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datalab-app-plugin-oms

A Python plugin for processing and visualising Online Mass Spectrometry (OMS) data within datalab instances.

The project is being developed as part of the FAST (Formation and Ageing for Sustainable Battery Technologies) Faraday work package, by datalab industries ltd..

Features

  • Processes and plots data from OMS.
  • Handles both the final .csv export of the experiment and the live updating .dat binary file. (See the documentation for more information).
  • Plots species concentrations on a linear or log scale.
  • Can perform calibrations given the relevant calibration data to convert pressure to nmol/s
  • Extracts useful parameters such as peak rate, total integral (total nmol over the course of the experiment), and the initial rate (the rate within a user defined time window) and stores these in the block metadata.

Usage

The plugin provides three parser functions for OMS file formats (see the documentation for format details):

parse_oms_csv(filename, auto_detect_header=True)

Parses the standard .csv export. Automatically detects the header size by searching for the "header" line in the first 10 lines, then reads the data table below it. Returns a DataFrame with a Time (s) column (converted from milliseconds) and one column per species.

parse_oms_dat(filepath, csv_filepath=None, num_species=None, species_names=None)

Parses the .dat binary file (46-byte records starting with V1 markers). Since the binary format does not contain species names or counts, the number of species is resolved in priority order:

  1. num_species — explicitly provided by the user.
  2. Companion .csv file — if csv_filepath is given (or a .csv with the same base name exists), the species count and names are read from its columns.
  3. Auto-detection — tests candidate species counts and picks the one that produces the smoothest signal.

When a companion CSV is available, species names are matched to binary channels by comparing first-row values. Returns a DataFrame indexed by Data Point (sequential index, since .dat files contain no timestamps).

Roadmap

This plugin is still in active development, here are some planned improvements: - ✓ Record and save key characteristics about the data (e.g Total integral or the gradient of peaks). - ✓ Automatic calibration by comparing to reference files. - Integrate other Mass Spectrometry manufacturers to allow comparison between instruments.

Installation

The datalab-app-plugin-oms package can be installed from datalab-industries/datalab-app-plugin-oms.

Development installation

We recommend you use uv for managing virtual environments and Python versions.

Once you have uv installed, you can clone this repository and install the package in a fresh virtual environment with:

git clone git@github.com:datalab-industries/datalab-app-plugin-oms
cd datalab-app-plugin-oms
uv sync --all-extras --dev

You can activate pre-commit in your cloned repository with uv run pre-commit install.

You can run the tests using pytest

uv run pytest

License

This plugin is released under the MIT license. Please see LICENSE for the full text of the license.

datalab-app-plugin-oms is a datalab plugin generated using the datalab-app-plugin-template template.

Releases are created via semantic version tags on GitHub, and will require manually updating the CHANGELOG.