Thyra

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

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)
  • 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)
  • 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

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

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}")

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

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

Development

git clone https://github.com/M4i-Imaging-Mass-Spectrometry/thyra.git
cd thyra
poetry install
poetry run pre-commit install
poetry 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 3, 2026
Data provided by the project maintainers, verified at the time the release was uploaded to PyPI.

Key dates

PyPI data
Data sourced directly from PyPI's database.
  • Released:
Newer release available (3.7.3)

1 maintainer

PyPI data
Data sourced directly from PyPI's database.
Avatar for Tomatokeftes from gravatar.com Tomatokeftes

Credits

Author/Maintainer: Theodoros Visvikis

GitHub Statistics

Data verified by PyPI on Aug 3, 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

MIT License (MIT)

Requires

Python <3.14, >=3.12

Tags

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

Classifiers

Report project as malware

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

thyra-3.1.0.tar.gz (11.6 MB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

thyra-3.1.0-py3-none-any.whl (11.7 MB view details)

Uploaded Python 3

File details

Details for the file thyra-3.1.0.tar.gz.

File metadata

  • Download URL: thyra-3.1.0.tar.gz
  • Upload date:
  • Size: 11.6 MB
  • Tags: Source
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for thyra-3.1.0.tar.gz
Algorithm Hash digest
SHA256 e156f95e307c2aff3b07ca4f2093c0e22e15eca65ca0f9d302c66e71448859ad
MD5 d4562e219d8709456b779531bc501565
BLAKE2b-256 246fb80402f64d2beb2f7bd02e7fd28a293079208837fc961b1e2268ee2277c1

See more details on using hashes here.

Provenance

The following attestation bundles were made for thyra-3.1.0.tar.gz:

Publisher: release.yml on M4i-Imaging-Mass-Spectrometry/thyra

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

File details

Details for the file thyra-3.1.0-py3-none-any.whl.

File metadata

  • Download URL: thyra-3.1.0-py3-none-any.whl
  • Upload date:
  • Size: 11.7 MB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? Yes
  • Uploaded via: twine/7.0.0 CPython/3.13.14

File hashes

Hashes for thyra-3.1.0-py3-none-any.whl
Algorithm Hash digest
SHA256 62eabdb5aec91469f3d5ae53eb6fc5a2d1e3ddd4d86a456bf4d011e6e24aa148
MD5 0f2a82ee080b056e917fcb1a61c7c3f1
BLAKE2b-256 e71aaeb657202c6c6287bec76c0dee033ae4b23b2e98f310f25a191e0473e7ac

See more details on using hashes here.

Provenance

The following attestation bundles were made for thyra-3.1.0-py3-none-any.whl:

Publisher: release.yml on M4i-Imaging-Mass-Spectrometry/thyra

Attestations: Values shown here reflect the state when the release was signed and may no longer be current.

Release history Release notifications | RSS feed

3.7.3

2 files

3.7.2

2 files

3.7.1

2 files

3.7.0

2 files

3.6.0

2 files

3.5.1

2 files

3.5.0

2 files

3.4.0

2 files

3.3.0

2 files

3.2.2

2 files

3.2.1

2 files

3.2.0

2 files

3.1.1

2 files

This release

3.1.0 This release

2 files

3.0.3

2 files

3.0.2

2 files

3.0.1

2 files

3.0.0

2 files

2.3.1

2 files

2.3.0

2 files

2.2.4

2 files

2.2.3

2 files

2.2.2

2 files

2.2.1

2 files

2.2.0

2 files

2.1.0

2 files

2.0.4

2 files

2.0.3

2 files

2.0.2

2 files

2.0.1

2 files

2.0.0

2 files

1.27.3

2 files

1.27.2

2 files

1.27.1

2 files

1.27.0

2 files

1.26.0

2 files

1.25.5

2 files

1.25.4

2 files

1.25.3

2 files

1.25.2

2 files

1.25.1

2 files

1.25.0

2 files

1.24.0

2 files

1.23.0

2 files

1.22.0

2 files

1.21.0

2 files

1.20.3

2 files

1.20.2

2 files

1.20.1

2 files

1.20.0

2 files

1.19.0

2 files

1.18.2

2 files

1.18.1

2 files

1.18.0

2 files

1.17.2

2 files

1.17.1

2 files

1.17.0

2 files

1.16.0

2 files

1.15.1

2 files

1.15.0

2 files

1.14.1

2 files

1.14.0

2 files

1.13.0

2 files

1.12.1

2 files

1.12.0

2 files

1.11.1

2 files

1.11.0

2 files

1.10.0

2 files

1.9.0

2 files

1.8.4

2 files

Anthropic, PBC Visionary sponsor Bloomberg Visionary sponsor Hudson River Trading Visionary sponsor Meta Visionary sponsor NVIDIA Visionary sponsor Microsoft Sustainability sponsor Depot Continuous Integration AWS Cloud computing and Security Sponsor Datadog Monitoring Fastly CDN Google Download Analytics Sentry Error logging StatusPage Status page