Reconstructing continuous distributions of 3D protein structure from cryo-EM images

Cryo-electron microscopy (cryo-EM) is a powerful technique for determining the structure of proteins and other macromolecular complexes at near-atomic resolution. In single particle cryo-EM, the central problem is to reconstruct the three-dimensional structure of a macromolecule from $10^{4-7}$ noisy and randomly oriented two-dimensional projections. However, the imaged protein complexes may exhibit structural variability, which complicates reconstruction and is typically addressed using discrete clustering approaches that fail to capture the full range of protein dynamics. Here, we introduce a novel method for cryo-EM reconstruction that extends naturally to modeling continuous generative factors of structural heterogeneity. This method encodes structures in Fourier space using coordinate-based deep neural networks, and trains these networks from unlabeled 2D cryo-EM images by combining exact inference over image orientation with variational inference for structural heterogeneity. We demonstrate that the proposed method, termed cryoDRGN, can perform ab initio reconstruction of 3D protein complexes from simulated and real 2D cryo-EM image data. To our knowledge, cryoDRGN is the first neural network-based approach for cryo-EM reconstruction and the first end-to-end method for directly reconstructing continuous ensembles of protein structures from cryo-EM images

Neural network regularization in the problem of few-view computed tomography

The computed tomography allows to reconstruct the inner morphological structure of an object without physical destructing. The accuracy of digital image reconstruction directly depends on the measurement conditions of tomographic projections, in particular, on the number of recorded projections. In medicine, to reduce the dose of the patient load there try to reduce the number of measured projections. However, in a few-view computed tomography, when we have a small number of projections, using standard reconstruction algorithms leads to the reconstructed images degradation. The main feature of our approach for few-view tomography is that algebraic reconstruction is being finalized by a neural network with keeping measured projection data because the additive result is in zero space of the forward projection operator. The final reconstruction presents the sum of the additive calculated with the neural network and the algebraic reconstruction. First is an element of zero space of the forward projection operator. The second is an element of orthogonal addition to the zero space. Last is the result of applying the algebraic reconstruction method to a few-angle sinogram. The dependency model between elements of zero space of forward projection operator and algebraic reconstruction is built with neural networks. It demonstrated that realization of the suggested approach allows achieving better reconstruction accuracy and better computation time than state-of-the-art approaches on test data from the Low Dose CT Challenge dataset without increasing reprojection error.This work was partly supported by RFBR (grants) 18-29-26020 and 19-01-00790

Tomographic Image Reconstruction of Fan-Beam Projections with Equidistant Detectors using Partially Connected Neural Networks

We present a neural network approach for tomographic imaging problem using interpolation methods and fan-beam projections. This approach uses a partially connected neural network especially assembled for solving tomographic\ud reconstruction with no need of training. We extended the calculations to perform reconstruction with interpolation and to allow tomography of fan-beam geometry. The main goal is to aggregate speed while maintaining or improving the quality of the tomographic reconstruction process