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This is Alistair's development version of ZhuangLab/matlab-storm. For release version, please see Zhanglab/matlab-storm.
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This collection of matlab, c, python, and CUDA code is designed to provide a basic interface for STORM data analysis using a Matlab(R) front-end interface. The Graphical User Interfaces (GUIs) should be usable to those with little programming experience. Many additional STORM related data processing functions are available to the experience matlab user.


Core code was contributed by Alistair Boettiger and Jeffrey Moffitt. All core code contained here is licensed under the creative commons CC BY NC. See individual help files for more information.

Some functions are dependent upon the sister repository storm-analysis, written primarily by Hazen Babcock and also available through git-hub as one of Zhuang Lab's repositories.

GPU code was contributed by Fang Huang and Keith Lidke. Please see Code Attribution below for information on citing this code.

Installation Instructions

  1. Clone this repository (see below) via git or copy the contents to your hard drive
    • New to Git? Recommended: Sign up for an account at and fork the matlab-storm project.
    • Install Windows Github on your local machine (or GitK).
    • Sign into to Windows Github on your local machine and clone the github project.
  2. Clone the storm-analysis repository via git or copy the contents to your hard drive.
  3. Copy startup_demo.m into your default matlab working directory. Typically this directory is "/My Documents/MATLAB"
  4. Change the paths within startup_demo.m to specify the locations of the matlab-storm and storm-analysis repositories, and set up a scratch folder. Then change the name of startup_demo.m to startup.m (or name it something else and instruct your existing startup.m script to call it).
  5. Launch matlab.

Instructions for Contributing to matlab-storm

Everyone is welcome to contribute to matlab-storm but any code contributed must follow several general 'clean code' standards.

  1. New functions should be written in the form described in /Templates/FunctionTemplate.m and placed in an appropriate folder in /Functions
  2. Modifications to existing functions should remain backwards compatible as much as possible.

Code Attribution

  1. Code repository

    title = {}

    version = {git commit ce8094b603}

    authors = {Alistair Boettiger and Jeff Moffitt}

Additional Software for Analysis

Some aspects of this analysis package depend on the Insight3 which can be provided by request (contact Matt Kilroy kilroy at For instructions on integrating this software with matlab-storm, contact Alistair or Jeff.

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