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Synthetic Dataset Creation » History » Version 9

Dmitry Lyumkis, 06/07/2010 11:30 AM

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h1. Synthetic Dataset Creation
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This method uses projections of a 3D model in order to create a synthetic dataset. Although it can be modified according to the options specified, the scheme consists of 12 basic steps, as shown and summarized below:
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!http://emg.nysbc.org/attachments/294/Supplementary_Figure_5_-_Synthetic_dataset_creation.png!
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# a model is chosen from which projectinos are created
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# the model is projected either in an even distribution or with axial preference
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# the projections are randomly rotated in the XY plane
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# the projections are randomly shifted in the XY plane
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# white Gaussian noise is added
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# a contrast transfer function is added according to the specified defocus parameter and the spherical aberration constant of the microscope
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# an envelope function is added according to an experimentally determined decay function from 3000 real micrographs (see Voss, N, Lyumkis, D. et al, JSB (2010) 169, 3, 389-98).
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# a second level of Gaussian noise is added, usually to bring the signal-to-noise ratio down to ~0.05, consistent with real ice data (see Baxter, WT, et al, JSB (2009) 166, 2, 126-32).
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# (optional) the CTF is estimated by ACE2 and corrected
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# (optional) the particle is band-pass filtered
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# final particle of 50S ribosomal subunit with a SNR of 0.05
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# particle is added to a growing stack of synthetic particles
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!http://emg.nysbc.org/attachments/277/Picture_81.png!