neuralib-parser 0.7.0

Parsers for output from open-source packages or specific devices

neuralib-parser

Data parsers for neuroscience research tools and file formats, providing unified interfaces for segmentation, morphology, imaging, tracking, and confocal microscopy data.

Overview

neuralib-parser provides Python parsers and data structures for output from open-source packages and specific imaging devices. It includes:

• Segmentation: Cellpose, StarDist cell segmentation
• Morphology: SWC neuron morphology files
• Imaging: Suite2p, Scanbox data formats
• Tracking: DeepLabCut, Facemap behavioral tracking
• Confocal Scans: Zeiss CZI, LSM file formats

Installation

From PyPI

pip install neuralib-parser

With Optional Dependencies

# StarDist support (requires numpy<2.0)
pip install neuralib-parser[stardist]

# Suite2p integration
pip install neuralib-parser[suite2p]

# Zeiss CZI format support
pip install neuralib-parser[czi]

# Scanbox reader
pip install neuralib-parser[sbx]

# All features (excludes stardist due to numpy<2.0 constraint)
pip install neuralib-parser[all]

From Source (uv recommended)

git clone https://github.com/ytsimon2004/neuralib2.git
cd neuralib2/packages/neuralib-parser
uv pip install -e .        # Basic installation
uv pip install -e ".[all]" # With optional features

Requirements

• Python 3.11 or 3.12
• Core dependencies: neuralib-utils, numpy
• See pyproject.toml for optional dependencies

Documentation

• Main Documentation: https://neuralib2.readthedocs.io/
• GitHub Repository: https://github.com/ytsimon2004/neuralib2
• Issue Tracker: https://github.com/ytsimon2004/neuralib2/issues

Important Notes

StarDist and NumPy 2.0

StarDist requires numpy<2.0 due to upstream compatibility. The stardist extra explicitly pins this constraint:

License

BSD 3-Clause License. See LICENSE file for details.

Contributing

Contributions are welcome! Please:

1. Fork the repository
2. Create a feature branch
3. Submit a pull request with clear description

For bug reports and feature requests, use the GitHub issue tracker.

Acknowledgments

This package provides interfaces to:

• Suite2p - Calcium imaging data analysis
• Scanbox - Two-photon imaging system
• StarDist - Cell segmentation
• Cellpose - Cell segmentation
• DeepLabCut - Pose estimation
• Facemap - Behavioral video analysis