neuralib-utils 0.7.0

Utilities for neuralib

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.toml for 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 anatomy
• neuralib-imaging: Cellular imaging and widefield imaging tools
• neuralib-parser: Data parsers for segmentation, morphology, Suite2p, Scanbox, CZI, StarDist
• neuralib-metric: Analysis metrics and computational tools

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.