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cryoJAX
Filters and masks
mjo22/cryojax
cryoJAX
mjo22/cryojax
Welcome to cryoJAX!
Examples
Examples
Getting started
Getting started
Simulate an image
JAX transformations
Render a volume
Load cryo-EM images
Your first program
Your first program
Write a STAR file of simulated data
API
API
cryojax.simulator
cryojax.simulator
Api
Representing volumes
Representing volumes
Scattering potential representations
Representing poses
Structural ensembles
Image formation
Image formation
Scattering potential 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
Filters and masks
cryojax.ndimage.transforms
cryojax.ndimage.transforms
Transforms
cryojax.coordinates
cryojax.coordinates
Creating coordinate systems
Transforming coordinate systems
cryojax.rotations
cryojax.rotations
Representing rotations
Helpers for converting angular parameterizations
cryojax.constants
cryojax.constants
Working with physical units
Scattering factor parameters
cryojax.jax_util
cryojax.jax_util
Helper functions for Equinox filtering
Grid search interface
Reparameterizing pytrees
Useful JAX functions
Filters and masks
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