Thyra

Tests PyPI Python 3.12+ License: MIT Code style: black Docs Open in Colab

Thyra (from Greek thyra, meaning "door" or "portal") -- a modern Python library for converting Mass Spectrometry Imaging (MSI) data into the standardized SpatialData/Zarr format, serving as your portal to spatial omics analysis workflows.

Read the documentation | Getting Started | Tutorial | CLI Reference | API Reference

Try it without any data

pip install thyra
thyra-example-data example_data/synthetic_brain.imzML   # generates a small synthetic dataset
thyra example_data/synthetic_brain.imzML example_data/synthetic_brain.zarr

See the Tutorial for a full walkthrough, including the published example dataset (10.5281/zenodo.18326569).

Features

  • Multiple Input Formats: ImzML, Bruker (.d directories), Waters (.raw directories), PHI SmartSoft-TOF ToF-SIMS (.raw files)
  • SpatialData Output: Modern, cloud-ready format with Zarr backend
  • Memory Efficient: Handles large datasets (100+ GB) through streaming processing
  • Optical Alignment: Automatic MSI-to-optical image registration for Bruker data
  • Multi-Region Support: Handles slides with multiple tissue sections
  • Resampling: Physics-aware mass axis resampling (on by default in the CLI; opt-in from the Python API)
  • Validated Metadata: Versioned, ontology-mapped metadata schema (PSI-MS, NCBITaxon, UBERON, CHEBI) with thyra validate and one-command METASPACE export
  • 3D Support: Process volume data or treat as 2D slices
  • Cross-Platform: Windows, macOS, and Linux

Installation

pip install thyra

Quick Start

Command Line

# Basic conversion (resampling enabled by default)
thyra input.imzML output.zarr

# Bruker data with verbose logging
thyra data.d output.zarr -v DEBUG

# PHI SmartSoft-TOF ToF-SIMS (a .raw file, not a directory)
thyra tofsims_run.raw output.zarr

# Disable resampling
thyra input.imzML output.zarr --no-resample

Thyra auto-detects the input format. Note that .raw is claimed by two vendors and resolved by shape: Waters writes a directory, PHI writes a single file. See Supported Formats.

Python API

from thyra import convert_msi

success = convert_msi("data/sample.imzML", "output/sample.zarr")

Working with the Output

import spatialdata as sd

sdata = sd.read_zarr("output/sample.zarr")
msi_table = sdata.tables["msi_dataset_z0"]

print(f"Shape: {msi_table.shape}")  # (pixels, m/z bins)
print(f"m/z range: {msi_table.var['mz'].min():.1f} -- {msi_table.var['mz'].max():.1f}")

Metadata

Every converted store carries a versioned, ontology-mapped metadata block (uns["msi_metadata"]), auto-populated from the source file:

thyra validate output.zarr                               # schema + ontology checks
thyra export-metaspace output.zarr --merge sample.json   # METASPACE submission JSON

See Metadata Schema.

Documentation

Full documentation: M4i-Imaging-Mass-Spectrometry.github.io/thyra

Supported Formats

Input Extension Status
ImzML .imzML Full support
Bruker .d Full support (timsTOF + Rapiflex)
Waters .raw Full support
PHI SmartSoft-TOF .raw Full support
Shimadzu .imdx, .kbd In development (workaround: imzML export from IMAGEREVEAL MS)

Output: SpatialData/Zarr -- cloud-ready, efficient, standardized

Development

git clone https://github.com/M4i-Imaging-Mass-Spectrometry/thyra.git
cd thyra
uv sync
uv run pre-commit install
uv run pytest

Contributing

See CONTRIBUTING.md for guidelines.

License

MIT -- see LICENSE.

Citation

@software{thyra2024,
  title = {Thyra: Modern Mass Spectrometry Imaging Data Conversion},
  author = {Visvikis, Theodoros},
  year = {2024},
  url = {https://github.com/M4i-Imaging-Mass-Spectrometry/thyra}
}

Acknowledgments

Visual identity

Logomark and logotype designed by Nepsis Scriptorium.

Instagram @nepsis.scriptorium Email nepsisscriptorium@gmail.com

Project links

Data verified by PyPI on Aug 28, 2026
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Credits

Author/Maintainer: Theodoros Visvikis

GitHub Statistics

Data verified by PyPI on Aug 28, 2026
The GitHub source repository was provided by the project maintainers and verified by PyPI at the time of upload. Stars, forks, and open issues/PRs are derived from that repository and have not been independently verified.

License expression

MIT
View SPDX License List

Requires

Python <3.14, >=3.12

Tags

bioinformatics bruker data-conversion imaging imzml mass-spectrometry msi omics scientific-computing spatial-omics spatialdata zarr

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