SLIM Curve: a package for exponential curve fitting of combined spectral lifetime image data
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README.md

SLIM Curve is a curve fitting library used for Fluorescent Lifetime Imaging or FLIM and Spectral Lifetime Imaging or SLIM. It is developed by Paul Barber and the Advanced Technology Group at the [Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology] (http://www.rob.ox.ac.uk/), University of Oxford, as well as the Laboratory for Optical and Computational Instrumentation at the University of Wisconsin-Madison. SLIM Curve is used for FLIM functionality in the Advanced Technology Group's Time Resolved Imaging (TRI2) software, as well as in the SLIM Curve plugin for ImageJ.

For exponential lifetime fitting there are two core algorithms within SLIM Curve:

  1. A triple integral method that does a very fast estimate of a single exponential lifetime component.
  2. The second is a Levenberg-Marquardt algorithm or LMA that uses an iterative, least-squares-minimization approach to generate a fit. This works with single, double and triple exponential models, as well as stretched exponential.

There is also code to perform 'global' analysis over a number of signals simultaneously (e.g. over an image), where the lifetimes can be considered constant across the data set, but the amplitudes are allowed to vary for each signal. There is also a completely generic global analysis function. A third algorithm is available to perform phasor analysis.

In addition there is a non-negative linear least squares algorithm that is useful for spectral unmixing in SLIM.

The code is written in C89 compatible C and is thread safe for fitting multiple pixels concurrently. Several files are provided as wrappers to call this library from Java code: EcfWrapper.c and .h provide a subset of function calls used by the ImageJ plugin; these may be invoked directly from Java using JNA. In addition there is a Java CurveFitter project that provides a wrapper to the SLIM Curve code. This invokes the C code using JNI, with loci_curvefitter_SLIMCurveFitter.c and .h.

Additionally, there is wrapper code in cLibrary.i to wrap the remaining external functions in GCI_Phasor.c and EcfGlobal.c. This code generates swig wrapper files which enable you to call these functions from Java. They are generated automatically in Eclipse when the slim-curve project is updated.

See also

Directory contents

  • lib - pre-compiled dll files for Windows 32 and 64 bit.
  • src - source files
  • src/main/c - The source files for the SLIM Curve library
  • src/main/cpp - The C++ include file for a SLIMCurve class for use in C++ projects
  • src/slim-curve-cmd/c - The source files for the standalone executable wrapper for the library
  • src/slim-curve-cmd/cpp - The source files for the standalone executable written in C++
  • src/matlab - Wrapper and example code for use of the library with Matlab
  • test_files - dat and ini settings file for testing

Building the source

To build the library and standalone program using CMake and gcc under Linux:

  1. Create a build folder, and cd to it

    mkdir build
    cd build
    
  2. Run CMake

    cmake ../CMakeLists.txt
    
  3. Run make

    make
    

On Windows you can use CMake to create a Visual Studio project for the library and test programs.

Running the standalone executable

  1. Copy the executable to the test_files folder for convenience

    cp slim-curve-cmd ../test_files
    
  2. Run the program with the test files

    cd ../test_files
    ./slim-curve-cmd test.ini transient.dat