Measuring optical properties of clear and turbid media with broadband spectral interferometry - data and analysis

This repository contains data of [1]. This repository is structured as follows:

There are three HDF5 data files for each substance: glycerol, ethanol and Intralipid. These contain the measured optical properties of these materials. These are the group index and the GVD, and for Intralipid the scattering attenuation. The data is given per wavenumber in µm-1, the GVD is given in fs2/mm, and the attenuation is given in µm-1.

The raw data is organized in the "data" folder. The raw measured spectral data are stored in the HDF5 files in their substance specific folders. These folders themselves are divided by subfolders by measurement date. The file name of the HDF5 files consists of the volume fraction of solute in water and the measurement number. The HDF5 files contain the transmission spectrum, the reference spectrum and the interference spectrum. The HDF5 files also contain metadata for each spectrum. Among the metadata are the integration time, a timestamp and the number of spectra that is used for averaging.

To retrieve the optical properties of a medium two measurements are needed. A measurement of the medium itself and a calibration measurement. Which calibration measurement belongs to which measurement is stored in the YAML format in the "settings" folder. Each YAML file contains two relative paths: one to the HDF5 file of the measurement and one to the HDF5 file of the calibration measurement.

In these files, some constants that were arbitrarily chosen during the analysis are saved. Most important are the wavelength bounds, the order of the polynomial fit to the spectral phase, the volume fraction and the cuvette width. The attenuation coefficient of Intralipid for wavelengths below about 500 nm is too high to reliably measure. The lower wavelength bound was increased from 460 nm for diluted Intralipid to 500 nm for undiluted Intralipid. See the YAML file which wavelength bounds was used. The order of the polynomial was set to 4 for the transparent media and 3 for Intralipid. The file name is the volume fraction of the sample diluted in water.

The data processing and analysis is performed with the code provided in "measurement.py". See the comments in the code for further details. To quickly visualize the group index, GVD and attenuation, for a single wavelength four sample scripts were provided. "plotConcentrationDependenceGlycerol.py", "plotConcetrationDependenceEthanol.py" and "plotConcentrationDependenceIntralipid" to view the concentration dependence of each optical property for the three substances. The wavelength can be changed from within the scripts. The wavenumber dependence of can be viewed with "plotWavenumberDependence.py". Which wavelength or volume fraction is viewed, can be adjusted in the Python scripts themselves. Some example plots are uploaded in the PDF format.

The datapoints of the measurements in the figures in the results section of the paper[1], are in the folder "figure data" within the "data" folder. These figures are Figures 5,6,7 and 8. In principle, these datapoints are also in the substance specific datasets described above.

[1] P.N.A. Speets and J. Kalkman, Measuring optical properties of clear and turbid media with broadband spectral interferometry, Applied Optics, 2023, DOI:10.1364/AO.488543.