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Overview of Core Functionality

smite (Single Molecule Imaging Toolbox Extraordinaire) is a collection of MATLAB tools developed to process, either through GUIs or via batch, fluorescent single molecule imaging data. This data is typically collected into .h5 (Hierarchical Data Format 5) files created by the sister software MATLAB Instrument Control (MIC), a collection of MATLAB classes for automated data collection on complex, multi-component custom built microscopes. This software can be obtained from the MIC GitHub distribution (https://github.com/LidkeLab/matlab-instrument-control.git).

smite is organized into a set of namespaces that group similar tools and concepts. The namespace +smi contains the highest level tools that will be the most common entry point for processing SMLM and SPT data sets.

List of smite namespaces and classes.

The core functionality of smite (contained in the namespace +smi) is

  • SMLM (Single Molecule Localization Microscopy), which processes 2D super-resolution (SR) data in .h5 files with standard contents. Data can also be stored in .mat files under a variable with a name like sequence;
  • Publish, which batch-processes SR data assuming the .h5 files follow a standard naming convention (obj.CoverslipDir/Cell*/Label*/Data*.h5);
  • SPT (Single Particle Tracking), which analyzes tracking data;
  • BaGoL (Bayesian Grouping of Localizations) explores the possible number of emitters and their positions that can explain the observed localizations and uncertainties in the data.

Note: A camera calibration file is used by SMLM (and hence Publish and SPT) as well.

Corresponding examples/extended examples are presented in:

  B=BaGoL()       % create object
  B.SMD=....      % set properties
  B.analyze_all() % run complete analysis

In all the examples and throughout smite, three main data structures are used to organize the analysis parameters and data:

  • SMF (Single Molecule Fitting), which uniquely and completely defines the data analysis parameters;
  • SMD (Single Molecule Data), which stores the data results;
  • TR (Tracking Results), which is a variation of SMD used for tracking data results.

Many further examples demonstrate various smite functionalities.