Welcome to irootlab page

irootLab is an open-source toolbox for vibrational spectroscopy data analysis in MATLAB. The project started in 2008 at Lancaster University, UK.

Downloads

Citation

If you find this software useful for you in your publication please cite the following paper:

Trevisan, J., Angelov, P.P., Scott, A.D., Carmichael, P.L. & Martin, F.L. (2013) "IRootLab: a free and open-source MATLAB toolbox for vibrational biospectroscopy data analysis". Bioinformatics 29(8), 1095-1097. doi: 10.1093/bioinformatics/btt084. http://bioinformatics.oxfordjournals.org/content/early/2013/03/12/bioinformatics.btt084.short

MATLAB code generation

irootlab is unique (to our knownledge) in its ability to generate MATLAB code as you operate on the toolbox GUIs. You can later take this auto-generated code as a basis for your own customized and/or systematic analysis.

Pipeline

irootlab provides routines in the following stages of the biospectroscopy data processing pipeline:

Visualization

Here are lots of different visualizations available. Here is a list of some of them:

Supported file types

As of today, the following file types are supported:

Quick starter

  1. Download the most recent ZIP file from the official website and extract the file into a directory of your 2. Start MATLAB 3 Change MATLAB's "Current directory" to the one created above (which should contain a file called "startup.m")
  2. In MATLAB's command line, enter

    startup

  3. The 'welcome' message shown contains links for some features (suggestion: check browse_demos)

System requirements

MATLAB

MATLAB (Windows/Linux/MacOS/etc), release >= r2007b tested

Specific features

Some routines contain "parfor" loops to speed up the process. To parallelize computation using parfor, the MATLAB Parallel Computing Toolbox (PCT) must be present. All routines that contain parfor loops can also run in serial mode without using the PCT.

Wavelet de-noising: this feature makes function calls to MATLAB Wavelet Toolbox.

Platform-specific binaries

Manual

irootlab manual

Tutorials

Here are some tutorials to take you through the steps of some possible pipelines and features.