Dataset Information

Macromolecule Particle Picking and Segmentation of a KLH Database by Unsupervised Cryo-EM Image Processing.

ABSTRACT: Segmentation is one of the most important stages in the 3D reconstruction of macromolecule structures in cryo-electron microscopy. Due to the variability of macromolecules and the low signal-to-noise ratio of the structures present, there is no generally satisfactory solution to this process. This work proposes a new unsupervised particle picking and segmentation algorithm based on the composition of two well-known image filters: Anisotropic (Perona-Malik) diffusion and non-negative matrix factorization. This study focused on keyhole limpet hemocyanin (KLH) macromolecules which offer both a top view and a side view. Our proposal was able to detect both types of views and separate them automatically. In our experiments, we used 30 images from the KLH dataset of 680 positive classified regions. The true positive rate was 95.1% for top views and 77.8% for side views. The false negative rate was 14.3%. Although the false positive rate was high at 21.8%, it can be lowered with a supervised classification technique.

SUBMITTER: Carrasco M

PROVIDER: S-EPMC6995569 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature

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Publications

Macromolecule Particle Picking and Segmentation of a KLH Database by Unsupervised Cryo-EM Image Processing.

Carrasco Miguel M Toledo Patricio P Tischler Nicole D ND

Biomolecules 20191130 12

Segmentation is one of the most important stages in the 3D reconstruction of macromolecule structures in cryo-electron microscopy. Due to the variability of macromolecules and the low signal-to-noise ratio of the structures present, there is no generally satisfactory solution to this process. This work proposes a new unsupervised particle picking and segmentation algorithm based on the composition of two well-known image filters: Anisotropic (Perona-Malik) diffusion and non-negative matrix facto ...[more]

PMID: 31801266

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Project description:BackgroundAn important task of macromolecular structure determination by cryo-electron microscopy (cryo-EM) is the identification of single particles in micrographs (particle picking). Due to the necessity of human involvement in the process, current particle picking techniques are time consuming and often result in 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 multiple techniques including: image averaging, normalization, cryo-EM image contrast enhancement correction (CEC), histogram equalization, restoration, adaptive histogram equalization, guided image filtering, and morphological operations. Image preprocessing 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 recognize particle-like objects from noisy cryo-EM micrographs without the need of labeled training data or human intervention making it a useful tool for cryo-EM protein structure determination.

Dataset Information

Macromolecule Particle Picking and Segmentation of a KLH Database by Unsupervised Cryo-EM Image Processing.

Publications

Macromolecule Particle Picking and Segmentation of a KLH Database by Unsupervised Cryo-EM Image Processing.

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