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mjo22
/
cryojax
Cryo electron microscopy image simulation and analysis built on JAX.
https://mjo22.github.io/cryojax/
GNU Lesser General Public License v2.1
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fix bug in loading from multiple mrcs
#275
DSilva27
closed
3 days ago
0
implement loading from different mrcfiles in RelionDataset
#274
DSilva27
closed
4 days ago
0
Load from multiple mrcs when getting items from RelionDataset
#273
DSilva27
closed
4 days ago
0
Small bug in how the name of the mrcs was defined inside the starfiles
#272
DSilva27
closed
1 week ago
1
Fix bug in new writer function
#271
mjo22
closed
1 week ago
0
Simplify writer by assuming function takes in particle stack
#270
mjo22
closed
1 week ago
0
Fix bugs in `RelionDataset`
#269
mjo22
closed
2 weeks ago
0
Make it optional to read in envelopes
#268
mjo22
closed
2 weeks ago
0
jax.tree_util -> jax.tree
#267
mjo22
opened
2 weeks ago
0
211 starfile writer
#266
DSilva27
closed
1 week ago
1
Get rid of `pose.offset_z_in_angstroms` in the `AbstractPose`?
#265
mjo22
opened
2 weeks ago
1
252 add envelope function to reliondataset
#264
DSilva27
closed
2 weeks ago
3
Change defocus parameter convention to mean defocus
#263
mjo22
closed
3 weeks ago
0
specify whether to use gemmis occupancy threshold when loading a pdb.
#262
Miro-Astore
opened
3 weeks ago
0
Allow varying defocus during imaging.
#261
Miro-Astore
opened
3 weeks ago
0
Update contrast_transfer_theory.py to allow defocus to be zero
#260
DSilva27
closed
3 weeks ago
1
Allow defocus to be zero in CTF definition
#259
DSilva27
closed
2 weeks ago
0
First pass at multislice implementation
#258
mjo22
opened
1 month ago
2
Optionally read arrays on the CPU in `RelionDataset`
#257
mjo22
closed
1 month ago
0
add option to only load starfile parameters in RelionDataset
#256
DSilva27
closed
1 month ago
6
Update documentation in `AbstractDataset` to show proper creation of a custom pytorch dataset
#255
mjo22
opened
1 month ago
1
Add option to not load particles in RelionDataset
#254
DSilva27
closed
1 month ago
0
Multislice
#253
geoffwoollard
closed
1 month ago
1
Add envelope function to RelionDataset
#252
DSilva27
closed
2 weeks ago
2
Multislice (old branch for reference of complex ctf)
#251
geoffwoollard
closed
1 month ago
1
Create cryojax.experimental submodule
#250
mjo22
closed
1 month ago
0
Bugfix: missing factor of 10 in loading from mdtraj
#249
ehthiede
closed
2 months ago
0
Unit Conversion for MDTraj
#248
ehthiede
closed
2 months ago
1
Fix mac install issues
#247
mjo22
closed
2 months ago
0
Contributor guidelines
#246
geoffwoollard
closed
2 months ago
1
implement bioem likelihood
#245
geoffwoollard
closed
2 weeks ago
2
Option to normalize signal in IndependentGaussianFourierModes distribution
#244
mjo22
closed
2 months ago
1
Add boolean option to normalize images before computing likelihoods
#243
mjo22
closed
2 months ago
1
Convert back to standard FFT convention
#242
mjo22
closed
3 months ago
0
Change FFT normalization convention to "ortho"
#241
mjo22
closed
3 months ago
0
Cleanup the radially averaged power spectrum
#240
mjo22
closed
3 months ago
0
Converting to ortho FFT Convention
#239
ehthiede
closed
2 months ago
2
Touch up filter and mask interface and add more cosine masks
#238
mjo22
closed
3 months ago
0
filters (fourier masking and real space masking)
#237
geoffwoollard
closed
2 weeks ago
4
More realistic water model
#236
geoffwoollard
opened
3 months ago
5
Complete documentation
#235
mjo22
opened
4 months ago
0
Developer guide
#234
mjo22
closed
2 months ago
1
Generate volumes using error functions
#233
mjo22
closed
4 months ago
0
Add feature to compute images from extracting surfaces on the ewald sphere
#232
mjo22
closed
1 month ago
1
Speedup in voxel grid computation
#231
mjo22
closed
4 months ago
0
demo tutorials for building intuition of forward model
#230
geoffwoollard
opened
4 months ago
0
Add new integrator to docs
#229
mjo22
closed
4 months ago
0
change type hint for upsampling_factor in GaussianMixtureProjection
#228
DSilva27
closed
4 months ago
1
Add atom potential integrator for mixtures of gaussians
#227
mjo22
closed
4 months ago
0
Make tutorial for simulating a starfile, and reading+reproducing that starfile
#226
DSilva27
closed
5 days ago
2
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