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2025-raman-spectrometer-comparison

Repo for the notebook pub "Comparison of spontaneous Raman spectrometers"

https://github.com/arcadia-science/2025-raman-spectrometer-comparison

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Repository

Repo for the notebook pub "Comparison of spontaneous Raman spectrometers"

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  • Open Issues: 0
  • Releases: 2
Created over 1 year ago · Last pushed about 1 year ago
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Readme License Citation Authors

README.md

Comparison of spontaneous Raman spectrometers

Arcadia Pub

tracked

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/

─ HoribaMacroRAM   ├── CC-124-TAP-2.txt   ├── acetonitrile.txt   └── chlamyspectra.tar ─ OpenRAMAN   ├── CC-124TAPPos-2-000002.csv   ├── acetonitrilennnsolid1000005.csv   ├── chlamyspectra.tar   └── neonnnnsolid1000005.csv ─ RenishawQontor   ├── CC-124TAPplate5x3points.txt   ├── acetonitrile5x.txt   ├── chlamyspectra.tar   └── glassslidebackground.txt ─ WasatchWP532X   ├── CC-124TAPPos-4-002001.csv   ├── acetonitrile.csv   └── chlamyspectra.tar ─ WasatchWP785X ├── CC-124TAPWP-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.

Owner

  • Name: Arcadia Science
  • Login: Arcadia-Science
  • Kind: organization
  • Location: United States of America

Citation (CITATION.cff) 

cff-version: 1.2.0
message: If you use this software, please cite the associated publication.
title: Comparison of spontaneous Raman spectrometers
doi: 10.57844/arcadia-b670-4291
authors:
- family-names: Essock-Burns
  given-names: Tara
  affiliation: Arcadia Science
  orcid: https://orcid.org/0000-0003-4159-6974
- family-names: Kolb
  given-names: Ilya
  affiliation: Arcadia Science
  orcid: https://orcid.org/0000-0001-5100-849X
- family-names: Lane
  given-names: Ryan
  affiliation: Arcadia Science
  orcid: https://orcid.org/0000-0002-5887-2069
- family-names: Mets
  given-names: David G.
  affiliation: Arcadia Science
  orcid: https://orcid.org/0000-0002-0803-0912
- family-names: Sharma
  given-names: Sunanda
  affiliation: Arcadia Science
  orcid: https://orcid.org/0000-0001-8822-7960
preferred-citation:
  title: Comparison of spontaneous Raman spectrometers
  type: article
  doi: 10.57844/arcadia-b670-4291
  authors:
  - family-names: Essock-Burns
    given-names: Tara
    affiliation: Arcadia Science
    orcid: https://orcid.org/0000-0003-4159-6974
  - family-names: Kolb
    given-names: Ilya
    affiliation: Arcadia Science
    orcid: https://orcid.org/0000-0001-5100-849X
  - family-names: Lane
    given-names: Ryan
    affiliation: Arcadia Science
    orcid: https://orcid.org/0000-0002-5887-2069
  - family-names: Mets
    given-names: David G.
    affiliation: Arcadia Science
    orcid: https://orcid.org/0000-0002-0803-0912
  - family-names: Sharma
    given-names: Sunanda
    affiliation: Arcadia Science
    orcid: https://orcid.org/0000-0001-8822-7960
  year: 2025

GitHub Events

Total
  • Release event: 3
  • Delete event: 7
  • Issue comment event: 9
  • Public event: 1
  • Push event: 21
  • Pull request review comment event: 3
  • Pull request event: 15
  • Pull request review event: 13
  • Create event: 12
Last Year
  • Release event: 3
  • Delete event: 7
  • Issue comment event: 9
  • Public event: 1
  • Push event: 21
  • Pull request review comment event: 3
  • Pull request event: 15
  • Pull request review event: 13
  • Create event: 12

Dependencies

.github/workflows/publish.yml actions
  • actions/checkout v4 composite
  • quarto-dev/quarto-actions/publish v2 composite
  • quarto-dev/quarto-actions/setup v2 composite
pyproject.toml pypi
.github/workflows/build.yml actions
  • actions/checkout v4 composite
  • actions/setup-python v5 composite
  • astral-sh/setup-uv v5 composite
  • peter-evans/create-pull-request v7 composite