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cryoJAX
Noise and likelihoods
michael-0brien/cryojax
Welcome to cryoJAX!
Overview
Examples
API
FAQ
cryoJAX
michael-0brien/cryojax
Welcome to cryoJAX!
Overview
Examples
Examples
Getting started
Getting started
Simulate an image
JAX transformations
Render a volume
Load cryo-EM images
Create custom image simulation methods
Your first program
Your first program
Write a STAR file of simulated data
Structural refinement using gradient descent
API
API
The simulator
The simulator
Your entry point
Representing volumes
Representing volumes
Representing poses
Modeling cryo-EM volumes
Image formation
Image formation
Volume projection and integration onto the plane
Contrast transfer functions
Scattering approximations
Detectors
Putting it all together
Putting it all together
Configuring an image
Image formation models
Noise and likelihoods
Support utilities
Support utilities
Basic loading of atoms, images, and volumes
Image and volume manipulation
Atom manipulation
Physical constants
Rotations in cryo-EM
Cryo-EM datasets and software compatibility
Extra JAX/Equinox
FAQ
Noise and likelihoods
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