HIA - Hyperspectral Image Analysis

The HIA program was developed by Francesco Masia and Wolfgang Langbein to analyze hyperspectral images, specifically for the application to coherent anti-Stokes Raman microscopy.

The details of the implemented algorithms are described in the following papers.

• Quantitative Chemical Imaging and Unsupervised Analysis Using Hyperspectral Coherent Anti-Stokes Raman Scattering Microscopy
  F. Masia, A. Glen, P. Stephens, P. Borri, and W. Langbein, Anal. Chem. 85, 10820 (2013). DOI 10.1021/ac402303g
• Sparse sampling for fast hyperspectral coherent anti-Stokes Raman scattering imaging
  F. Masia, P. Borri, and W. Langbein, Opt. Express 22, 4021 (2014). DOI 10.1364/OE.22.004021
• Hyperspectral image analysis for CARS, SRS, and Raman data
  F. Masia, A.Karuna, P. Borri, and W. Langbein, J. Raman Spect. 46, 727 (2015) DOI 10.1002/jrs.4729

The program was used in the following papers

• Hyperspectral and differential CARS microscopy for quantitative chemical imaging in human adipocytes
  C. Di Napoli, I. Pope, F. Masia,  P. Watson, W. Langbein, P. Borri, Biomedical Optics Express 5, 1378 (2014) DOI 10.1364/BOE.5.001378
  
• Hyperspectral volumetric coherent anti-Stokes Raman scattering microscopy: Quantitative volume determination and NaCl as non-resonant standard
  A. Karuna, F. Masia, P. Borri, and W. Langbein, J. Raman Spect. (2016) DOI 10.1002/jrs.4876
  
• Quantitative Spatiotemporal Chemical Profiling of Individual Lipid Droplets by Hyperspectral CARS Microscopy in Living Human Adipose-Derived Stem Cells
  C. Di Napoli, I. Pope, F. Masia, W. Langbein, P. Watson, and P. Borri Anal. Chem. (2016 DOI: 10.1021/acs.analchem.5b04468

Please acknowledge the usage of the HIA software and cite our related publications.

Installing & Running the Hyperspectral Imaging Analysis (HIA) software

• Download the version of HIA you want to use from the below list (the latest version is recommended).
  
• Extract all the files in a folder.
  
• The file “HIA.chm” is a help file with the instructions to use the program and the description of the functions.
• The software is written in MATLAB, compiled for Windows 7 64bit, and requires a MATLAB run-time compiler to be installed. The specific compiler version is given in the help file of the HIA version. 
• The library "minilzo.dll" (from version 2.4), the java class “DropTargetList.class”, the "bioformats.package.jar" (from version 2.3) and the parallel computing profile “HIA.settings” must be in the same folder as the executable.
• To run the software, launch the batch file “run HIA.bat”. This will open a cmd window which can show any MATLAB error occurred during the analysis. Please use this feature to identify and report bugs.
  
• Examples of Raman and CARS analysis are available, see links below in the different versions.
  

Versions

• 16/12/2016
  
• Version 2.4 released HIA_v2_4.zip
• Change Log
• 24/03/2016
• Version 2.3 released HIA_v2_3.zip
• Example of Raman Analysis
• Change Log
• 23/09/2015
  
• Version 2.2 released HIA_v2_2.zip
• Change Log
• 29/06/2015
• Version 2.1 released HIA_v2_1.zip
• Example of CARS analysis
• 30/04/2015
• Version 2.0 released HIA_Software_JRS.zip