Spatial Analysis Tutorials

Spatial Analysis Tutorials#

Welcome to the spatial analysis tutorials! This section contains both beginner and advanced materials.

Beginner Tutorials#

Start here if you’re new to spatial analysis:

  1. SpatialData Objects: Introduction to working with spatial data structures

  2. Static Plotting: Learn how to create static visualizations

  3. Interactive Plotting with Napari: Explore interactive visualization using Napari

  4. Simple Analysis using scverse tools: Basic analysis techniques using the scverse toolkit

Advanced Tutorials#

Once you’re comfortable with the basics, explore these more complex topics:

  1. Transformations: Learn about spatial transformations and coordinate systems

  2. Niche Calculation Tutorial: Advanced analysis of spatial niches and microenvironments

These advanced tutorials assume familiarity with the concepts covered in the beginner section.

Environment setup instructions#

In order to work with SpatialData, we will need to install some more packages. To avoid installation conflicts, we suggest to create a new environment, very similar to what was required for the first day.

conda create -y --name workshop_2025_spatial python=3.12
conda activate workshop_2025_spatial
pip install jupyterlab notebook
pip install spatialdata spatialdata-io spatialdata-plot napari-spatialdata squidpy pyproj
conda install -y ipykernel
python -m ipykernel install --user --name workshop_2025_spatial

We will use this environment throughout the afternoon.

Data#

We will work with publicly available data throughout the workshop:

  • 10X Genomics datasets (hosts raw that that can be converted with spatialdata-io)

  • SpatialData-DB (hosts already converted SpatialData objects)

    • An example of how to work with the SpatialData-DB can be found here.

References#

Contents