv.org/content/10.1...
cryoJAX is a modular framework for implementing forward models of cryo-EM image formation. these can be used to build powerful data analyses!
Link to the repo: github.com/michael-0bri...
a toy demonstration: in only a few blocks of code, we can use cryoJAX and JAX automatic differentiation to implement a gradient-based optimization that recovers conformation A starting from conformation B. check out the code (roughly) used here: michael-0brien.github.io/cryojax/exam...
www.biorxiv.org
Michael O’Brien
Michael O’Brien
Happy to share our cryoEM Ensemble Optimization method! 🎉It infers optimal structures and their weights directly from individual cryoEM images - no maps just physics! with David Sliva-Sánchez, @erikhthiede.bsky.social & Roy Lederman www.biorxiv.org/content/10.6...
