Reconstruction-Aware Cryo-EM Particle Picking
Abstract
Cryo-electron microscopy (cryo-EM) determines the structures of proteins and macromolecular assemblies at near-atomic resolution, and the final 3D reconstruction depends on extracting a clean particle stack from noisy micrographs. This extraction decomposes into three sub-tasks, namely particle picking, contamination removal, and 2D class selection. Each of them, however, is trained and evaluated in isolation, and none is optimized for the reconstruction. We instead integrate the three sub-tasks into a single pipeline posed against downstream reconstruction quality. We instantiate the pipeline with a state-of-the-art component for each sub-task, CryoTransformer picking permissively, MicrographCleaner masking contamination, and CryoSift selecting 2D classes by a continuous quality score, and close the loop with a fine-tuning step that returns the surviving particles to the picker. The pipeline achieves a better 3D resolution than every picker we compare. We also show that the best 2D F1 is not the best resolution, so particle selection is better treated as one reconstruction-aware pipeline judged by the map it delivers.
Related
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BibTeX
@misc{itsuji2026reconstructionaware,
title = {{Reconstruction-Aware Cryo-EM Particle Picking}},
author = {Riku Itsuji and Yuanhao Wang and Xingjian Li and Seonghui Min and Hideo Saito and Min Xu},
howpublished = {arXiv},
year = {2026},
month = aug,
doi = {10.48550/arxiv.2608.28838},
eprint = {2608.28838},
archivePrefix = {arXiv},
url = {https://arxiv.org/abs/2608.28838},
note = {CC BY-NC-ND 4.0},
}
RIS
TY - UNPB
TI - Reconstruction-Aware Cryo-EM Particle Picking
AU - Riku Itsuji
AU - Yuanhao Wang
AU - Xingjian Li
AU - Seonghui Min
AU - Hideo Saito
AU - Min Xu
PY - 2026
DA - 2026/08/28
PB - arXiv
DO - 10.48550/arxiv.2608.28838
UR - https://arxiv.org/abs/2608.28838
AB - Cryo-electron microscopy (cryo-EM) determines the structures of proteins and macromolecular assemblies at near-atomic resolution, and the final 3D reconstruction depends on extracting a clean particle stack from noisy micrographs. This extraction decomposes into three sub-tasks, namely particle picking, contamination removal, and 2D class selection. Each of them, however, is trained and evaluated in isolation, and none is optimized for the reconstruction. We instead integrate the three sub-tasks into a single pipeline posed against downstream reconstruction quality. We instantiate the pipeline with a state-of-the-art component for each sub-task, CryoTransformer picking permissively, MicrographCleaner masking contamination, and CryoSift selecting 2D classes by a continuous quality score, and close the loop with a fine-tuning step that returns the surviving particles to the picker. The pipeline achieves a better 3D resolution than every picker we compare. We also show that the best 2D F1 is not the best resolution, so particle selection is better treated as one reconstruction-aware pipeline judged by the map it delivers.
ER -