I attempted to use ptyRAD to reconstruct simulated data with the following parameters: voltage = 200 kV, convergence angle = 25 mrad, scan step size = 0.32 Å, C10 = 75 Å, and dk = 0.0488 Å⁻¹. The simulated sample was a single-crystal Si [110] incorporating 16 frozen-phonon configurations (with no other perturbations or aberrations).
During the reconstruction, I tried increasing dz to observe the phase wrapping phenomenon (which might be linked to the "donut" artifacts often seen in reconstructions). However, as dz increased, no phase wrapping occurred; the phase of the single slice did not exceed 2π (or even π), as shown in the figure below. Furthermore, the peak phase value (and contrast) decreased, indicating a deterioration in reconstruction quality.
Additionally, a new issue arose: when I performed single-slice reconstruction, the results were extremely poor. Not only was the atomic structure unclear, but inexplicable artifacts also appeared on the left and right sides in the summary figure.
I would like to understand why I did not observe phase wrapping—could it be due to incorrect parameter settings? (I have attached my reconstruction parameters) I would also like to know the origin of the artifacts appearing on the left and right sides when dz = 220 Å.
Any suggestions would be greatly appreciated.
config_Si_sim_opt75_frozenphonon16.yaml
config_Si_sim_opt75_frozenphonon16_dz20.yaml
config_Si_sim_opt75_frozenphonon16_dz50.yaml
config_Si_sim_opt75_frozenphonon16_dz80.yaml
config_Si_sim_opt75_frozenphonon16_dz220.yaml
I attempted to use ptyRAD to reconstruct simulated data with the following parameters: voltage = 200 kV, convergence angle = 25 mrad, scan step size = 0.32 Å, C10 = 75 Å, and dk = 0.0488 Å⁻¹. The simulated sample was a single-crystal Si [110] incorporating 16 frozen-phonon configurations (with no other perturbations or aberrations).
During the reconstruction, I tried increasing dz to observe the phase wrapping phenomenon (which might be linked to the "donut" artifacts often seen in reconstructions). However, as dz increased, no phase wrapping occurred; the phase of the single slice did not exceed 2π (or even π), as shown in the figure below. Furthermore, the peak phase value (and contrast) decreased, indicating a deterioration in reconstruction quality.
Additionally, a new issue arose: when I performed single-slice reconstruction, the results were extremely poor. Not only was the atomic structure unclear, but inexplicable artifacts also appeared on the left and right sides in the summary figure.
I would like to understand why I did not observe phase wrapping—could it be due to incorrect parameter settings? (I have attached my reconstruction parameters) I would also like to know the origin of the artifacts appearing on the left and right sides when dz = 220 Å.
Any suggestions would be greatly appreciated.
config_Si_sim_opt75_frozenphonon16.yaml
config_Si_sim_opt75_frozenphonon16_dz20.yaml
config_Si_sim_opt75_frozenphonon16_dz50.yaml
config_Si_sim_opt75_frozenphonon16_dz80.yaml
config_Si_sim_opt75_frozenphonon16_dz220.yaml