slx2imzml

A Python package for converting SCiLS Lab files (.slx) to open-standard imzML files for mass spectrometry imaging (MSI) data analysis.

Overview

This package reads proprietary SCiLS Lab files (using API clients) and exports regions as accessible imzML files that are compatible with M²aia and other open-source MSI analysis tools. The converter supports both continuous centroid and profile spectrum modes.

Features

• Multi-format Export: Converts SCiLS Lab regions to imzML format with continuous profile/centroid spectrum support
• Additional Outputs: Exports spot images, optical images, and region masks as NRRD files
• Flexible Configuration: JSON-based export configuration for customizing output
• M²aia Compatibility: Generated imzML files are fully compatible with M²aia software
• Batch Processing: Process multiple regions and datasets in a single run

Installation

Prerequisites

• Python ≥ 3.6
• SCiLS Lab Python API (Bruker Daltonics)

Install from Source

git clone <repository-url>
cd slx2imzml
pip install -e .

Dependencies

The package automatically installs the following dependencies:

• numpy - Numerical computations
• pandas - Data manipulation
• jinja2 - XML template rendering
• matplotlib - Plotting utilities
• SimpleITK - Medical image processing
• scilslab - SCiLS Lab API integration

Usage

Command Line Interface

slx2imzml export_instructions.json

Export Instructions Format

Create a JSON configuration file to specify export parameters:

{
  "description": "Export configuration for SCiLS to imzML conversion",
  "slice_thickness": 10,
  "data_exports": [
    {
      "filename": "path/to/your/file.slx",
      "final_features": [],
      "final_regions": [["Region1", "region_id_1"]],
      "final_spot_images": ["normalization1", "normalization2"],
      "final_optical_images": ["optical1"],
      "final_labels": [],
      "final_regions_as_labels": []
    }
  ]
}

Output Files

For each processed region, the tool generates:

• imzML Files: region_name.imzML and region_name.ibd - imzML format files
• NRRD Files:
  • region_name.mask.nrrd - Region mask as multilabel image
  • region_name.spot_image_name.nrrd - Spot images (e.g., normalizations)
  • region_name.optical_image_name.nrrd - Optical reference images

The naming is based on the regions_name defined in SCiLS Lab.

Technical Details

Spectrum Modes

• Continuous Profile/Centroid: Full spectrum data export (when final_features is empty)
• Continuous Centroid: Feature-based export with specified m/z values

Coordinate System

The converter preserves spatial information including:

• Pixel spacing in micrometers
• Origin coordinates
• Direction matrix for proper spatial positioning

Data Processing

1. Region Processing: Extracts spectral data for each specified region
2. Feature Selection: Applies feature lists or exports full spectra
3. Spatial Mapping: Maintains pixel-to-coordinate transformations
4. Format Conversion: Generates imzML/ibd file pairs with proper metadata

File Structure

slx2imzml/
├── __init__.py              # Package initialization
├── ImzMLIO.py              # Main conversion logic
├── ImzMLWriter.py          # imzML file writing utilities
├── ScilsLabFileHelper.py   # SCiLS Lab data access helpers
└── imzMLTemplate.j2        # Jinja2 template for imzML XML

Contributing

This project is developed at Hochschule Mannheim in connection with the M²aia project for open-source mass spectrometry imaging analysis.

License

MIT License - See LICENSE file for details.

Related Projects

• M²aia - Open-source software for mass spectrometry imaging
• imzML - Open standard for mass spectrometry imaging data

Support

For questions and issues, please contact the author or visit the M²aia project website.