Blob-B-Gone: a lightweight framework for removing blob artifacts from 2D/3D MINFLUX single-particle tracking data

• Published in: Frontiers in bioinformatics 2023, Vol.3, p.1268899-1268899
• Main Authors: Vogler, Bela T L, Reina, Francesco, Eggeling, Christian
• Format: Article
• Language: English
• Subjects: annotation; artifact removal; clustering; MINFLUX; point clouds; single-particle tracking
• ISSN: 2673-7647; 2673-7647
• DOI: 10.3389/fbinf.2023.1268899

In this study, we introduce Blob-B-Gone, a lightweight framework to computationally differentiate and eventually remove dense isotropic localization accumulations (blobs) caused by artifactually immobilized particles in MINFLUX single-particle tracking (SPT) measurements. This approach uses purely geometrical features extracted from MINFLUX-detected single-particle trajectories, which are treated as point clouds of localizations. Employing clustering, we perform single-shot separation of the feature space to rapidly extract blobs from the dataset without the need for training. We automatically annotate the resulting sub-sets and, finally, evaluate our results by means of principal component analysis (PCA), highlighting a clear separation in the feature space. We demonstrate our approach using two- and three-dimensional simulations of freely diffusing particles and blob artifacts based on parameters extracted from hand-labeled MINFLUX tracking data of fixed 23-nm bead samples and two-dimensional diffusing quantum dots on model lipid membranes. Applying Blob-B-Gone, we achieve a clear distinction between blob-like and other trajectories, represented in F1 scores of 0.998 (2D) and 1.0 (3D) as well as 0.995 (balanced) and 0.994 (imbalanced). This framework can be straightforwardly applied to similar situations, where discerning between blob and elongated time traces is desirable. Given a number of localizations sufficient to express geometric features, the method can operate on any generic point clouds presented to it, regardless of its origin.