neuralib-utils
Core utilities and foundational tools for the neuralib ecosystem, providing I/O operations, data manipulation, type definitions, visualization helpers, and common infrastructure for neuroscience research workflows.
Overview
neuralib-utils is the foundational package for neuralib, providing essential utilities that other neuralib packages
depend on. It includes:
- File I/O: Efficient HDF5 lazy loading, JSON/CSV handling, dataset management
- Type System: Unified type aliases supporting both pandas and polars DataFrames
- Utilities: Logging, colored output, DataFrame operations, GPU monitoring, profiling
- Plotting: Publication-quality plotting tools (PSTH, Venn diagrams, colormaps)
- Dashboard: Bokeh-based web UI framework for interactive data visualization
- Image Utilities: Array manipulation, labeling, color management, normalization
- External Tools: Google Sheets and Slack integrations
This package serves as the core dependency for all other neuralib packages (neuralib-atlas, neuralib-imaging, etc.).
Installation
From PyPI
pip install neuralib-utils
With Optional Dependencies
# Dashboard support (Bokeh)
pip install neuralib-utils[dashboard]
# Plotting support (matplotlib, seaborn)
pip install neuralib-utils[plot]
# Optional tools (Google Sheets, Slack, GPU monitoring)
pip install neuralib-utils[opt]
# All features
pip install neuralib-utils[all]
From Source (uv recommended)
git clone https://github.com/ytsimon2004/neuralib2.git
cd neuralib2/packages/neuralib-utils
uv pip install -e . # Basic installation
uv pip install -e ".[all]" # With all features
Requirements
- Python 3.11 or 3.12
- Core dependencies:
numpy,scipy,pandas,polars,h5py,rich,tqdm - See
pyproject.tomlfor full dependency list
Documentation
- Main Documentation: https://neuralib2.readthedocs.io/
- GitHub Repository: https://github.com/ytsimon2004/neuralib2
- Issue Tracker: https://github.com/ytsimon2004/neuralib2/issues
Related Packages
neuralib-utils is the foundation for the neuralib ecosystem:
neuralib-atlas: Brain atlas tools and hierarchical representations of mouse brain anatomyneuralib-imaging: Cellular imaging and widefield imaging toolsneuralib-parser: Data parsers for segmentation, morphology, Suite2p, Scanbox, CZI, StarDistneuralib-metric: Analysis metrics and computational tools
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.
1 maintainer
Metadata
1 maintainer
Release files for neuralib-utils 0.7.3
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