SMITE: Single Molecule Imaging Toolbox Extraordinaire (MATLAB)

Fluorescence single molecule imaging comprises a variety of techniques that involve detecting individual fluorescent molecules. Many of these techniques involve localizing individual fluorescent molecules with precisions below the diffraction limit, which limits the spatial resolution of (visible) light-based microscopes. These methodologies are widely used to image biological structures at the nanometer scale by fluorescently tagging the structures of interest, elucidating details of the biological behavior observed. Two common techniques are single-molecule localization microscopy (SMLM), (Betzig et al., 2006; Fazel & Wester, 2022; Hell, 2007; Lidke et al., 2005; Rust et al., 2006; van de Linde et al., 2011) which is used to produce 2D or 3D super-resolution images of static or nearly static structures, and single-particle tracking (SPT) (Shen et al., 2017), which follows the time course of one or a very small number of moving tagged molecules. SMLM often involves distributions of particles at medium to high density, while SPT works in a very low density domain. These procedures all require intensive numerical computation, and the methods are tightly interwoven.