Jupyter Notebook Examples

These example notebooks demonstrate how to use Celldega for spatial transcriptomics analysis and visualization. Each notebook is designed to be run in a Jupyter environment and showcases different features of the library.

Tutorials

Comprehensive tutorials that walk through complete workflows:

• Scanpy-Squidpy Xenium Pancreas - Full analysis workflow using Scanpy and Squidpy with Xenium data
• Chromium Pre-process - Pre-processing Chromium single-cell RNA-seq data
• Single-cell Clustergram Chromium - Creating clustergram visualizations for single-cell data
• Visium-HD Landscape Pre-process - Pre-processing Visium HD data for Landscape visualization

Brief Notebooks

Focused examples demonstrating specific features:

• Landscape View Xenium - Basic Landscape visualization of Xenium data
• Landscape-Heatmap Visium-HD - Combined Landscape and heatmap visualization
• UMAP-Cluster Pancreas Xenium - UMAP clustering with Xenium pancreas data
• Visium-HD Landscape Mouse Lung - Visium HD visualization example
• Custom Segmentation - Using custom cell segmentation with Celldega
• Yearbook-Query - Using single-cell Yearbook view

Running the Notebooks

Prerequisites

Install Celldega and its dependencies:

pip install celldega

For full analysis workflows, you may also need:

pip install scanpy squidpy

Online Resources

You can also run Celldega notebooks in the cloud:

• Google Colab - Xenium Landscape Visualizations
• ObservableHQ - Celldega Landscape Xenium