Open-Source Phase Retrieval
- Suite of open-source STEM phase retrieval algorithms:
- “in-focus” techniques: center-of-mass (COM) imaging and direct ptychography (SSB/WDD)
- “out-of-focus” techniques: tilt-corrected BF-STEM (parallax) and iterative ptychography
- User-friendly and GPU-accelerated code
ptycho = py4DSTEM.process.phase.SingleslicePtychography(
datacube=dataset,
energy = 80e3,
semiangle_cutoff = 21.4,
device = 'gpu', # GPU acceleration
storage = 'cpu', # on-demand data streaming
).preprocess(
plot_center_of_mass = False,
).reconstruct(
num_iter = 8,
step_size = 0.5,
gaussian_filter_sigma = 0.2, # regularizations
).visualize(
)
Example Materials-Science Reconstructions
- Reconstructions of a variety of materials classes[4]
- 2D materials as-well as “thick” objects (multislice)
- Reconstructions using a number of different detectors
- low (4D Camera, K3) / high (EMPAD, Arina) dynamic range
- even on a CMOS detector!
Ti islands on graphene
few-layer hBN
low-voltage CMOS detector
STO bottom-layer
STO middle-layer
STO top-layer
Core-shell bottom-layer
Core-shell middle-layer
Core-shell top-layer
Example Life-Sciences Reconstructions
- Reconstructions of a variety of dose-sensitive samples[5]
- plunge-frozen in vitreous ice → single-particle analysis
Virus-like particles (tilt-corrected BF-STEM)
Apoferritin proteins (iterative ptychography)
Tobacco mosaic virus (iterative ptychography)
https://github.com/py4dstem/py4DSTEM_tutorials/tree/main/notebooks ↩︎
Iterative Phase Retrieval Algorithms for Scanning Transmission Electron Microscopy, arXiv:2309.05250 ↩︎
4D-STEM dataset used was recorded by Zhen Chen, at Cornell: Electron ptychography of 2D materials to deep sub-ångström resolution ↩︎
Materials-science sample & imaging credit: K.Reidy, D. Byrne, F. Allen, B. Cohen, H. Shih, D. Kepaptsoglou, C. Ophus, S. Ribet ↩︎
Life-sciences sample & imaging credit: Y. Yu, K. Küçükoglu, S. Ribet ↩︎