Deep learning improves macromolecule identification in 3D cellular cryo-electron tomograms.

Cryogenic electron tomography (cryo-ET) visualizes the 3D spatial distribution of macromolecules at nanometer resolution inside native cells. However, automated identification of macromolecules inside cellular tomograms is challenged by noise and reconstruction artifacts, as well as the presence of many molecular species in the crowded volumes. Here, we present DeepFinder, a computational procedure that uses artificial neural networks to simultaneously localize multiple classes of macromolecules. Once trained, the inference stage of DeepFinder is faster than template matching and performs better than other competitive deep learning methods at identifying macromolecules of various sizes in both synthetic and experimental datasets. On cellular cryo-ET data, DeepFinder localized membrane-bound and cytosolic ribosomes (roughly 3.2 MDa), ribulose 1,5-bisphosphate carboxylase-oxygenase (roughly 560 kDa soluble complex) and photosystem II (roughly 550 kDa membrane complex) with an accuracy comparable to expert-supervised ground truth annotations. DeepFinder is therefore a promising algorithm for the semiautomated analysis of a wide range of molecular targets in cellular tomograms.

A Monte Carlo framework for missing wedge restoration and noise removal in cryo-electron tomography.

We propose a statistical method to address an important issue in cryo-electron tomography image analysis: reduction of a high amount of noise and artifacts due to the presence of a missing wedge (MW) in the spectral domain. The method takes as an input a 3D tomogram derived from limited-angle tomography, and gives as an output a 3D denoised and artifact compensated volume. The artifact compensation is achieved by filling up the MW with meaningful information. To address this inverse problem, we compute a Minimum Mean Square Error (MMSE) estimator of the uncorrupted image. The underlying high-dimensional integral is computed by applying a dedicated Markov Chain Monte-Carlo (MCMC) sampling procedure based on the Metropolis-Hasting (MH) algorithm. The proposed MWR (Missing Wedge Restoration) algorithm can be used to enhance visualization or as a pre-processing step for image analysis, including segmentation and classification of macromolecules. Results are presented for both synthetic data and real 3D cryo-electron images.