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LimbLab

LimbLab

Work fast, code less. Analyze your 3D limb data with ease. Aesthetic out of the box.

🚀 Quick Start

Get started with LimbLab in minutes:

# Install LimbLab
pip install limb

# Create your first experiment
limb create-experiment my_experiment

# Process your data
limb clean-volume my_experiment raw_data.tif DAPI
limb extract-surface my_experiment --auto
limb stage my_experiment
limb align my_experiment

# Visualize results
limb vis isosurfaces my_experiment DAPI

Need help? Check out our tutorials or user guide.

Documentation Overview

Docs

Tutorials

What is LimbLab?

LimbLab is a comprehensive library for processing and analyzing 3D limb development data. Designed specifically for the scientific community working with mouse limb models, it provides a complete pipeline from raw data to publication-ready visualizations.

Key Features

🔬 Limb-Specific Tools

  • Semi automate limb staging using 3D morphology

  • Limb 3D Reference alignment for comparative analysis

  • Specialized algorithms for limb development data

🎨 Aesthetic Out-of-the-Box Publication-ready visualizations

⚙️ Customizable Built on Vedo for extensibility

🔬 Trusted by Research Active use in research laboratories

Complete Analysis Pipeline

LimbLab provides a complete pipeline for 3D limb data analysis:

1. Data Preparation

# Create experiment structure
limb create-experiment my_study

# Process raw volumes
limb clean-volume my_study dapi.tif DAPI
limb clean-volume my_study gene.tif GENE

2. 3D Analysis

# Extract surface mesh
limb extract-surface my_study --auto

# Determine developmental stage
limb stage my_study

# Align with reference
limb align my_study

3. Visualization

# Create 3D visualizations
limb vis isosurfaces my_study GENE
limb vis slices my_study GENE
limb vis raycast my_study GENE

System Requirements

Minimum Requirements

  • OS: Windows 10+, macOS 10.14+, Ubuntu 18.04+
  • Python: 3.8 or higher
  • RAM: 8GB minimum, 16GB recommended
  • Storage: 10GB free space
  • GPU: Optional (CUDA support for acceleration)
  • OS: Latest stable release
  • Python: 3.9 or 3.10
  • RAM: 32GB or more
  • Storage: SSD with 50GB+ free space
  • GPU: NVIDIA GTX 1060 or better (for acceleration)

Installation

Quick Install

pip install limb

License & Citation

License

LimbLab is released under the MIT License, allowing free use in both academic and commercial applications.

Citation

If you use LimbLab in your research, please cite:

@software{limblab2024,
  title={LimbLab: A comprehensive library for 3D limb development analysis},
  author={Vinyo, Laura and Contributors},
  year={2024},
  url={https://github.com/lauavinyo/limb}
}

LimbLab - Empowering 3D limb development research

Made with ❤️ by the Sharpe Lab