AutoCryoPicker: An Unsupervised Learning Approach for Fully Automated Single Particle Picking in Cryo-EM Images

Abstract

BackgroundAn important task of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is the identification of single particles in micrographs (particle picking). Currently, particle picking is laborious, time consuming, and potentially biased due to the need of human intervention to initialize the particle picking. The results typically include many false positives and negatives. Adjusting the parameters to eliminate false positives often excludes true particles in certain orientations. The supervised machine learning (e.g. deep learning) methods for particle picking often need a large training dataset, which requires extensive manual annotation. Other reference-dependent methods rely on low-resolution templates for particle detection, matching and picking, and therefore, are not fully automated. These issues motivate us to develop a fully automated, unbiased framework for particle picking. ResultsWe design a fully automated, unsupervised approach for single particle picking in cryo-EM micrographs. Our approach consists of three stages: image preprocessing, particle clustering, and particle picking. The image preprocessing is based on image averaging, normalization, cryo-EM image contrast enhancement correction (CEC), histogram equalization, restoration, adaptive histogram equalization, guided image filtering, and morphological operations significantly improves the quality of original cryo-EM images. Our particle clustering method is based on an intensity distribution model which is much faster and more accurate than traditional K-means and Fuzzy C-Means (FCM) algorithms for single particle clustering. Our particle picking method, based on image cleaning and shape detection with a modified Circular Hough Transform algorithm, effectively detects the shape and the center of each particle and creates a bounding box encapsulating the particles. ConclusionsAutoCryoPicker can automatically and effectively recognizes particle-like objects from in noisy cryo-EM micrographs without the need of labeled training data and human intervention and therefore is a useful tool for cryo-EM protein structure determination.