neuralib-imaging
Tools for cellular imaging and widefield imaging analysis, providing spike inference, image registration, and widefield data processing for neuroscience research.
Overview
neuralib-imaging provides Python tools for analyzing calcium imaging and widefield imaging data. It includes:
- Spike Inference: CASCADE (deep learning), OASIS deconvolution
- Registration: Coordinate transformation and atlas alignment
- Widefield Analysis: FFT processing, SVD decomposition, hemodynamic correction
- Visualization: Interactive napari-based viewers and plotting tools
Installation
From PyPI
pip install neuralib-imaging
With Optional Dependencies
# CASCADE spike inference (requires TensorFlow)
pip install neuralib-imaging[cascade]
# Widefield analysis (requires napari, bokeh, scikit-learn)
pip install neuralib-imaging[widefield]
# All features
pip install neuralib-imaging[all]
From Source (uv recommended)
git clone https://github.com/ytsimon2004/neuralib2.git
cd neuralib2/packages/neuralib-imaging
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,numba,matplotlib - See
pyproject.tomlfor optional dependencies
Documentation
- Main Documentation: https://neuralib2.readthedocs.io/
- GitHub Repository: https://github.com/ytsimon2004/neuralib2
- Issue Tracker: https://github.com/ytsimon2004/neuralib2/issues
License
BSD 3-Clause License. See LICENSE file for details.
Contributing
Contributions are welcome! Please:
- Fork the repository
- Create a feature branch
- Submit a pull request with clear description
For bug reports and feature requests, use the GitHub issue tracker.
Acknowledgments
This package integrates with:
1 maintainer
Metadata
1 maintainer
Release files for neuralib-imaging 0.7.2
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| File | Size | Uploaded | Provenance | Actions |
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