biostudies-literatureBromberg RU.S. Department of EnergyOffice of ScienceNational Institutes of HealthNational Institute of General Medical SciencesNIGMS NIH HHSCancer Prevention and Research Institute of Texas107945https://www.ebi.ac.uk/biostudies/studies/S-EPMC10200766biostudies-literatureUnknown215(2)Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed images is usually corrected for motion between frames prior to particle stack creation. However, the contrast transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step. Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of lower resoJournal of structural biologyCryoEM single particle reconstruction with a complex-valued particle stack.PMC10200766R21GM126406R01GM118619R44 GM137671R21 GM126406R01 GM117080R35 GM145365DE-SC0019600R35GM145365R43 GM137671R01GM117080R01 GM118619DE-SC0021600R44GM137671Borek DGuo YOtwinowski ZBromberg RfalseCryoEM single particle reconstruction with a complex-valued particle stack.Single particle reconstruction (SPR) in cryoEM is an image processing task with an elaborate hierarchy that starts with many very noisy multi-frame images. Efficient representation of the intermediary image structures is critical for keeping the calculations manageable. One such intermediary structure is called a particle stack and contains cut-out images of particles in square boxes of predefined size. The micrograph that is the source of the boxed images is usually corrected for motion between frames prior to particle stack creation. However, the contrast transfer function (CTF) or its Fourier Transform point spread function (PSF) are not considered at this step. Historically, the particle stack was intended for large particles and for a tighter PSF, which is characteristic of lower reso2023-01-01T00:00:00Z2023 Jun2025-04-05T08:50:26.305Z2025-02-19T01:16:04.879ZS-EPMC102007663688956010.1016/j.jsb.2023.107945