Cala

Features

Cala is a neural endoscope image processing tool designed for neuroscience research, with a focus on long-term massive recordings. It features a no-code approach through configuration files, making it accessible to researchers of all programming backgrounds.

Requirements

• Python 3.11, 3.12, or 3.13
• Dependencies are handled through pdm

Installation

pip install cala==0.1.0

Quick Start

1. Prepare your video files
2. Create a configuration file (YAML format)
3. Run the pipeline:

python main.py --visual --config cala_config.yaml

Architecture

Cala uses a graph-&-state based architecture with three key components:

1. Configuration System

   • Supports YAML and env-based configuration
   • No-code pipeline setup
   • Flexible node configuration

2. Processing Nodes

   • Modular transformation units
   • Managed automatically by the runner
   • Connected to storage through parameter types

3. Storage System

   • Automatically created and updated by the distributor
   • Leverages Zarr for large-scale data storage

Schematics of the architecture can be found here.

Documentation

Detailed documentation is available in three main sections:

1. User Guide: Step-by-step guide for using Cala

   • Configuration file setup
   • Pipeline structure
   • Processing nodes
   • Advanced features

2. Developer Guide: Information for extending Cala

   • Adding new nodes
   • Working with stores
   • Best practices

3. API Reference: Available on Read the Docs

Roadmap

EOM 04/2025: UI first iteration complete

Contributing

We welcome contributions! Please fork this repository and submit a pull request if you would like to contribute to the project. You can also open issues for bug reports, feature requests, or discussions.

Test Coverage Status

https://app.codecov.io/gh/Aharoni-Lab/cala

License

Contact

For questions or support, please reach out to Raymond Chang at [email protected].