Missing Wedge Completion via Unsupervised Learning with Coordinate Networks

• Published in: International journal of molecular sciences 2024-05, Vol.25 (10), p.5473
• Main Authors: Van Veen, Dave, Galaz-Montoya, Jesús G, Shen, Liyue, Baldwin, Philip, Chaudhari, Akshay S, Lyumkis, Dmitry, Schmid, Michael F, Chiu, Wah, Pauly, John
• Format: Article
• Language: English
• Subjects: Accuracy; Algorithms; artificial intelligence; BASIC BIOLOGICAL SCIENCES; coordinate networks; Cryoelectron Microscopy - methods; cryogenic electron microscopy (cryoEM); cryogenic electron tomography (cryoET); Data collection; Datasets; Deep Learning; Electron Microscope Tomography - methods; ENGINEERING; Image Processing, Computer-Assisted - methods; Imaging, Three-Dimensional - methods; machine learning; Methods; missing wedge; Neural networks; Neural Networks, Computer; Radiation; reconstruction; simulation; Tomography; unsupervised learning; Unsupervised Machine Learning
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms25105473

Cryogenic electron tomography (cryoET) is a powerful tool in structural biology, enabling detailed 3D imaging of biological specimens at a resolution of nanometers. Despite its potential, cryoET faces challenges such as the missing wedge problem, which limits reconstruction quality due to incomplete data collection angles. Recently, supervised deep learning methods leveraging convolutional neural networks (CNNs) have considerably addressed this issue; however, their pretraining requirements render them susceptible to inaccuracies and artifacts, particularly when representative training data is scarce. To overcome these limitations, we introduce a proof-of-concept unsupervised learning approach using coordinate networks (CNs) that optimizes network weights directly against input projections. This eliminates the need for pretraining, reducing reconstruction runtime by 3-20× compared to supervised methods. Our in silico results show improved shape completion and reduction of missing wedge artifacts, assessed through several voxel-based image quality metrics in real space and a novel directional Fourier Shell Correlation (FSC) metric. Our study illuminates benefits and considerations of both supervised and unsupervised approaches, guiding the development of improved reconstruction strategies.