A Local Agreement Filtering Algorithm for Transmission EM Reconstructions |
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Authors: | Kailash Ramlaul Colin M Palmer Christopher HS Aylett |
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Institution: | 1. Section for Structural Biology, Department of Medicine, Imperial College Road, South Kensington, London SW7 2BB, United Kingdom;2. Scientific Computing Department, Science and Technology Facilities Council, Research Complex at Harwell, Didcot OX11 0FA, United Kingdom |
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Abstract: | We present LAFTER, an algorithm for de-noising single particle reconstructions from cryo-EM.Single particle analysis entails the reconstruction of high-resolution volumes from tens of thousands of particle images with low individual signal-to-noise. Imperfections in this process result in substantial variations in the local signal-to-noise ratio within the resulting reconstruction, complicating the interpretation of molecular structure. An effective local de-noising filter could therefore improve interpretability and maximise the amount of useful information obtained from cryo-EM maps.LAFTER is a local de-noising algorithm based on a pair of serial real-space filters. It compares independent half-set reconstructions to identify and retain shared features that have power greater than the noise. It is capable of recovering features across a wide range of signal-to-noise ratios, and we demonstrate recovery of the strongest features at Fourier shell correlation (FSC) values as low as 0.144 over a 2563-voxel cube. A fast and computationally efficient implementation of LAFTER is freely available.We also propose a new way to evaluate the effectiveness of real-space filters for noise suppression, based on the correspondence between two FSC curves: 1) the FSC between the filtered and unfiltered volumes, and 2) Cref, the FSC between the unfiltered volume and a hypothetical noiseless volume, which can readily be estimated from the FSC between two half-set reconstructions. |
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Keywords: | 2D/3D 2/3-Dimensional Cryo-EM Electron Cryo-Microscopy CDF Cumulative distribution function EM Electron microscopy FSC Fourier shell correlation LAFTER Local Agreement Filter for Transmission EM Reconstructions RMSD Root mean squared deviation SNR Signal to noise ratio xFSC Cross-FSC Cryo-EM Local resolution Noise suppression Real-space filter |
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