Setup

This document details how to create a local copy of this pub’s codebase, setup your compute environment, and reproduce the pub itself. This will enable you to experiment with the analysis in the pub and, optionally, contribute revisions to it.

Obtain local copy

The codebase is hosted on GitHub and can be found here.

To obtain a local copy of this repo, you can either clone it directly or fork it to your own GitHub account, then clone your fork. If you aren’t sure what’s best, our suggestion is to clone directly unless you both (1) want to propose a revision for the publication and (2) are not an employee of Arcadia Science.

To clone:

git clone https://github.com/Arcadia-Science/raman-mapping-algae.git

Installation

Important

The publication is rendered with Quarto. If you don’t have it installed (check with quarto --version), you can install it here.

This repository uses conda to manage the computational and build environment. If you don’t have it installed (check with conda --version), you can find operating system-specific instructions for installing miniconda here. After installing, run the following commands to create and activate the environment.

conda env create -n raman-mapping-algae --file env.yml
conda activate raman-mapping-algae

Now, install any internal packages in the repository:

pip install -e .

And finally, if you plan to submit a pull request, install the pre-commit hooks:

pre-commit install

What’s next?

With a copy of the code and compute environment set up on your local machine, you can now reproduce or modify a local copy of the publication however you see fit. Read on to get started.

Reproduce

The best way to ensure you’ve correctly set up your code and compute environment is to reproduce this work. Fortunately, the analysis, and therefore the publication itself, can be reproduced with the following command:

make execute

(Make sure you’re in the conda environment you created above)

This will execute and render the notebook index.ipynb, then build the publication site. To preview the site, use

make preview

This will open a local instance of the publication in your default browser.

Modify

To modify or extend any analyses, open up index.ipynb with Jupyter or your favorite IDE. To preview changes as you modify the notebook, run make preview again and leave the command running. As you make changes to the notebook, the preview site will automatically reload.

Data files

The data/ directory contains the following files, each tied to specific sections and figures of the publication:

File	Used for
UV-Vis 5_1_2025 7_19_21 PM.tsv	UV-Vis absorbance figure of pigment standards (introductory pigment characterization)
Cells- 473nm-Map-ForPeng 1.txt	All 473 nm Raman analysis: spectra, intensity masking, baseline correction, univariate maps, PCA, NMF
Cells- 532nm-Map-ForPeng 1.txt	All 532 nm Raman analysis: spectra, intensity masking, baseline correction, univariate maps
2024-11-12_CC-1373_TAP_slide_10_singlecellmap.txt	All 785 nm Raman analysis: spectra, intensity masking, baseline correction, univariate maps
2024-11-12_TAP_slide_single.txt	785 nm background spectrum used to subtract glass + medium fluorescence

Publish

If you’ve improved the publication, consider contributing so we can update the hosted publication with your edits (big or small!). To get started, see our contributing guide.