thyra 1.24.0

A modern Python library for converting Mass Spectrometry Imaging (MSI) data into SpatialData/Zarr format - your portal to spatial omics

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 | CLI Reference | API Reference

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 (enabled by default)
• 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

• Getting Started -- installation, first conversion, common workflows
• CLI Reference -- all command-line options
• Output Format -- understanding the zarr structure
• Coordinate Systems -- the "global" contract Thyra writes for downstream consumers
• API Reference -- Python API documentation

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

• Built with SpatialData ecosystem
• Powered by Zarr for efficient storage
• Uses pyimzML for ImzML parsing