SPEX - Spatial Omics Analysis Library

This library implements methods developed for the SPEX software platform, enabling users to apply state-of-the-art tissue segmentation techniques on their own image data.

📦 Installation

Upgrade pip and install dependencies:

pip install --upgrade pip setuptools wheel packaging
pip install pytest

🛠️ System Requirements

Before using OpenCV-related features, install the required system libraries:

sudo apt install -y libgl1-mesa-glx libjpeg-dev zlib1g-dev libpng-dev libgl1 libfftw3-dev build-essential python3-dev
 

Install the package locally:

pip install .

📂 Examples

Use the methods directly in your own analysis pipelines. Example notebooks are available:

• ▶️ Google Colab Run on Colab

• 🖥️ JupyterLab Server View on Server password "spexspex"

Notebooks include:

• Model downloading (in case Cellpose server access fails)
• Visualization examples
• End-to-end segmentation pipelines

⚙️ Compatibility

• ✅ Tested with Python 3.11
• ⚠️ Compatibility with other Python versions is not guaranteed
• ⚙️ Includes integrated Cellpose support, with fallback model handling (in notebooks)