iCDF – a program to import netCDF files in MATLAB

Version 1.0 (release 261007) - by

Klavs M. Sørensen, Thomas Skov & Rasmus Bro

About iCDF

The most common chromatographic format is a so-called netCDF format, which is a format that most manufacturers of chromatographic software support. However, the transfer to other software packages is not straightforward and requires advanced toolboxes and often basic knowledge in programming. An often cited netCDF toolbox for MATLAB version 6 [1,3] uses rather advanced features but also commercial black box environments [e.g. ref 2] and licensed software are available. None of these solutions, however, are accessible to laymen. In order to stimulate research in advanced chemometric data analysis, a free and documented toolbox, iCDF, has been developed, which makes the import of data a simple operation.

  • iCDF is currently for XC-MS data (X: GC, LC, HPLC), but soon it will be able to import data using other detectors as well.

  • iCDF for MATLAB is freely available

  • iCDF can be used to open netCDF files from many different instruments (e.g. Agilent, Bruker) and many chromatographic software packages (e.g. ChemStation).

When you start to install the program (iCDF.msi) the files will be placed in the folder:

C:\Program Files\LIFE\iCDF Matlab Toolbox

Add this folder to the path in Matlab and run the program in Matlab by typing or type help iCDF_load for information of input and output:

[matrix,TIC,axis_min,axis_mz] = iCDF_load(filename)
If you also have the stats toolbox there will a function called icdf that is NOT related to this program. Our iCDF file must be written like this; iCDF (capital CDF) to be able to work. This file is NOT an m-file and thus if you type help iCDF the icdf (stats toolbox) will open. Write 'which iCDF' to make sure you call the right function using iCDF_load.

If you use iCDF for MATLAB we would appreciate a reference to the program. This may for example be:
Skov T and Bro R. (2008) Solving fundamental problems in chromatographic analysis
Analytical and Bioanalytical Chemistry, 390 (1): 281-285

You can read more about iCDF and how to analyze chromatographic data here. If you have any questions, suggestions or comments please feel free to email us.


References on the netCDF format

[1] Rew R, Davis G (1990) NetCDF - An Interface for Scientific Data Access. IEEE Computer Graphics and Applications 10 (4): 76-82. Unidata. [July 2007, URL: http://www.unidata.ucar.edu/software/netcdf/]

[2] Bunk B, Kucklick M, Jonas R, Munch R, Schobert M, Jahn D, Hiller K (2006) MetaQuant: a tool for the automatic quantification of GC/MS-based metabolome data. Bioinformatics, 22 (23): 2962-2965.

[3] US Geological Survey (USGS), Woods Hole, NetCDF toolbox for MATLAB 6. [July 2007, URL: http://mexcdf.sourceforge.net/index.html]