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cryoJAX
Utilities for converting between angular parametrizations
michael-0brien/cryojax
cryoJAX
michael-0brien/cryojax
Welcome to cryoJAX!
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
Advanced usage
Advanced usage
Structural refinement using gradient descent
API
API
cryojax.simulator
cryojax.simulator
Api
Representing volumes
Representing volumes
Representing poses
Modeling cryo-EM volumes
Image formation
Image formation
Volume integration methods
Contrast transfer functions
Scattering approximations
Putting it all together
Putting it all together
Configuring an image
Rendering an image
Distributions: noisy images and likelihoods
cryojax.dataset
cryojax.dataset
RELION compatibility
cryojax.io
cryojax.io
Reading and writing MRC files
Reading atomic structures
cryojax.ndimage
cryojax.ndimage
Utility functions for image and volume arrays
cryojax.ndimage.operators
cryojax.ndimage.operators
Operators
cryojax.ndimage.transforms
cryojax.ndimage.transforms
Image transforms (filters and masks)
cryojax.coordinates
cryojax.coordinates
Creating coordinate systems
Transforming coordinate systems
cryojax.rotations
cryojax.rotations
Representing rotations
Utilities for converting between angular parametrizations
cryojax.constants
cryojax.constants
Working with physical units
Scattering factor parameters
Converting between common conventions
cryojax.atom_util
cryojax.atom_util
Utilities for atom manipulation
cryojax.jax_util
cryojax.jax_util
Helper functions for Equinox filtering
Grid search interface
Reparameterizing pytrees
Useful JAX functions
Utilities for converting between angular parametrizations
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