Tutorials

This section contains various tutorials showcasing spatial molecular data analysis with squidpy.

Analysis of spatial datasets using squidpy

This section contains tutorials showcasing core Squidpy functionalities by applying them to a diverse set of different spatial datasets.

Analyze Imaging Mass Cytometry data

Analyze seqFISH data

Analyze Slide-seqV2 data

Analyze Visium fluorescence data

Analyze Visium H&E data

Analyze MIBI-TOF image data

Analyze 4i data

Analyze Nanostring data

Analyze Vizgen data

Vizgen Mouse Liver Squidpy Vignette

Analyze Xenium data

Advanced Tutorials

This section contains tutorials showcasing advanced squidpy functionalities, such as:

• loading spatial data.

• interactive visualization.

• working with z-stacks.

Import spatial data in AnnData and Squidpy

ImageContainer object

Interactive visualization with Napari

Use z-stacks with ImageContainer

External tutorials

This section contains tutorials showcasing how squidpy can interface with external libraries.

Predict cluster labels spots using Tensorflow

Cell-type deconvolution using Tangram

Nuclei segmentation using Cellpose

Nuclei segmentation using StarDist

Feature extraction using CellProfiler