Example of hyperspectral image analysis using the software HIA2.1

Unzip Data.zip
Data.txt: hyperspectral CARS intensity images of a U2OS cell acquired with the multimodal CARS microscope at School of Biosciences (Cardiff University) using spectral focusing. Software: MultiCARS.
Offset.txt: CARS intensity image of the same cell taken at zero temporal overlap of the Pump and Stokes pulses. Software: MultiCARS.
gwratio.dat: Glass/Water CARS ratio spectrum

1. Import hyperspectral data

2. Remove offset

3. SVD denoising


4. Calculate CARS ratio


5. Correction for uneven background


6. Field retrieval


7. Save compressed data


8. FSC3


Recommended settings for improved reproducibility

We noticed improved reproducibility of the factorization of the example data using the FSC3 settings shown below. Settings can be imported in the v2.1 using the 'Load FSC3 parameters' function on the FSC3 panel menu and selecting the file 'FSC3_2p1.par'.

These settings produce some results were the water is factorized in only one component and DNA and lipid are factorized separately from the cytosolic protein.

07/05/2015, Francesco Masia. Updated by FM 26/06/2015