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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First pass at multislice implementation #258

Open mjo22 opened 3 months ago

mjo22 commented 3 months ago

This should be pretty much good to go. I think it would be good to formalize the multislice.ipynb into a more complete tutorial for the PR.

Fresnel propagator units look reasonable, amplitude contrast is implemented (needs references), and we have a naive implementation of variable slice thickness.

Anti-aliasing can be done with padding, but if there is another implementation that we should use instead we can do that.

The main issue is that things are slow because we rasterize a voxel-grid every time we want an image. Perhaps in the future an interpolation method should be used on a pre-rasterized grid.

Questions:

geoffwoollard commented 3 months ago

Let me work on a tutorial for the PR

mjo22 commented 2 months ago

Two comments