Tutorials

Notebooks tailored to showcase specific functionalities of the SpatialData ecosystem.

• I. Use SpatialData with your data: the SpatialData object.

• II. Use SpatialData with your data: SpatialElements and tables

• Transformations and coordinate systems

• Spatial query

• Annotating regions of interest with napari

• Use landmark annotations to align multiple -omics layers

• Working with annotations in SpatialData

• Integrate/aggregate signals across spatial layers

• Squidpy integration

• Deep learning example on image tiles

Visualizations

Many different technologies can be visualised out-of-the-box. See below for a couple of examples. See the example datasets for additional technologies represented in SpatialData.

• Technology focus: 10x Genomics Visium

• Technology focus: MIBI-TOF

• Technology focus: MERFISH

• Technology focus: CosMx

• Technology focus: Visium HD

• Technology focus: Xenium

Advanced

Advanced tutorials that showcase more complex functionalities of the SpatialData ecosystem.

• Implicit performance improvements when plotting raster data