An Algorithm for Enhancing the Image Contrast of Electron Tomography

Dongsheng Lei,Xiaobo Zhai,Rongfang Bie,Jianfang Liu,Yadong Yu,Hao Wu,Gang Ren

doi:10.1038/s41598-018-34652-9

Dongsheng Lei, Xiaobo Zhai + Show 5 more

Open Access

https://doi.org/10.1038/s41598-018-34652-9

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Abstract

Three-dimensional (3D) reconstruction of a single protein molecule is essential for understanding the relationship between the structural dynamics and functions of the protein. Electron tomography (ET) provides a tool for imaging an individual particle of protein from a series of tilted angles. Individual-particle electron tomography (IPET) provides an approach for reconstructing a 3D density map from a single targeted protein particle (without averaging from different particles of this type of protein), in which the target particle was imaged from a series of tilting angles. However, owing to radiation damage limitations, low-dose images (high noise, and low image contrast) are often challenging to be aligned for 3D reconstruction at intermediate resolution (1–3 nm). Here, we propose a computational method to enhance the image contrast, without increasing any experimental dose, for IPET 3D reconstruction. Using an edge-preserving smoothing-based multi-scale image decomposition algorithm, this method can detect the object against a high-noise background and enhance the object image contrast without increasing the noise level or significantly decreasing the image resolution. The method was validated by using both negative staining (NS) ET and cryo-ET images. The successful 3D reconstruction of a small molecule (<100 kDa) indicated that this method can be used as a supporting tool to current ET 3D reconstruction methods for studying protein dynamics via structure determination from each individual particle of the same type of protein.

Highlights

In solution, protein particles travel in following the Brownian motion and their structures are vibrated in following the thermodynamics
The analyses showed that the Fourier ring correlation (FRC) curves were similar to the curves before applied the enhancement (Fig. 2B)
The Fourier shell correlation (FSC) analyses of the 3D reconstructions showed no significant change in resolution (Fig. 3B), but the SNR levels were increased by 50%, (Table 2), which was consistent to the larger protein (ModB2C2)

Summary

Introduction

Protein particles travel in following the Brownian motion and their structures are vibrated in following the thermodynamics. A combination of multi-scale operations was used[20] The limitations of these methods include some halo artifacts existing near the boundaries from using previous models[21]. To overcome these limitations, several optimized edge-preserving smoothing filters have been reported[16,22,23,24]. Several optimized edge-preserving smoothing filters have been reported[16,22,23,24] Among these methods, the bilateral filter (BLF)[23] and weighted least squares (WLS) filter[22] are two of the most effective tools for multi-scale decomposition, especially for detail extraction and noise removal. Compared with the BLF filter, the WLS filter is more convenient, flexible and appropriate for extracting multi-scale details

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Conclusion