Welcome to saSPT’s documentation!

saspt is a Python tool for analyzing single particle tracking (SPT) experiments. It uses state arrays, a kind of variational Bayesian framework that learns intelligible models given raw trajectories from an SPT experiment.

There are a lot of great SPT analysis tools out there. We found it useful to write saspt because:

  • it is simple and flexible enough to accommodate a wide variety of underlying stochastic models;

  • its outputs are familiar numpy and pandas objects;

  • it imposes no prior beliefs on the number of dynamic states;

  • it uses tried-and-true Bayesian methods (marginalization over nuisance parameters) to deal with measurement error in a natural way.

I originally wrote saspt to deal with live cell protein tracking experiments. In the complex intracellular environment, a protein can occupy a large and unknown number of molecular states with distinct dynamics. saspt provides a simple way to measure the number, characteristics, and fractional occupations of these states. It is also “smart” enough to deal with situations where there may not be discrete states.

If you want to jump right into working with saspt, see Quickstart. If you want a more detailed explanation of why saspt exists, see Background. If you want to dig into the guts of the actual model and inference algorithm, see The state array model.

(saspt stands for “state arrays for single particle tracking”.)

What does saSPT do?

saspt takes a set of trajectories from a tracking experiment, and identifies a mixture model to explain them. It is designed to work natively with numpy and pandas objects.

What doesn’t saSPT do?

  1. saspt doesn’t do tracking; it takes trajectories as input. (See: Q. Does saspt provide a way to do tracking?)

  2. saspt doesn’t model transitions between states. For that purpose, we recommend the excellent vbSPT package.

  3. saspt doesn’t check the quality of the input data.

  4. saspt expects you to know the parameters for your imaging experiment, including pixel size, frame rate, and focal depth.

Currently saspt only supports a small range of physical models. That may change as the package grows.

Contents

Indices and tables