End-to-end reconstruction for cryo electron ptychographic single-particle analysis
- 1Friedrich-Alexander Universitaet Erlangen-Nuernberg
Abstract
Cryo-electron ptychographic (cryo-ptycho) single-particle analysis (SPA) is a diffractive imaging method for protein structure determination. Current reconstruction workflows sequentially reconstruct a 2D phase micrograph from each scan, and then apply conventional SPA software to the resulting projections to obtain a 3D potential map. Here, we introduce End2EndPtychoSPA, an end-to-end reconstruction algorithm that directly fits a 3D electrostatic potential volume and particle poses to 4D-STEM diffraction data using a differentiable multislice forward model. On simulated haemoglobin data where the sequential route recovers initial poses, End2EndPtychoSPA with a learnable vitreous-ice layer reaches 3.22 A resolution against the ground truth (FSC 0.5), compared with 3.41 A for the sequential route. We also compare End2EndPtychoSPA with the sequential route on four published experimental cryo-ptycho SPA datasets. On apoferritin (11,552 particles), the End2EndPtychoSPA map improves agreement with an external atomic model over both our matched sequential route on the same particles and the deposited EMD-19425 half-map mean, and shifts the unmasked half-map FSC 0.143 crossing from 6.83 A to 5.99 A. On T20S, TMV and Phi92, End2EndPtychoSPA does not yet improve upon the 2D route.
Related
- Diffractograph: single-particle reconstruction using electron-diffraction data
- Particle picking and centering in cryo-electron micrographs via a vanishing radial kernel
- Reconstruction-Aware Cryo-EM Particle Picking
- AreTomoLive: automated reconstruction of comprehensively corrected and denoised cryo-electron tomograms in real time and at high throughput
- Identical-location electron microscopy for the discovery of heterogeneous catalysts' dynamics at the single-particle level.
BibTeX
@misc{you2026endtoend,
title = {{End-to-end reconstruction for cryo electron ptychographic single-particle analysis}},
author = {S. You and N. Palatkin and S. Shao and P. M. Pelz},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.31.763295},
url = {https://www.biorxiv.org/content/10.64898/2026.10.31.763295v1},
note = {CC BY},
}
RIS
TY - UNPB
TI - End-to-end reconstruction for cryo electron ptychographic single-particle analysis
AU - S. You
AU - N. Palatkin
AU - S. Shao
AU - P. M. Pelz
PY - 2026
DA - 2026/10/31
PB - bioRxiv
DO - 10.64898/2026.10.31.763295
UR - https://www.biorxiv.org/content/10.64898/2026.10.31.763295v1
AB - Cryo-electron ptychographic (cryo-ptycho) single-particle analysis (SPA) is a diffractive imaging method for protein structure determination. Current reconstruction workflows sequentially reconstruct a 2D phase micrograph from each scan, and then apply conventional SPA software to the resulting projections to obtain a 3D potential map. Here, we introduce End2EndPtychoSPA, an end-to-end reconstruction algorithm that directly fits a 3D electrostatic potential volume and particle poses to 4D-STEM diffraction data using a differentiable multislice forward model. On simulated haemoglobin data where the sequential route recovers initial poses, End2EndPtychoSPA with a learnable vitreous-ice layer reaches 3.22 A resolution against the ground truth (FSC 0.5), compared with 3.41 A for the sequential route. We also compare End2EndPtychoSPA with the sequential route on four published experimental cryo-ptycho SPA datasets. On apoferritin (11,552 particles), the End2EndPtychoSPA map improves agreement with an external atomic model over both our matched sequential route on the same particles and the deposited EMD-19425 half-map mean, and shifts the unmasked half-map FSC 0.143 crossing from 6.83 A to 5.99 A. On T20S, TMV and Phi92, End2EndPtychoSPA does not yet improve upon the 2D route.
ER -