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 and further developed 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
• Bessel-beam hyperspectral CARS microscopy with sparse sampling: Enabling high-content high-throughput label-free quantitative chemical imaging
  F. Masia, P. Watson, W. Langbein, and P. Borri
  Anal. Chem. 90, 3775 (2018) DOI 10.1021/acs.analchem.7b04039
• Label-free quantitative chemical imaging and classication analysis of adipogensis using mouse embryonic stem cells
  F. Masia, A. Glen, P. Stephens, W. Langbein, and P. Borri
  J. Biophotonics 11, e201700219 (2018) DOI 10.1002/jbio.201700219
• Hyperspectral Analysis Applied to Micro-Brillouin Maps of Amyloid-Beta Plaques in Alzheimer’s Brain
  F. Palombo, F. Masia, S. Mattana, F. Tamagnini, P. Borri, W. Langbein, and D. Fioretto
  Analyst 143, 6095 (2018) DOI 10.1039/c8an01291a
• Label-free volumetric quantitative imaging of the human somatic cell  division by hyperspectral coherent anti-Stokes Raman scattering
  A. Karuna, F. Masia, M. Wiltshire, R. Errington, P. Borri, and W. Langbein
  Anal. Chem. (2019) DOI 10.1021/acs.analchem.8b04706
• Dynamic label-free imaging of lipid droplets and their link to fatty acid and pyruvate oxidation in mouse eggs
  J. Bradley, I. Pope, W. Langbein, P. Borri, and K. Swann
  J. Cell Science 132, jcs228999 (2019) DOI 10.1242/jcs.228999
• Quantitative Label-Free Imaging of Lipid Domains in Single Bilayers by Hyperspectral Coherent Raman Scattering
  A. Nahmad-Rohen, D. Regan, F. Masia, C. McPhee, I. Pope, W. Langbein, and P. Borri\\
  Anal. Chem. 92, 14657 (2020), DOI 10.1021/acs.analchem.0c03179
• Identifying subpopulations in multicellular systems by quantitative chemical imaging using label-free hyperspectral CARS microscopy
  I. Pope, F. Masia, K. Ewan, A. Jimenez-Pascual, T.C. Dale, F.A. Siebzehnrubl, P. Borri, and W. Langbein
  Analyst 146, 2277 (2021), DOI 10.1039/D0AN02381G
• Quantification of the nonlinear susceptibility of the hydrogen and deuterium stretch vibration for biomolecules in coherent Raman micro-spectroscopy
  D. Boorman, I. Pope, F. Masia, P. Watson, P. Borri, and W. Langbein
  J. Raman Spectr. 52, 1540 (2021),  DOI 10.1002/jrs.6164
• Hyperspectral CARS microscopy and quantitative unsupervised analysis of deuterated and non-deuterated fatty acid storage in human cells
  D. Boorman, I. Pope, F. Masia, W. Langbein, S. Hood, P. Borri, and P. Watson
  J. Chem. Phys. 155, 224202 (2021) DOI 10.1063/5.0065950
• uFLIM - Unsupervised analysis of FLIM-FRET microscopy data
  F. Masia,  W. Dewitte, P. Borri, and W. Langbein
  arXiv 2102.11002, Medical Image Analysis 82, 102579 (2022) DOI 10.1016/j.media.2022.102579
• Low-energy electron microscopy intensity-voltage data – factorization, sparse sampling, and classification
  F. Masia, W. Langbein; S. Fischer, J-O. Krisponeit, J. Falta
  arXiv 2203.12353, J. Microscopy 289, 91 (2023) DOI 10.1111/jmi.13155

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.
• From version 2.5, to open the Andor data *.sif, it requires the installation of the Andor Matlab SIF i/o toolbox (AndorMatlabSIFIOSetup-2.102.30000.0). The installation folder must be the Runtime compiler folder, for example YourDrive\Program Files\MATLAB\MATLAB Runtime\v91. Choose installation for 64 bit matlab when asked
• 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

• Version 2.6 coming soon
  
• 01/12/2020
• Utility to compare two FSC3 results
• FSC3Comparison
  
• 25/02/2017
  
• Version 2.5
• HIA_v2_5.zip
• Help file
• Change Log
• 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