Installation

The neura-library provides a flexible and modular installation pipeline for a wide range of tools used in systems neuroscience research.

Requirements

  • Python >= 3.10

  • Supported OS: OS Independent

  • Recommended: virtual environment (e.g. uv, conda)

Basic Installation

To install the core functionality of the library:

pip install neura-library

Optional Modules

You can extend the functionality by installing optional modules:

Module-based

Atlas Tools:

pip install "neura-library[atlas]"

Scanner Support:

pip install "neura-library[scanner]"

Imaging Utilities:

pip install "neura-library[imaging]"

Image Processing Libraries:

pip install "neura-library[imagelib]"

Functionality-based

  • Rastermap: pip install "neura-library[rastermap]"

  • Cascade (TensorFlow): pip install "neura-library[cascade]"

  • Cellpose: pip install "neura-library[cellpose]"

  • StarDist: pip install "neura-library[stardist]"

  • Slack integration: pip install "neura-library[slack]"

  • Google Sheets API: pip install "neura-library[gspread]"

Warning

For those heavy Functionality-based wrapper usage (i.e., Rastermap, Cascade, Cellpose, StarDist), Create a separate conda environment for the specific job is recommended (avoid dependencies conflict)

For example you need to run cellpose:

conda create -n neuralib_seg python=3.10
conda activate neuralib_seg
pip install neura-library[cellpose]

All-In-One Installation

To install everything, including all optional features:

pip install "neura-library[all]"

Development Installation

For contributing and development:

pip install "neura-library[dev]"

This installs all tools plus development utilities like pre-commit and ruff.

Documentation Build

To build the documentation locally:

pip install "neura-library[doc]"