Comparison of spontaneous Raman spectrometers

Purpose

This code repository contains all materials required for creating and hosting the publication entitled, "Comparison of spontaneous Raman spectrometers".

Data Description

For each Raman spectroscopy instrument we tested, we acquired spectra of acetonitrile (a standard) and several different strains of unicellular algae within the genus, Chlamydomonas. The sample preparation for the cell cultures is described in the notebook pub, as is a table of acquisition settings and descriptions of each spectrometer. The data is organized into directories for each instrument, expanded below.

Organization

$ tree -L 2 data/

─ Horiba_MacroRAM
  ├── CC-124-TAP-2.txt
  ├── acetonitrile.txt
  └── chlamy_spectra.tar
─ OpenRAMAN
  ├── CC-124_TAP_Pos-2-000_002.csv
  ├── acetonitrile_n_n_n_solid_10000_0_5.csv
  ├── chlamy_spectra.tar
  └── neon_n_n_n_solid_10000_0_5.csv
─ Renishaw_Qontor
  ├── CC-124_TAP_plate_5x_3_points.txt
  ├── acetonitrile_5x.txt
  ├── chlamy_spectra.tar
  └── glass_slide_background.txt
─ Wasatch_WP532X
  ├── CC-124_TAP_Pos-4-002_001.csv
  ├── acetonitrile.csv
  └── chlamy_spectra.tar
─ Wasatch_WP785X
  ├── CC-124_TAP_WP-02071.csv
  ├── acetonitrile.csv
  └── chlamy_spectra.tar

Working with the data

The module, load_spectra.py, was created to facilitate loading each group of spectral data. This module provides three separate functions:

• load_acetonitrile_spectra() -> returns the set of acetonitrile spectra measured by each instrument, and a corresponding pandas DataFrame.
• load_cc124_tap_spectra() -> returns the set of spectra for one particular strain of algal cells grown in one particular media (strain CC-124, grown in TAP) measured by each instrument, and a corresponding pandas DataFrame.
• load_chlamy_spectra() -> returns the full set of spectra of all three algal strains grown in two different types of media measured by each instrument, and a corresponding pandas DataFrame.

See the notebook pub for example usage of these functions.

Reproduce

Please see SETUP.qmd.

Contribute

Please see CONTRIBUTING.qmd.