Awesome

storm-analysis

This is a repository of code developed in the Zhuang Lab for analysis of STORM movies. Some algorithms were developed in other groups and ported to Python.

Installation

You will need Python and you will need the storm-analysis directory in your Python path.

Pre-compiled libraries (using MinGW) are provided for 64-bit Windows. For other operating systems you will need to compile the libraries and executables yourself as described in the README files in the relevant folders. There are also compile_bat.bat files which have examples of how to compile everything.

To use the software on 64-bit Windows you will need the windows_dll directory to be in your PATH.

Directory Layout

3d_daostorm - The core code to perform 3D-DAOSTORM analysis as described in this publication 3D-DAOSTORM

L1H - The core code to perform l1H analysis as described in this publication L1H

decon-storm - Matlab, C and Python code for DeconSTORM analysis as described in this publication DeconSTORM

fista - The core code to perform FISTA image deconvolution as described in this publication Beck and Teboulle

frc - The core code to perform FRC analysis as described in this publication Nieuwenhuizen et al

rcc - The core code to perform RCC drift correction as described in this publication Wang et al

rolling_ball_bgr - The core code to perform rolling ball based background estimation.

sCMOS - The core code to perform analysis of data from a sCMOS camera as described in this publication Huang et al

sa_library - A collection of Python (and C) libraries that provide functionality whose utility is not limited to just a support role for 3D-DAOSTORM (and other analysis approaches).

sa_utilities - A collection of Python and C programs that perform functions such as tracking single molecules across multiple frames or determining and applying drift correction. These are used by 3D-DAOSTORM, but as with the functions in the library directory they are considered to be of more general utility.

simulator - A simple simulator for generating test data.

tests - Simple tests of 3D-DAOSTORM and sCMOS to verify that they work.

visualizer - A PyQt4 based application that draws the found localizations on frame in which they were found.

wavelet_bgr - The core code to perform wavelet based background estimation as described in this publication Galloway et al.

windows_dll - The other DLLs that you will need to get the 3D-DAOSTORM analysis to work on windows.

Files

compile_all_linux.sh - Batch file to compile all the C libraries for a linux environment.

General Notes

Questions should be addressed to Hazen Babcock (hbabcock at fas.harvard.edu)